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[hg] galaxy 3764: Add 'filter transcripts via tracking' tool to ...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/4e5ca6c44804 changeset: 3764:4e5ca6c44804 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Mon May 10 12:42:05 2010 -0400 description: Add 'filter transcripts via tracking' tool to RNA-seq tools. This tool is useful for operating on output files from cufftools suite. diffstat: tool_conf.xml.sample | 1 + tools/ngs_rna/filter_transcripts_via_tracking.py | 70 +++++++++++++++++++++++ tools/ngs_rna/filter_transcripts_via_tracking.xml | 32 ++++++++++ 3 files changed, 103 insertions(+), 0 deletions(-) diffs (121 lines): diff -r 1110a91888e2 -r 4e5ca6c44804 tool_conf.xml.sample --- a/tool_conf.xml.sample Mon May 10 11:55:08 2010 -0400 +++ b/tool_conf.xml.sample Mon May 10 12:42:05 2010 -0400 @@ -239,6 +239,7 @@ <tool file="ngs_rna/cufflinks_wrapper.xml" /> <tool file="ngs_rna/cuffcompare_wrapper.xml" /> <tool file="ngs_rna/cuffdiff_wrapper.xml" /> + <tool file="ngs_rna/filter_transcripts_via_tracking.xml" /> </section> <section name="NGS: SAM Tools" id="samtools"> <tool file="samtools/sam_bitwise_flag_filter.xml" /> diff -r 1110a91888e2 -r 4e5ca6c44804 tools/ngs_rna/filter_transcripts_via_tracking.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ngs_rna/filter_transcripts_via_tracking.py Mon May 10 12:42:05 2010 -0400 @@ -0,0 +1,70 @@ +#!/usr/bin/env python +import os, sys, tempfile + +assert sys.version_info[:2] >= ( 2, 4 ) + +def __main__(): + """ + Utility script for analyzing Cufflinks data: uses a tracking file (produced by cuffcompare) to filter a GTF file of transcripts (usually the transcripts + produced by cufflinks). Filtering is done by extracting transcript IDs from tracking file and then filtering the GTF so that the output GTF contains only + transcript found in the tracking file. Because a tracking file has multiple samples, a sample number is used to filter transcripts for + a particular sample. + """ + # Read parms. + tracking_file_name = sys.argv[1] + transcripts_file_name = sys.argv[2] + output_file_name = sys.argv[3] + sample_number = int ( sys.argv[4] ) + + # Open files. + transcripts_file = open( transcripts_file_name, 'r' ) + output_file = open( output_file_name, 'w' ) + + # Read transcript IDs from tracking file. + transcript_ids = {} + for i, line in enumerate( file( tracking_file_name ) ) : + # Split line into elements. Line format is + # [Transfrag ID] [Locus ID] [Ref Gene ID] [Ref Transcript ID] [Class code] [qJ:<gene_id>|<transcript_id>|<FMI>|<FPKM>|<conf_lo>|<conf_hi>] + line = line.rstrip( '\r\n' ) + elems = line.split( '\t' ) + + # Get transcript info. + if sample_number == 1: + transcript_info = elems[4] + elif sample_number == 2: + transcript_info = elems[5] + if not transcript_info.startswith('q'): + # No transcript for this sample. + continue + + # Get and store transcript id. + transcript_id = transcript_info.split('|')[1] + transcript_id = transcript_id.strip('"') + transcript_ids[transcript_id] = "" + + # Filter transcripts file using transcript_ids + for i, line in enumerate( file( transcripts_file_name ) ): + # GTF format: chrom source, name, chromStart, chromEnd, score, strand, frame, attributes. + elems = line.split( '\t' ) + + # Get attributes. + attributes_list = elems[8].split(";") + attributes = {} + for name_value_pair in attributes_list: + pair = name_value_pair.strip().split(" ") + name = pair[0].strip() + if name == '': + continue + # Need to strip double quote from values + value = pair[1].strip(" \"") + attributes[name] = value + + # Get element's transcript id. + transcript_id = attributes['transcript_id'] + if transcript_id in transcript_ids: + output_file.write(line) + + # Clean up. + output_file.close() + +if __name__ == "__main__": __main__() diff -r 1110a91888e2 -r 4e5ca6c44804 tools/ngs_rna/filter_transcripts_via_tracking.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ngs_rna/filter_transcripts_via_tracking.xml Mon May 10 12:42:05 2010 -0400 @@ -0,0 +1,32 @@ +<tool id="filter_combined_via_tracking" name="Filter Combined Transcripts" version="0.1"> + <description>using tracking file</description> + <command interpreter="python"> + filter_transcripts_via_tracking.py + $tracking_file + $transcripts_file + $filtered_transcripts + $sample_num + </command> + <inputs> + <param format="gtf" name="transcripts_file" type="data" label="Cufflinks assembled transcripts" help=""/> + <param format="tabular" name="tracking_file" type="data" label="Cuffcompare tracking file" help=""/> + <param name="sample_num" type="select" label="Sample Number"> + <option value="1">1</option> + <option value="2">2</option> + </param> + </inputs> + + <outputs> + <data format="gtf" name="filtered_transcripts"/> + </outputs> + + <tests> + </tests> + + <help> + Uses a tracking file (produced by cuffcompare) to filter a GTF file of transcripts (usually the transcripts produced by + cufflinks). Filtering is done by extracting transcript IDs from tracking file and then filtering the + GTF so that the output GTF contains only transcript found in the tracking file. Because a tracking file has multiple + samples, a sample number is used to filter transcripts for a particular sample. + </help> +</tool>

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[hg] galaxy 3763: right welcome.html at last
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/1110a91888e2 changeset: 3763:1110a91888e2 user: fubar/ross period lazarus at gmail d0t com date: Mon May 10 11:55:08 2010 -0400 description: right welcome.html at last diffstat: static/welcome.html | 4 ++-- 1 files changed, 2 insertions(+), 2 deletions(-) diffs (15 lines): diff -r df72c7a8d5cf -r 1110a91888e2 static/welcome.html --- a/static/welcome.html Mon May 10 11:49:25 2010 -0400 +++ b/static/welcome.html Mon May 10 11:55:08 2010 -0400 @@ -8,9 +8,9 @@ <body> <div class="document"> <div class="warningmessagelarge"> - <strong>Welcome to Galaxy at the Channing Laboratory</strong> + <strong>Hello world! It's running...</strong> <hr> - Your jobs will run under SGE on the cluster. + To customize this page edit <code>static/welcome.html</code> </div> <br/> <img src="images/noodles.png" alt="WWFSMD?" style="display: block; margin-left: auto; margin-right: auto;" />

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[hg] galaxy 3762: Revert inadvertantly updated tool_conf.xml.sam...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/df72c7a8d5cf changeset: 3762:df72c7a8d5cf user: fubar/ross period lazarus at gmail d0t com date: Mon May 10 11:49:25 2010 -0400 description: Revert inadvertantly updated tool_conf.xml.sample and welcome.html diffstat: static/welcome.html | 3 +- tool_conf.xml.sample | 231 +++++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 233 insertions(+), 1 deletions(-) diffs (256 lines): diff -r ecbd01636a92 -r df72c7a8d5cf static/welcome.html --- a/static/welcome.html Mon May 10 11:22:50 2010 -0400 +++ b/static/welcome.html Mon May 10 11:49:25 2010 -0400 @@ -10,9 +10,10 @@ <div class="warningmessagelarge"> <strong>Welcome to Galaxy at the Channing Laboratory</strong> <hr> + Your jobs will run under SGE on the cluster. </div> <br/> - <img src="images/Armitagep_manhattan.png" alt="manhattan plot" style="display: block; margin-left: auto; margin-right: auto;" /> + <img src="images/noodles.png" alt="WWFSMD?" style="display: block; margin-left: auto; margin-right: auto;" /> <hr/> This project is supported in part by <a target="_blank" class="reference" href="http://www.nsf.gov">NSF</a>, <a target="_blank" class="reference" href="http://www.genome.gov">NHGRI</a>, and <a target="_blank" class="reference" href="http://www.huck.psu.edu">the Huck Institutes of the Life Sciences</a>. </div> diff -r ecbd01636a92 -r df72c7a8d5cf tool_conf.xml.sample --- a/tool_conf.xml.sample Mon May 10 11:22:50 2010 -0400 +++ b/tool_conf.xml.sample Mon May 10 11:49:25 2010 -0400 @@ -23,6 +23,237 @@ <tool file="data_source/hbvar.xml" /> <tool file="validation/fix_errors.xml" /> </section> + <section name="Send Data" id="send"> + <tool file="data_destination/epigraph.xml" /> + <tool file="data_destination/epigraph_test.xml" /> + </section> + <section name="ENCODE Tools" id="EncodeTools"> + <tool file="encode/gencode_partition.xml" /> + <tool file="encode/random_intervals.xml" /> + </section> + <section name="Lift-Over" id="liftOver"> + <tool file="extract/liftOver_wrapper.xml" /> + </section> + <section name="Text Manipulation" id="textutil"> + <tool file="filters/fixedValueColumn.xml" /> + <tool file="stats/column_maker.xml" /> + <tool file="filters/catWrapper.xml" /> + <tool file="filters/cutWrapper.xml" /> + <tool file="filters/mergeCols.xml" /> + <tool file="filters/convert_characters.xml" /> + <tool file="filters/CreateInterval.xml" /> + <tool file="filters/cutWrapper.xml" /> + <tool file="filters/changeCase.xml" /> + <tool file="filters/pasteWrapper.xml" /> + <tool file="filters/remove_beginning.xml" /> + <tool file="filters/randomlines.xml" /> + <tool file="filters/headWrapper.xml" /> + <tool file="filters/tailWrapper.xml" /> + <tool file="filters/trimmer.xml" /> + <tool file="stats/dna_filtering.xml" /> + <tool file="new_operations/tables_arithmetic_operations.xml" /> + </section> + <section name="Filter and Sort" id="filter"> + <tool file="stats/filtering.xml" /> + <tool file="filters/sorter.xml" /> + <tool file="filters/grep.xml" /> + </section> + <section name="Join, Subtract and Group" id="group"> + <tool file="filters/joiner.xml" /> + <tool file="filters/compare.xml"/> + <tool file="new_operations/subtract_query.xml"/> + <tool file="stats/grouping.xml" /> + <tool file="new_operations/column_join.xml" /> + </section> + <section name="Convert Formats" id="convert"> + <tool file="filters/axt_to_concat_fasta.xml" /> + <tool file="filters/axt_to_fasta.xml" /> + <tool file="filters/axt_to_lav.xml" /> + <tool file="filters/bed2gff.xml" /> + <tool file="fasta_tools/fasta_to_tabular.xml" /> + <tool file="filters/gff2bed.xml" /> + <tool file="filters/lav_to_bed.xml" /> + <tool file="maf/maf_to_bed.xml" /> + <tool file="maf/maf_to_interval.xml" /> + <tool file="maf/maf_to_fasta.xml" /> + <tool file="fasta_tools/tabular_to_fasta.xml" /> + <tool file="fastx_toolkit/fastq_to_fasta.xml" /> + <tool file="filters/wiggle_to_simple.xml" /> + <tool file="filters/sff_extractor.xml" /> + <tool file="filters/gtf2bedgraph.xml" /> + </section> + <section name="Extract Features" id="features"> + <tool file="filters/ucsc_gene_bed_to_exon_bed.xml" /> + <tool file="extract/extract_GFF_Features.xml" /> + </section> + <section name="Fetch Sequences" id="fetchSeq"> + <tool file="extract/extract_genomic_dna.xml" /> + </section> + <section name="Fetch Alignments" id="fetchAlign"> + <tool file="maf/interval2maf_pairwise.xml" /> + <tool file="maf/interval2maf.xml" /> + <tool file="maf/maf_split_by_species.xml"/> + <tool file="maf/interval_maf_to_merged_fasta.xml" /> + <tool file="maf/genebed_maf_to_fasta.xml"/> + <tool file="maf/maf_stats.xml"/> + <tool file="maf/maf_thread_for_species.xml"/> + <tool file="maf/maf_limit_to_species.xml"/> + <tool file="maf/maf_limit_size.xml"/> + <tool file="maf/maf_by_block_number.xml"/> + <tool file="maf/maf_reverse_complement.xml"/> + <tool file="maf/maf_filter.xml"/> + </section> + <section name="Get Genomic Scores" id="scores"> + <tool file="stats/wiggle_to_simple.xml" /> + <tool file="stats/aggregate_binned_scores_in_intervals.xml" /> + <tool file="extract/phastOdds/phastOdds_tool.xml" /> + </section> + <section name="Operate on Genomic Intervals" id="bxops"> + <tool file="new_operations/intersect.xml" /> + <tool file="new_operations/subtract.xml" /> + <tool file="new_operations/merge.xml" /> + <tool file="new_operations/concat.xml" /> + <tool file="new_operations/basecoverage.xml" /> + <tool file="new_operations/coverage.xml" /> + <tool file="new_operations/complement.xml" /> + <tool file="new_operations/cluster.xml" id="cluster" /> + <tool file="new_operations/join.xml" /> + <tool file="new_operations/get_flanks.xml" /> + <tool file="new_operations/flanking_features.xml" /> + <tool file="annotation_profiler/annotation_profiler.xml" /> + </section> + <section name="Statistics" id="stats"> + <tool file="stats/gsummary.xml" /> + <tool file="filters/uniq.xml" /> + <tool file="stats/cor.xml" /> + <tool file="regVariation/t_test_two_samples.xml" /> + <tool file="regVariation/compute_q_values.xml" /> + </section> + <section name="Graph/Display Data" id="plots"> + <tool file="plotting/histogram2.xml" /> + <tool file="plotting/scatterplot.xml" /> + <tool file="plotting/bar_chart.xml" /> + <tool file="plotting/xy_plot.xml" /> + <tool file="plotting/boxplot.xml" /> + <tool file="visualization/GMAJ.xml" /> + <tool file="visualization/LAJ.xml" /> + <tool file="visualization/build_ucsc_custom_track.xml" /> + </section> + <section name="Regional Variation" id="regVar"> + <tool file="regVariation/windowSplitter.xml" /> + <tool file="regVariation/featureCounter.xml" /> + <tool file="regVariation/quality_filter.xml" /> + <tool file="regVariation/maf_cpg_filter.xml" /> + <tool file="regVariation/getIndels_2way.xml" /> + <tool file="regVariation/getIndels_3way.xml" /> + <tool file="regVariation/getIndelRates_3way.xml" /> + <tool file="regVariation/substitutions.xml" /> + <tool file="regVariation/substitution_rates.xml" /> + <tool file="regVariation/microsats_alignment_level.xml" /> + <tool file="regVariation/microsats_mutability.xml" /> + <tool file="regVariation/delete_overlapping_indels.xml" /> + <tool file="regVariation/compute_motifs_frequency.xml" /> + <tool file="regVariation/compute_motif_frequencies_for_all_motifs.xml" /> + <tool file="regVariation/categorize_elements_satisfying_criteria.xml" />s + <tool file="regVariation/draw_stacked_barplots.xml" /> + </section> + <section name="Multiple regression" id="multReg"> + <tool file="regVariation/linear_regression.xml" /> + <tool file="regVariation/best_regression_subsets.xml" /> + <tool file="regVariation/rcve.xml" /> + </section> + <section name="Multivariate Analysis" id="multVar"> + <tool file="multivariate_stats/pca.xml" /> + <tool file="multivariate_stats/cca.xml" /> + <tool file="multivariate_stats/kpca.xml" /> + <tool file="multivariate_stats/kcca.xml" /> + </section> + <section name="Evolution" id="hyphy"> + <tool file="hyphy/hyphy_branch_lengths_wrapper.xml" /> + <tool file="hyphy/hyphy_nj_tree_wrapper.xml" /> + <tool file="hyphy/hyphy_dnds_wrapper.xml" /> + <tool file="evolution/mutate_snp_codon.xml" /> + <tool file="evolution/codingSnps.xml" /> + <tool file="evolution/add_scores.xml" /> + </section> + <section name="Metagenomic analyses" id="tax_manipulation"> + <tool file="taxonomy/gi2taxonomy.xml" /> + <tool file="taxonomy/t2t_report.xml" /> + <tool file="taxonomy/t2ps_wrapper.xml" /> + <tool file="taxonomy/find_diag_hits.xml" /> + <tool file="taxonomy/lca.xml" /> + <tool file="taxonomy/poisson2test.xml" /> + </section> + <section name="FASTA manipulation" id="fasta_manipulation"> + <tool file="fasta_tools/fasta_compute_length.xml" /> + <tool file="fasta_tools/fasta_filter_by_length.xml" /> + <tool file="fasta_tools/fasta_concatenate_by_species.xml" /> + <tool file="fasta_tools/fasta_to_tabular.xml" /> + <tool file="fasta_tools/tabular_to_fasta.xml" /> + <tool file="fastx_toolkit/fasta_formatter.xml" /> + <tool file="fastx_toolkit/fasta_nucleotide_changer.xml" /> + <tool file="fastx_toolkit/fastx_collapser.xml" /> + </section> + <section name="NGS: QC and manipulation" id="cshl_library_information"> + <label text="Illumina data" id="illumina" /> + <tool file="fastq/fastq_groomer.xml" /> + <tool file="fastq/fastq_paired_end_splitter.xml" /> + <tool file="fastq/fastq_paired_end_joiner.xml" /> + <tool file="fastq/fastq_stats.xml" /> +  + <label text="Roche-454 data" id="454" /> + <tool file="metag_tools/short_reads_figure_score.xml" /> + <tool file="metag_tools/short_reads_trim_seq.xml" /> + <tool file="fastq/fastq_combiner.xml" /> + <label text="AB-SOLiD data" id="solid" /> + <tool file="next_gen_conversion/solid2fastq.xml" /> + <tool file="solid_tools/solid_qual_stats.xml" /> + <tool file="solid_tools/solid_qual_boxplot.xml" /> + <label text="Generic FASTQ manipulation" id="generic_fastq" /> + <tool file="fastq/fastq_filter.xml" /> + <tool file="fastq/fastq_trimmer.xml" /> + <tool file="fastq/fastq_trimmer_by_quality.xml" /> + <tool file="fastq/fastq_manipulation.xml" /> + <tool file="fastq/fastq_to_fasta.xml" /> + <tool file="fastq/fastq_to_tabular.xml" /> + <tool file="fastq/tabular_to_fastq.xml" /> + </section> + <section name="NGS: Mapping" id="solexa_tools"> + <tool file="sr_mapping/lastz_wrapper.xml" /> + <tool file="sr_mapping/lastz_paired_reads_wrapper.xml" /> + <tool file="sr_mapping/bowtie_wrapper.xml" /> + <tool file="sr_mapping/bowtie_color_wrapper.xml" /> + <tool file="sr_mapping/bwa_wrapper.xml" /> + <tool file="metag_tools/megablast_wrapper.xml" /> + <tool file="metag_tools/megablast_xml_parser.xml" /> + <tool file="sr_mapping/PerM.xml" /> + </section> + <section name="NGS: Expression Analysis" id="ngs-rna-tools"> + <tool file="ngs_rna/tophat_wrapper.xml" /> + <tool file="ngs_rna/cufflinks_wrapper.xml" /> + <tool file="ngs_rna/cuffcompare_wrapper.xml" /> + <tool file="ngs_rna/cuffdiff_wrapper.xml" /> + </section> + <section name="NGS: SAM Tools" id="samtools"> + <tool file="samtools/sam_bitwise_flag_filter.xml" /> + <tool file="samtools/sam2interval.xml" /> + <tool file="samtools/sam_to_bam.xml" /> + <tool file="samtools/sam_merge.xml" /> + <tool file="samtools/sam_pileup.xml" /> + <tool file="samtools/pileup_parser.xml" /> + <tool file="samtools/pileup_interval.xml" /> + </section> + <section name="NGS: Peak Calling" id="peak_calling"> + <tool file="peak_calling/macs_wrapper.xml" /> + <tool file="genetrack/genetrack_indexer.xml" /> + <tool file="genetrack/genetrack_peak_prediction.xml" /> + </section> <section name="SNP/WGA: Data; Filters" id="rgdat"> <label text="Data: Import and upload" id="rgimport" /> <tool file="data_source/upload.xml"/>

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[hg] galaxy 3761: Bug in SGE external metadata
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/ecbd01636a92 changeset: 3761:ecbd01636a92 user: Nate Coraor <nate(a)bx.psu.edu> date: Mon May 10 11:22:50 2010 -0400 description: Bug in SGE external metadata diffstat: lib/galaxy/jobs/runners/sge.py | 3 +-- 1 files changed, 1 insertions(+), 2 deletions(-) diffs (17 lines): diff -r f53d06cf2f93 -r ecbd01636a92 lib/galaxy/jobs/runners/sge.py --- a/lib/galaxy/jobs/runners/sge.py Mon May 10 11:13:51 2010 -0400 +++ b/lib/galaxy/jobs/runners/sge.py Mon May 10 11:22:50 2010 -0400 @@ -166,12 +166,11 @@ script = sge_template % (job_wrapper.galaxy_lib_dir, os.path.abspath( job_wrapper.working_directory ), command_line) if self.app.config.set_metadata_externally: - output_fnames = [ str( o ) for o in job_wrapper.get_output_fnames() ] script += "cd %s\n" % os.path.abspath( os.getcwd() ) script += "%s\n" % job_wrapper.setup_external_metadata( exec_dir = os.path.abspath( os.getcwd() ), tmp_dir = self.app.config.new_file_path, dataset_files_path = self.app.model.Dataset.file_path, - output_fnames = output_fnames, + output_fnames = job_wrapper.get_output_fnames(), set_extension = False, kwds = { 'overwrite' : False } ) #we don't want to overwrite metadata that was copied over in init_meta(), as per established behavior fh = file( jt.remoteCommand, "w" )

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[hg] galaxy 3760: Add external metadata to SGE
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/f53d06cf2f93 changeset: 3760:f53d06cf2f93 user: Nate Coraor <nate(a)bx.psu.edu> date: Mon May 10 11:13:51 2010 -0400 description: Add external metadata to SGE diffstat: lib/galaxy/jobs/runners/sge.py | 9 +++++++++ 1 files changed, 9 insertions(+), 0 deletions(-) diffs (19 lines): diff -r 6aa1379d35e0 -r f53d06cf2f93 lib/galaxy/jobs/runners/sge.py --- a/lib/galaxy/jobs/runners/sge.py Mon May 10 10:17:11 2010 -0400 +++ b/lib/galaxy/jobs/runners/sge.py Mon May 10 11:13:51 2010 -0400 @@ -165,6 +165,15 @@ jt.nativeSpecification = ' '.join(nativeSpec) script = sge_template % (job_wrapper.galaxy_lib_dir, os.path.abspath( job_wrapper.working_directory ), command_line) + if self.app.config.set_metadata_externally: + output_fnames = [ str( o ) for o in job_wrapper.get_output_fnames() ] + script += "cd %s\n" % os.path.abspath( os.getcwd() ) + script += "%s\n" % job_wrapper.setup_external_metadata( exec_dir = os.path.abspath( os.getcwd() ), + tmp_dir = self.app.config.new_file_path, + dataset_files_path = self.app.model.Dataset.file_path, + output_fnames = output_fnames, + set_extension = False, + kwds = { 'overwrite' : False } ) #we don't want to overwrite metadata that was copied over in init_meta(), as per established behavior fh = file( jt.remoteCommand, "w" ) fh.write( script ) fh.close()

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[hg] galaxy 3759: SNP/WGA tool changes only
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/6aa1379d35e0 changeset: 3759:6aa1379d35e0 user: fubar/ross period lazarus at gmail d0t com date: Mon May 10 10:17:11 2010 -0400 description: SNP/WGA tool changes only Updates to functional test outputs Minor tweaks to some tests All now pass when run using -sid but there's something busted when a full functional test is run diffstat: static/welcome.html | 5 +- test-data/rgCaCotest1_CaCo_log.txt | 20 +- test-data/rgGLMtest1_GLM_log.txt | 28 +- test-data/rgQQtest1.pdf | 52 +- test-data/rgTDTtest1_TDT_log.txt | 18 +- test-data/rgtestouts/rgClean/rgCleantest1.log | 28 +- test-data/rgtestouts/rgEigPCA/Rplots.pdf | 46 +- test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.R | 2 +- test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.html | 35 +- test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_PCAPlot.pdf | 50 +- test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_log.txt | 6 +- test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls | 80 +- test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls.par | 6 +- test-data/rgtestouts/rgGRR/Log_rgGRRtest1.txt | 8 +- test-data/rgtestouts/rgGRR/rgGRRtest1.html | 14 +- test-data/rgtestouts/rgGRR/rgGRRtest1.svg | 118 +- test-data/rgtestouts/rgGRR/rgGRRtest1_table.xls | 1560 +++++----- test-data/rgtestouts/rgHaploView/1_rgHaploViewtest1.pdf | 0 test-data/rgtestouts/rgHaploView/1_rgHaploViewtest1.png | 0 test-data/rgtestouts/rgHaploView/2_HapMap_YRI_22.pdf | 0 test-data/rgtestouts/rgHaploView/2_HapMap_YRI_22.png | 0 test-data/rgtestouts/rgHaploView/Chromosome22YRI.LD.PNG | 0 test-data/rgtestouts/rgHaploView/Log_rgHaploViewtest1.txt | 16 +- test-data/rgtestouts/rgHaploView/alljoin.pdf | 0 test-data/rgtestouts/rgHaploView/allnup.pdf | 0 test-data/rgtestouts/rgHaploView/rgHaploViewtest1.html | 16 +- test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.LD.PNG | 0 test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TAGS | 14 +- test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TESTS | 10 +- test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bed | 2 +- test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim | 4 +- test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log | 96 +- test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.map | 4 +- test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.ped | 80 +- test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in | 4 +- test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.out | 4 +- test-data/rgtestouts/rgManQQ/Allelep_manhattan.png | 0 test-data/rgtestouts/rgManQQ/Allelep_qqplot.png | 0 test-data/rgtestouts/rgManQQ/Armitagep_manhattan.png | 0 test-data/rgtestouts/rgManQQ/Armitagep_qqplot.png | 0 test-data/rgtestouts/rgManQQ/rgManQQtest1.R | 4 +- test-data/rgtestouts/rgManQQ/rgManQQtest1.html | 4 +- test-data/rgtestouts/rgPedSub/rgPedSubtest1.log | 8 +- test-data/rgtestouts/rgQC/FQNormtinywga_s_het_cum.jpg | 0 test-data/rgtestouts/rgQC/FQNormtinywga_s_het_cum.pdf | 182 +- test-data/rgtestouts/rgQC/Ranked_Subject_Missing_Genotype.xls | 36 +- test-data/rgtestouts/rgQC/SubjectDetails_rgQCtest1.xls | 72 +- test-data/rgtestouts/rgQC/ldp_tinywga.bed | 2 +- test-data/rgtestouts/rgQC/ldp_tinywga.bim | 10 +- test-data/rgtestouts/rgQC/ldp_tinywga.log | 18 +- test-data/rgtestouts/rgQC/rgQCtest1.html | 208 +- test-data/rgtestouts/rgQC/tinywga.het | 80 +- test-data/rgtestouts/rgQC/tinywga.log | 6 +- test-data/rgtestouts/rgQC/tinywga.prune.in | 10 +- test-data/rgtestouts/rgQC/tinywga.prune.out | 10 +- test-data/rgtestouts/rgQC/tinywga_All_3x3.pdf | 0 test-data/rgtestouts/rgQC/tinywga_All_Paged-0.jpg | 0 test-data/rgtestouts/rgQC/tinywga_All_Paged-1.jpg | 0 test-data/rgtestouts/rgQC/tinywga_All_Paged-2.jpg | 0 test-data/rgtestouts/rgQC/tinywga_All_Paged-3.jpg | 0 test-data/rgtestouts/rgQC/tinywga_All_Paged-4.jpg | 0 test-data/rgtestouts/rgQC/tinywga_All_Paged.pdf | 0 test-data/rgtestouts/rgQC/tinywga_fracmiss.jpg | 0 test-data/rgtestouts/rgQC/tinywga_fracmiss.pdf | 50 +- test-data/rgtestouts/rgQC/tinywga_fracmiss_cum.jpg | 0 test-data/rgtestouts/rgQC/tinywga_fracmiss_cum.pdf | 52 +- test-data/rgtestouts/rgQC/tinywga_s_het.jpg | 0 test-data/rgtestouts/rgQC/tinywga_s_het.pdf | 343 +- test-data/rgtestouts/rgQC/tinywga_s_het_cum.jpg | 0 test-data/rgtestouts/rgQC/tinywga_s_het_cum.pdf | 182 +- test-data/rgtestouts/rgfakePed/rgfakePedtest1.lped | 2 +- test-data/rgtestouts/rgfakePed/rgfakePedtest1.ped | 80 +- test-data/rgtestouts/rgfakePhe/rgfakePhetest1.pphe | 80 +- tool-data/annotation_profiler_options.xml.sample | 2 +- tool_conf.xml.sample | 231 - tools/rgenetics/rgGRR.py | 12 +- tools/rgenetics/rgGRR.xml | 10 +- tools/rgenetics/rgHaploView.xml | 4 +- tools/rgenetics/rgQC.xml | 2 +- tools/rgenetics/rgtest.sh | 6 +- tools/rgenetics/rgutils.py | 20 +- 81 files changed, 2045 insertions(+), 2007 deletions(-) diffs (truncated from 5750 to 3000 lines): diff -r acaf971320bd -r 6aa1379d35e0 static/welcome.html --- a/static/welcome.html Mon May 10 10:03:00 2010 -0400 +++ b/static/welcome.html Mon May 10 10:17:11 2010 -0400 @@ -8,12 +8,11 @@ <body> <div class="document"> <div class="warningmessagelarge"> - <strong>Hello world! It's running...</strong> + <strong>Welcome to Galaxy at the Channing Laboratory</strong> <hr> - To customize this page edit <code>static/welcome.html</code> </div> <br/> - <img src="images/noodles.png" alt="WWFSMD?" style="display: block; margin-left: auto; margin-right: auto;" /> + <img src="images/Armitagep_manhattan.png" alt="manhattan plot" style="display: block; margin-left: auto; margin-right: auto;" /> <hr/> This project is supported in part by <a target="_blank" class="reference" href="http://www.nsf.gov">NSF</a>, <a target="_blank" class="reference" href="http://www.genome.gov">NHGRI</a>, and <a target="_blank" class="reference" href="http://www.huck.psu.edu">the Huck Institutes of the Life Sciences</a>. </div> diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgCaCotest1_CaCo_log.txt --- a/test-data/rgCaCotest1_CaCo_log.txt Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgCaCotest1_CaCo_log.txt Mon May 10 10:17:11 2010 -0400 @@ -1,6 +1,6 @@ @----------------------------------------------------------@ -| PLINK! | v1.06 | 24/Apr/2009 | +| PLINK! | v1.07 | 10/Aug/2009 | |----------------------------------------------------------| | (C) 2009 Shaun Purcell, GNU General Public License, v2 | |----------------------------------------------------------| @@ -10,24 +10,24 @@ Skipping web check... [ --noweb ] Writing this text to log file [ rgCaCotest1.log ] -Analysis started: Thu Mar 25 21:01:31 2010 +Analysis started: Sun May 9 21:23:49 2010 Options in effect: --noweb - --bfile /opt/galaxy/test-data/tinywga + --bfile /share/shared/galaxy/test-data/tinywga --out rgCaCotest1 --model -Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] -25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ] -Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] -40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] +Reading map (extended format) from [ /share/shared/galaxy/test-data/tinywga.bim ] +25 markers to be included from [ /share/shared/galaxy/test-data/tinywga.bim ] +Reading pedigree information from [ /share/shared/galaxy/test-data/tinywga.fam ] +40 individuals read from [ /share/shared/galaxy/test-data/tinywga.fam ] 40 individuals with nonmissing phenotypes Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) Missing phenotype value is also -9 10 cases, 30 controls and 0 missing 21 males, 19 females, and 0 of unspecified sex -Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] +Reading genotype bitfile from [ /share/shared/galaxy/test-data/tinywga.bed ] Detected that binary PED file is v1.00 SNP-major mode Before frequency and genotyping pruning, there are 25 SNPs 27 founders and 13 non-founders found @@ -40,7 +40,7 @@ Full-model association tests, minimum genotype count: --cell 5 Writing full model association results to [ rgCaCotest1.model ] -Analysis finished: Thu Mar 25 21:01:31 2010 +Analysis finished: Sun May 9 21:23:49 2010 ###maxp=0.667360,minp=-0.000000,prange=1.167360,scalefact=856.633772 -Rgenetics V000.1 April 2007 http://rgenetics.org Galaxy Tools, rgCaCo.py started 25/03/2010 21:01:31 +Rgenetics V000.1 April 2007 http://rgenetics.org Galaxy Tools, rgCaCo.py started 09/05/2010 21:23:49 diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgGLMtest1_GLM_log.txt --- a/test-data/rgGLMtest1_GLM_log.txt Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgGLMtest1_GLM_log.txt Mon May 10 10:17:11 2010 -0400 @@ -1,11 +1,11 @@ -rgGLM.py called with ['/opt/galaxy/tools/rgenetics/rgGLM.py', '/opt/galaxy/test-data/tinywga', '/opt/galaxy/test-data/tinywga', 'rgGLMtest1', 'c1', '', '/opt/galaxy/test-data/rgGLMtest1_GLM.xls', '/opt/galaxy/test-data/rgGLMtest1_GLM_log.txt', 'tinywga', '', '', '', '1', '1', '0', '0', '/opt/galaxy/test-data/rgGLM_GLM_topTable.gff'] -vcl=['plink', '--noweb', '--bfile', '/opt/galaxy/test-data/tinywga', '--pheno-name', '"c1"', '--pheno', '/opt/galaxy/test-data/tinywga.pphe', '--out', 'tinywga', '--mind 1', '--geno 1', '--maf 0', '--linear'] -xformQassoc got resf=/tmp/tmpCB6CwWrgGLM/tinywga.assoc.linear, outfname=/opt/galaxy/test-data/rgGLMtest1_GLM.xls +rgGLM.py called with ['/share/shared/galaxy/tools/rgenetics/rgGLM.py', '/share/shared/galaxy/test-data/tinywga', '/share/shared/galaxy/test-data/tinywga', 'rgGLMtest1', 'c1', '', '/share/shared/galaxy/test-data/rgGLMtest1_GLM.xls', '/share/shared/galaxy/test-data/rgGLMtest1_GLM_log.txt', 'tinywga', '', '', '', '1', '1', '0', '0', '/share/shared/galaxy/test-data/rgGLMtest1_GLM_topTable.gff'] +vcl=['plink', '--noweb', '--bfile', '/share/shared/galaxy/test-data/tinywga', '--pheno-name', '"c1"', '--pheno', '/share/shared/galaxy/test-data/tinywga.pphe', '--out', 'tinywga', '--mind 1', '--geno 1', '--maf 0', '--linear'] +xformQassoc got resf=/tmp/tmpXKEn_LrgGLM/tinywga.assoc.linear, outfname=/share/shared/galaxy/test-data/rgGLMtest1_GLM.xls ###maxp=1.188425,minp=0.046772,prange=1.641653,scalefact=609.142127 @----------------------------------------------------------@ -| PLINK! | v1.06 | 24/Apr/2009 | +| PLINK! | v1.07 | 10/Aug/2009 | |----------------------------------------------------------| | (C) 2009 Shaun Purcell, GNU General Public License, v2 | |----------------------------------------------------------| @@ -15,31 +15,31 @@ Skipping web check... [ --noweb ] Writing this text to log file [ tinywga.log ] -Analysis started: Thu Mar 25 21:01:31 2010 +Analysis started: Sun May 9 21:23:49 2010 Options in effect: --noweb - --bfile /opt/galaxy/test-data/tinywga + --bfile /share/shared/galaxy/test-data/tinywga --pheno-name c1 - --pheno /opt/galaxy/test-data/tinywga.pphe + --pheno /share/shared/galaxy/test-data/tinywga.pphe --out tinywga --mind 1 --geno 1 --maf 0 --linear -Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] -25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ] -Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] -40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] +Reading map (extended format) from [ /share/shared/galaxy/test-data/tinywga.bim ] +25 markers to be included from [ /share/shared/galaxy/test-data/tinywga.bim ] +Reading pedigree information from [ /share/shared/galaxy/test-data/tinywga.fam ] +40 individuals read from [ /share/shared/galaxy/test-data/tinywga.fam ] 40 individuals with nonmissing phenotypes Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) Missing phenotype value is also -9 10 cases, 30 controls and 0 missing 21 males, 19 females, and 0 of unspecified sex -Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] +Reading genotype bitfile from [ /share/shared/galaxy/test-data/tinywga.bed ] Detected that binary PED file is v1.00 SNP-major mode -Reading alternate phenotype from [ /opt/galaxy/test-data/tinywga.pphe ] +Reading alternate phenotype from [ /share/shared/galaxy/test-data/tinywga.pphe ] 40 individuals with non-missing alternate phenotype Assuming a quantitative trait Missing phenotype value is -9 @@ -54,5 +54,5 @@ Converting data to Individual-major format Writing linear model association results to [ tinywga.assoc.linear ] -Analysis finished: Thu Mar 25 21:01:31 2010 +Analysis finished: Sun May 9 21:23:49 2010 diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgQQtest1.pdf --- a/test-data/rgQQtest1.pdf Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgQQtest1.pdf Mon May 10 10:17:11 2010 -0400 @@ -2,8 +2,8 @@ %âãÏÓ\r 1 0 obj << -/CreationDate (D:20100325210132) -/ModDate (D:20100325210132) +/CreationDate (D:20100509212350) +/ModDate (D:20100509212350) /Title (R Graphics Output) /Producer (R 2.10.1) /Creator (R) @@ -331,10 +331,42 @@ 8 0 obj << /Type /Encoding -/BaseEncoding /WinAnsiEncoding -/Differences [ 45/minus 96/quoteleft -144/dotlessi /grave /acute /circumflex /tilde /macron /breve /dotaccent -/dieresis /.notdef /ring /cedilla /.notdef /hungarumlaut /ogonek /caron /space] +/BaseEncoding /PDFDocEncoding +/Differences [ + 0/.notdef 1/.notdef 2/.notdef 3/.notdef 4/.notdef 5/.notdef 6/.notdef 7/.notdef + 8/.notdef 9/.notdef 10/.notdef 11/.notdef 12/.notdef 13/.notdef 14/.notdef 15/.notdef + 16/.notdef 17/.notdef 18/.notdef 19/.notdef 20/.notdef 21/.notdef 22/.notdef 23/.notdef + 24/.notdef 25/.notdef 26/.notdef 27/.notdef 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142/.notdef 143/.notdef + 144/dotlessi 145/grave 146/acute 147/circumflex 148/tilde 149/macron 150/breve 151/dotaccent + 152/dieresis 153/.notdef 154/ring 155/cedilla 156/.notdef 157/hungarumlaut 158/ogonek 159/caron + 160/space 161/exclamdown 162/cent 163/sterling 164/Euro 165/yen 166/Scaron 167/section + 168/scaron 169/copyright 170/ordfeminine 171/guillemotleft 172/logicalnot 173/hyphen 174/registered 175/macron + 176/degree 177/plusminus 178/twosuperior 179/threesuperior 180/Zcaron 181/mu 182/paragraph 183/periodcentered + 184/zcaron 185/onesuperior 186/ordmasculine 187/guillemotright 188/OE 189/oe 190/Ydieresis 191/questiondown + 192/Agrave 193/Aacute 194/Acircumflex 195/Atilde 196/Adieresis 197/Aring 198/AE 199/Ccedilla + 200/Egrave 201/Eacute 202/Ecircumflex 203/Edieresis 204/Igrave 205/Iacute 206/Icircumflex 207/Idieresis + 208/Eth 209/Ntilde 210/Ograve 211/Oacute 212/Ocircumflex 213/Otilde 214/Odieresis 215/multiply + 216/Oslash 217/Ugrave 218/Uacute 219/Ucircumflex 220/Udieresis 221/Yacute 222/Thorn 223/germandbls + 224/agrave 225/aacute 226/acircumflex 227/atilde 228/adieresis 229/aring 230/ae 231/ccedilla + 232/egrave 233/eacute 234/ecircumflex 235/edieresis 236/igrave 237/iacute 238/icircumflex 239/idieresis + 240/eth 241/ntilde 242/ograve 243/oacute 244/ocircumflex 245/otilde 246/odieresis 247/divide + 248/oslash 249/ugrave 250/uacute 251/ucircumflex 252/udieresis 253/yacute 254/thorn 255/ydieresis + +] >> endobj 9 0 obj @@ -370,9 +402,9 @@ 0000000293 00000 n 0000006405 00000 n 0000006612 00000 n -0000006869 00000 n -0000006952 00000 n -0000007049 00000 n +0000009405 00000 n +0000009488 00000 n +0000009585 00000 n trailer << /Size 12 @@ -380,5 +412,5 @@ /Root 2 0 R >> startxref -7151 +9687 %%EOF diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgTDTtest1_TDT_log.txt --- a/test-data/rgTDTtest1_TDT_log.txt Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgTDTtest1_TDT_log.txt Mon May 10 10:17:11 2010 -0400 @@ -1,6 +1,6 @@ @----------------------------------------------------------@ -| PLINK! | v1.06 | 24/Apr/2009 | +| PLINK! | v1.07 | 10/Aug/2009 | |----------------------------------------------------------| | (C) 2009 Shaun Purcell, GNU General Public License, v2 | |----------------------------------------------------------| @@ -10,25 +10,25 @@ Skipping web check... [ --noweb ] Writing this text to log file [ rgTDTtest1.log ] -Analysis started: Thu Mar 25 21:01:31 2010 +Analysis started: Sun May 9 21:23:49 2010 Options in effect: --noweb - --bfile /opt/galaxy/test-data/tinywga + --bfile /share/shared/galaxy/test-data/tinywga --out rgTDTtest1 --mind 0.5 --tdt -Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] -25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ] -Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] -40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] +Reading map (extended format) from [ /share/shared/galaxy/test-data/tinywga.bim ] +25 markers to be included from [ /share/shared/galaxy/test-data/tinywga.bim ] +Reading pedigree information from [ /share/shared/galaxy/test-data/tinywga.fam ] +40 individuals read from [ /share/shared/galaxy/test-data/tinywga.fam ] 40 individuals with nonmissing phenotypes Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) Missing phenotype value is also -9 10 cases, 30 controls and 0 missing 21 males, 19 females, and 0 of unspecified sex -Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] +Reading genotype bitfile from [ /share/shared/galaxy/test-data/tinywga.bed ] Detected that binary PED file is v1.00 SNP-major mode Before frequency and genotyping pruning, there are 25 SNPs 27 founders and 13 non-founders found @@ -48,6 +48,6 @@ 0 Mendel errors detected in total Writing TDT results (asymptotic) to [ rgTDTtest1.tdt ] -Analysis finished: Thu Mar 25 21:01:31 2010 +Analysis finished: Sun May 9 21:23:49 2010 ###maxp=0.590405,minp=-0.000000,prange=1.090405,scalefact=917.090439 diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgClean/rgCleantest1.log --- a/test-data/rgtestouts/rgClean/rgCleantest1.log Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgClean/rgCleantest1.log Mon May 10 10:17:11 2010 -0400 @@ -1,7 +1,7 @@ -rgClean.py started, called as /opt/galaxy/tools/rgenetics/rgClean.py /opt/galaxy/test-data tinywga rgCleantest1 1 1 0 0 1 1 /opt/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.pbed /opt/galaxy/test-data/rgtestouts/rgClean 0 0 0 0 +rgClean.py started, called as /share/shared/galaxy/tools/rgenetics/rgClean.py /share/shared/galaxy/test-data tinywga rgCleantest1 1 1 0 0 1 1 /share/shared/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.pbed /share/shared/galaxy/test-data/rgtestouts/rgClean 0 0 0 0 @----------------------------------------------------------@ -| PLINK! | v1.06 | 24/Apr/2009 | +| PLINK! | v1.07 | 10/Aug/2009 | |----------------------------------------------------------| | (C) 2009 Shaun Purcell, GNU General Public License, v2 | |----------------------------------------------------------| @@ -10,14 +10,14 @@ @----------------------------------------------------------@ Skipping web check... [ --noweb ] -Writing this text to log file [ /opt/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.log ] -Analysis started: Thu Mar 25 21:01:24 2010 +Writing this text to log file [ /share/shared/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.log ] +Analysis started: Sun May 9 21:23:43 2010 Options in effect: --noweb ---bfile /opt/galaxy/test-data/tinywga +--bfile /share/shared/galaxy/test-data/tinywga --make-bed ---out /opt/galaxy/test-data/rgtestouts/rgClean/rgCleantest1 +--out /share/shared/galaxy/test-data/rgtestouts/rgClean/rgCleantest1 --set-hh-missing --mind 1 --geno 1 @@ -25,16 +25,16 @@ --hwe 0 --me 1 1 -Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] -25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ] -Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] -40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] +Reading map (extended format) from [ /share/shared/galaxy/test-data/tinywga.bim ] +25 markers to be included from [ /share/shared/galaxy/test-data/tinywga.bim ] +Reading pedigree information from [ /share/shared/galaxy/test-data/tinywga.fam ] +40 individuals read from [ /share/shared/galaxy/test-data/tinywga.fam ] 40 individuals with nonmissing phenotypes Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) Missing phenotype value is also -9 10 cases, 30 controls and 0 missing 21 males, 19 females, and 0 of unspecified sex -Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] +Reading genotype bitfile from [ /share/shared/galaxy/test-data/tinywga.bed ] Detected that binary PED file is v1.00 SNP-major mode Before frequency and genotyping pruning, there are 25 SNPs 27 founders and 13 non-founders found @@ -57,10 +57,10 @@ 0 Mendel errors detected in total 0 families ( 0 individuals ) removed due to Mendel errors 0 markers removed due to Mendel errors, 25 remaining -Writing pedigree information to [ /opt/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.fam ] -Writing map (extended format) information to [ /opt/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.bim ] -Writing genotype bitfile to [ /opt/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.bed ] +Writing pedigree information to [ /share/shared/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.fam ] +Writing map (extended format) information to [ /share/shared/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.bim ] +Writing genotype bitfile to [ /share/shared/galaxy/test-data/rgtestouts/rgClean/rgCleantest1.bed ] Using (default) SNP-major mode Converting data to SNP-major format -Analysis finished: Thu Mar 25 21:01:24 2010 +Analysis finished: Sun May 9 21:23:43 2010 diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgEigPCA/Rplots.pdf --- a/test-data/rgtestouts/rgEigPCA/Rplots.pdf Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgEigPCA/Rplots.pdf Mon May 10 10:17:11 2010 -0400 @@ -2,8 +2,8 @@ %âãÏÓ\r 1 0 obj << -/CreationDate (D:20100325210125) -/ModDate (D:20100325210125) +/CreationDate (D:20100509212343) +/ModDate (D:20100509212343) /Title (R Graphics Output) /Producer (R 2.10.1) /Creator (R) @@ -34,10 +34,42 @@ 5 0 obj << /Type /Encoding -/BaseEncoding /WinAnsiEncoding -/Differences [ 45/minus 96/quoteleft -144/dotlessi /grave /acute /circumflex /tilde /macron /breve /dotaccent -/dieresis /.notdef /ring /cedilla /.notdef /hungarumlaut /ogonek /caron /space] +/BaseEncoding /PDFDocEncoding +/Differences [ + 0/.notdef 1/.notdef 2/.notdef 3/.notdef 4/.notdef 5/.notdef 6/.notdef 7/.notdef + 8/.notdef 9/.notdef 10/.notdef 11/.notdef 12/.notdef 13/.notdef 14/.notdef 15/.notdef + 16/.notdef 17/.notdef 18/.notdef 19/.notdef 20/.notdef 21/.notdef 22/.notdef 23/.notdef + 24/.notdef 25/.notdef 26/.notdef 27/.notdef 28/.notdef 29/.notdef 30/.notdef 31/.notdef + 32/space 33/exclam 34/quotedbl 35/numbersign 36/dollar 37/percent 38/ampersand 39/quoteright + 40/parenleft 41/parenright 42/asterisk 43/plus 44/comma 45/minus 46/period 47/slash + 48/zero 49/one 50/two 51/three 52/four 53/five 54/six 55/seven + 56/eight 57/nine 58/colon 59/semicolon 60/less 61/equal 62/greater 63/question + 64/at 65/A 66/B 67/C 68/D 69/E 70/F 71/G + 72/H 73/I 74/J 75/K 76/L 77/M 78/N 79/O + 80/P 81/Q 82/R 83/S 84/T 85/U 86/V 87/W + 88/X 89/Y 90/Z 91/bracketleft 92/backslash 93/bracketright 94/asciicircum 95/underscore + 96/quoteleft 97/a 98/b 99/c 100/d 101/e 102/f 103/g + 104/h 105/i 106/j 107/k 108/l 109/m 110/n 111/o + 112/p 113/q 114/r 115/s 116/t 117/u 118/v 119/w + 120/x 121/y 122/z 123/braceleft 124/bar 125/braceright 126/asciitilde 127/.notdef + 128/.notdef 129/.notdef 130/.notdef 131/.notdef 132/.notdef 133/.notdef 134/.notdef 135/.notdef + 136/.notdef 137/.notdef 138/.notdef 139/.notdef 140/.notdef 141/.notdef 142/.notdef 143/.notdef + 144/dotlessi 145/grave 146/acute 147/circumflex 148/tilde 149/macron 150/breve 151/dotaccent + 152/dieresis 153/.notdef 154/ring 155/cedilla 156/.notdef 157/hungarumlaut 158/ogonek 159/caron + 160/space 161/exclamdown 162/cent 163/sterling 164/Euro 165/yen 166/Scaron 167/section + 168/scaron 169/copyright 170/ordfeminine 171/guillemotleft 172/logicalnot 173/hyphen 174/registered 175/macron + 176/degree 177/plusminus 178/twosuperior 179/threesuperior 180/Zcaron 181/mu 182/paragraph 183/periodcentered + 184/zcaron 185/onesuperior 186/ordmasculine 187/guillemotright 188/OE 189/oe 190/Ydieresis 191/questiondown + 192/Agrave 193/Aacute 194/Acircumflex 195/Atilde 196/Adieresis 197/Aring 198/AE 199/Ccedilla + 200/Egrave 201/Eacute 202/Ecircumflex 203/Edieresis 204/Igrave 205/Iacute 206/Icircumflex 207/Idieresis + 208/Eth 209/Ntilde 210/Ograve 211/Oacute 212/Ocircumflex 213/Otilde 214/Odieresis 215/multiply + 216/Oslash 217/Ugrave 218/Uacute 219/Ucircumflex 220/Udieresis 221/Yacute 222/Thorn 223/germandbls + 224/agrave 225/aacute 226/acircumflex 227/atilde 228/adieresis 229/aring 230/ae 231/ccedilla + 232/egrave 233/eacute 234/ecircumflex 235/edieresis 236/igrave 237/iacute 238/icircumflex 239/idieresis + 240/eth 241/ntilde 242/ograve 243/oacute 244/ocircumflex 245/otilde 246/odieresis 247/divide + 248/oslash 249/ugrave 250/uacute 251/ucircumflex 252/udieresis 253/yacute 254/thorn 255/ydieresis + +] >> endobj xref @@ -55,5 +87,5 @@ /Root 2 0 R >> startxref -618 +3154 %%EOF diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.R --- a/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.R Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.R Mon May 10 10:17:11 2010 -0400 @@ -16,4 +16,4 @@ legend("top",legend=llist,pch=glist,col=glist,title="Sample") grid(nx = 10, ny = 10, col = "lightgray", lty = "dotted") dev.off() -#R script autogenerated by rgenetics/rgutils.py on 25/03/2010 21:01:25 +#R script autogenerated by rgenetics/rgutils.py on 09/05/2010 21:23:43 diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.html --- a/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.html Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1.html Mon May 10 10:17:11 2010 -0400 @@ -9,30 +9,27 @@ </head> <body> <div class="document"> -<h4>Output from rgEigPCA.py run at 25/03/2010 21:01:25<br/> +<h4>Output from rgEigPCA.py run at 09/05/2010 21:23:43<br/> </h4> -newfilepath=/opt/galaxy/test-data/rgtestouts/rgEigPCA, rexe=R(click on the image below to see a much higher quality PDF version)<table border="0" cellpadding="10" cellspacing="10"><tr><td> +newfilepath=/share/shared/galaxy/test-data/rgtestouts/rgEigPCA, rexe=R(click on the image below to see a much higher quality PDF version)<table border="0" cellpadding="10" cellspacing="10"><tr><td> <a href="rgEigPCAtest1_PCAPlot.pdf"><img src="rgEigPCAtest1_PCAPlot.pdf.png" alt="Samples plotted in first 2 eigenvector space" hspace="10" align="left" /></a></td></tr></table><br/> -<div class="document">All Files:<ol><li><a href="rgEigPCAtest1_eval.xls">rgEigPCAtest1_eval.xls (507 B)</a></li> -<li><a href="rgEigPCAtest1_pca.xls.par">rgEigPCAtest1_pca.xls.par (311 B)</a></li> +<div class="document">All Files:<ol><li><a href="rgEigPCAtest1.html">rgEigPCAtest1.html </a></li> +<li><a href="rgEigPCAtest1_pca.xls.par">rgEigPCAtest1_pca.xls.par (338 B)</a></li> +<li><a href="rgEigPCAtest1.txt">rgEigPCAtest1.txt (3.3 KB)</a></li> +<li><a href="rgEigPCAtest1_log.txt">rgEigPCAtest1_log.txt (6.1 KB)</a></li> +<li><a href="rgEigPCAtest1_PCAPlot.pdf">rgEigPCAtest1_PCAPlot.pdf (10.4 KB)</a></li> +<li><a href="rgEigPCAtest1_eval.xls">rgEigPCAtest1_eval.xls (507 B)</a></li> +<li><a href="rgEigPCAtest1_pca.xls">rgEigPCAtest1_pca.xls (1.2 KB)</a></li> +<li><a href="rgEigPCAtest1.R">rgEigPCAtest1.R (1.6 KB)</a></li> +<li><a href="Rplots.pdf">Rplots.pdf (3.3 KB)</a></li> +<li><a href="rgEigPCAtest1_pca.xls.evec">rgEigPCAtest1_pca.xls.evec (3.3 KB)</a></li> <li><a href="rgEigPCAtest1_PCAPlot.pdf.png">rgEigPCAtest1_PCAPlot.pdf.png (27.1 KB)</a></li> -<li><a href="rgEigPCAtest1_log.txt">rgEigPCAtest1_log.txt (6.0 KB)</a></li> -<li><a href="rgEigPCAtest1.html">rgEigPCAtest1.html </a></li> -<li><a href="rgEigPCAtest1_eigensoftplot.pdf.xtxt">rgEigPCAtest1_eigensoftplot.pdf.xtxt (257 B)</a></li> -<li><a href="rgEigPCAtest1_eigensoftplot.pdf.ps">rgEigPCAtest1_eigensoftplot.pdf.ps (13.6 KB)</a></li> -<li><a href="rgEigPCAtest1_pca.xls.evec">rgEigPCAtest1_pca.xls.evec (3.3 KB)</a></li> -<li><a href="rgEigPCAtest1_pca.xls">rgEigPCAtest1_pca.xls (1.3 KB)</a></li> -<li><a href="rgEigPCAtest1_PCAPlot.pdf">rgEigPCAtest1_PCAPlot.pdf (7.9 KB)</a></li> -<li><a href="rgEigPCAtest1.txt">rgEigPCAtest1.txt (3.3 KB)</a></li> -<li><a href="rgEigPCAtest1_eigensoftplot.pdf.pdf">rgEigPCAtest1_eigensoftplot.pdf.pdf (2.1 KB)</a></li> -<li><a href="rgEigPCAtest1.R">rgEigPCAtest1.R (1.6 KB)</a></li> -<li><a href="Rplots.pdf">Rplots.pdf (813 B)</a></li> </ol></div><div class="document">Log rgEigPCAtest1_log.txt contents follow below<p/><pre>parameter file: rgEigPCAtest1_pca.xls.par ### THE INPUT PARAMETERS ##PARAMETER NAME: VALUE -genotypename: /opt/galaxy/test-data/tinywga.ped -snpname: /opt/galaxy/test-data/tinywga.map -indivname: /opt/galaxy/test-data/tinywga.ped +genotypename: /share/shared/galaxy/test-data/tinywga.ped +snpname: /share/shared/galaxy/test-data/tinywga.map +indivname: /share/shared/galaxy/test-data/tinywga.ped evecoutname: rgEigPCAtest1_pca.xls.evec evaloutname: rgEigPCAtest1_eval.xls altnormstyle: NO @@ -156,5 +153,5 @@ Correlation between eigenvector 3 (of 4) and Case/Control status is 0.193 Correlation between eigenvector 4 (of 4) and Case/Control status is -0.069 </pre></div>If you need to rerun this analysis, the command line used was -smartpca.perl -i /opt/galaxy/test-data/tinywga.ped -a /opt/galaxy/test-data/tinywga.map -b /opt/galaxy/test-data/tinywga.ped -o rgEigPCAtest1_pca.xls -p rgEigPCAtest1_eigensoftplot.pdf -e rgEigPCAtest1_eval.xls -l rgEigPCAtest1_log.txt -k 4 -m 2 -t 2 -s 2 +smartpca.perl -i /share/shared/galaxy/test-data/tinywga.ped -a /share/shared/galaxy/test-data/tinywga.map -b /share/shared/galaxy/test-data/tinywga.ped -o rgEigPCAtest1_pca.xls -p rgEigPCAtest1_eigensoftplot.pdf -e rgEigPCAtest1_eval.xls -l rgEigPCAtest1_log.txt -k 4 -m 2 -t 2 -s 2 <p/></div></body></html> diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_PCAPlot.pdf --- a/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_PCAPlot.pdf Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_PCAPlot.pdf Mon May 10 10:17:11 2010 -0400 @@ -2,8 +2,8 @@ %âãÏÓ\r 1 0 obj << -/CreationDate (D:20100325210125) -/ModDate (D:20100325210125) +/CreationDate (D:20100509212343) +/ModDate (D:20100509212343) /Title (R Graphics Output) /Producer (R 2.10.1) /Creator (R) @@ -410,10 +410,42 @@ 8 0 obj << /Type /Encoding -/BaseEncoding /WinAnsiEncoding -/Differences [ 45/minus 96/quoteleft -144/dotlessi /grave /acute /circumflex /tilde /macron /breve /dotaccent -/dieresis 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95/underscore + 96/quoteleft 97/a 98/b 99/c 100/d 101/e 102/f 103/g + 104/h 105/i 106/j 107/k 108/l 109/m 110/n 111/o + 112/p 113/q 114/r 115/s 116/t 117/u 118/v 119/w + 120/x 121/y 122/z 123/braceleft 124/bar 125/braceright 126/asciitilde 127/.notdef + 128/.notdef 129/.notdef 130/.notdef 131/.notdef 132/.notdef 133/.notdef 134/.notdef 135/.notdef + 136/.notdef 137/.notdef 138/.notdef 139/.notdef 140/.notdef 141/.notdef 142/.notdef 143/.notdef + 144/dotlessi 145/grave 146/acute 147/circumflex 148/tilde 149/macron 150/breve 151/dotaccent + 152/dieresis 153/.notdef 154/ring 155/cedilla 156/.notdef 157/hungarumlaut 158/ogonek 159/caron + 160/space 161/exclamdown 162/cent 163/sterling 164/Euro 165/yen 166/Scaron 167/section + 168/scaron 169/copyright 170/ordfeminine 171/guillemotleft 172/logicalnot 173/hyphen 174/registered 175/macron + 176/degree 177/plusminus 178/twosuperior 179/threesuperior 180/Zcaron 181/mu 182/paragraph 183/periodcentered + 184/zcaron 185/onesuperior 186/ordmasculine 187/guillemotright 188/OE 189/oe 190/Ydieresis 191/questiondown + 192/Agrave 193/Aacute 194/Acircumflex 195/Atilde 196/Adieresis 197/Aring 198/AE 199/Ccedilla + 200/Egrave 201/Eacute 202/Ecircumflex 203/Edieresis 204/Igrave 205/Iacute 206/Icircumflex 207/Idieresis + 208/Eth 209/Ntilde 210/Ograve 211/Oacute 212/Ocircumflex 213/Otilde 214/Odieresis 215/multiply + 216/Oslash 217/Ugrave 218/Uacute 219/Ucircumflex 220/Udieresis 221/Yacute 222/Thorn 223/germandbls + 224/agrave 225/aacute 226/acircumflex 227/atilde 228/adieresis 229/aring 230/ae 231/ccedilla + 232/egrave 233/eacute 234/ecircumflex 235/edieresis 236/igrave 237/iacute 238/icircumflex 239/idieresis + 240/eth 241/ntilde 242/ograve 243/oacute 244/ocircumflex 245/otilde 246/odieresis 247/divide + 248/oslash 249/ugrave 250/uacute 251/ucircumflex 252/udieresis 253/yacute 254/thorn 255/ydieresis + +] >> endobj 9 0 obj << @@ -441,8 +473,8 @@ 0000000293 00000 n 0000007168 00000 n 0000007363 00000 n -0000007620 00000 n -0000007716 00000 n +0000010156 00000 n +0000010252 00000 n trailer << /Size 11 @@ -450,5 +482,5 @@ /Root 2 0 R >> startxref -7818 +10354 %%EOF diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_log.txt --- a/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_log.txt Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_log.txt Mon May 10 10:17:11 2010 -0400 @@ -1,9 +1,9 @@ parameter file: rgEigPCAtest1_pca.xls.par ### THE INPUT PARAMETERS ##PARAMETER NAME: VALUE -genotypename: /opt/galaxy/test-data/tinywga.ped -snpname: /opt/galaxy/test-data/tinywga.map -indivname: /opt/galaxy/test-data/tinywga.ped +genotypename: /share/shared/galaxy/test-data/tinywga.ped +snpname: /share/shared/galaxy/test-data/tinywga.map +indivname: /share/shared/galaxy/test-data/tinywga.ped evecoutname: rgEigPCAtest1_pca.xls.evec evaloutname: rgEigPCAtest1_eval.xls altnormstyle: NO diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls --- a/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgEigPCA/rgEigPCAtest1_pca.xls Mon May 10 10:17:11 2010 -0400 @@ -3,43 +3,43 @@ 7.7400 7.2550 4.2710 - 0.3015 0.2159 0.0173 0.3393 - -0.2453 -0.0165 -0.0856 0.0221 - 0.0268 -0.0008 0.3404 -0.0369 - 0.3015 0.2159 0.0173 0.3393 - -0.2453 -0.0165 -0.0856 0.0221 - 0.0268 -0.0008 0.3404 -0.0369 - 0.3015 0.2159 0.0173 0.3393 - -0.2453 -0.0165 -0.0856 0.0221 - 0.0268 -0.0008 0.3404 -0.0369 - 0.3015 0.2159 0.0173 0.3393 - -0.2453 -0.0165 -0.0856 0.0221 - 0.0268 -0.0008 0.3404 -0.0369 - 0.3015 0.2159 0.0173 0.3393 - -0.2453 -0.0165 -0.0856 0.0221 - 0.0268 -0.0008 0.3404 -0.0369 - 0.3015 0.2159 0.0173 0.3393 - -0.2453 -0.0165 -0.0856 0.0221 - 0.0268 -0.0008 0.3404 -0.0369 - 0.3015 0.2159 0.0173 0.3393 - -0.1608 -0.0349 0.0222 0.1244 - -0.1027 0.2939 -0.1091 -0.1832 - 0.2593 -0.1916 -0.2862 -0.1609 - 0.0302 0.2348 0.0136 0.1216 - -0.2453 -0.0165 -0.0856 0.0221 - 0.3015 0.2159 0.0173 0.3393 - -0.1608 -0.0349 0.0222 0.1244 - -0.1027 0.2939 -0.1091 -0.1832 - 0.2593 -0.1916 -0.2862 -0.1609 - -0.2453 -0.0165 -0.0856 0.0221 - -0.2493 -0.2867 -0.1811 0.1404 - 0.3015 0.2159 0.0173 0.3393 - -0.1027 0.2939 -0.1091 -0.1832 - 0.2593 -0.1916 -0.2862 -0.1609 - 0.0302 0.2348 0.0136 0.1216 - -0.2453 -0.0165 -0.0856 0.0221 - -0.2453 -0.0165 -0.0856 0.0221 - 0.3015 0.2159 0.0173 0.3393 - 0.2593 -0.1916 -0.2862 -0.1609 - 0.0302 0.2348 0.0136 0.1216 - 0.2593 -0.1916 -0.2862 -0.1609 + 0.0000 0.0000 0.0000 0.0000 + 0.0000 0.0000 0.0000 0.0000 + 0.0000 0.0000 0.0000 0.0000 + 0.0000 0.0000 0.0000 0.0000 + 0.0000 0.0000 0.0000 0.0000 + 0.0000 0.0000 0.0000 0.0000 + 0.0000 0.0000 0.0000 0.0000 + 0.0000 0.0000 0.0000 0.0000 + 0.0000 0.0000 0.0000 0.0000 + 0.0000 0.0000 0.0000 0.0000 + 0.0000 0.0000 0.0000 0.0000 + 0.0000 0.0000 0.0000 0.0000 + 0.0000 0.0000 0.0000 0.0000 + 0.0000 0.0000 0.0000 0.0000 + 0.0000 0.0000 0.0000 0.0000 + 0.0000 0.0000 0.0000 0.0000 + 0.0000 0.0000 0.0000 0.0000 + 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/opt/galaxy/test-data/tinywga.ped -snpname: /opt/galaxy/test-data/tinywga.map -indivname: /opt/galaxy/test-data/tinywga.ped +genotypename: /share/shared/galaxy/test-data/tinywga.ped +snpname: /share/shared/galaxy/test-data/tinywga.map +indivname: /share/shared/galaxy/test-data/tinywga.ped evecoutname: rgEigPCAtest1_pca.xls.evec evaloutname: rgEigPCAtest1_eval.xls altnormstyle: NO diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgGRR/Log_rgGRRtest1.txt --- a/test-data/rgtestouts/rgGRR/Log_rgGRRtest1.txt Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgGRR/Log_rgGRRtest1.txt Mon May 10 10:17:11 2010 -0400 @@ -1,13 +1,13 @@ Reading genotypes for 40 subjects and 5 markers Calculating 780 pairs... Estimated time is 0.00 to 0.00 seconds ... -T1: 0.00229454040527 T2: 0.0166795253754 T3: 0.000442743301392 TOT: 0.0201091766357 0 pairs with no (or not enough) comparable genotypes (0.0%) +T1: 0.00482821464539 T2: 0.0623338222504 T3: 0.000771522521973 TOT: 0.0691449642181 0 pairs with no (or not enough) comparable genotypes (0.0%) Relstate dupe: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 -Relstate parentchild: mean(mean)=1.82 sdev(mean)=0.14, mean(sdev)=0.33 sdev(sdev)=0.22 +Relstate parentchild: mean(mean)=1.73 sdev(mean)=0.20, mean(sdev)=0.38 sdev(sdev)=0.23 Relstate sibpairs: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 Relstate halfsibs: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 -Relstate parents: mean(mean)=1.62 sdev(mean)=0.21, mean(sdev)=0.53 sdev(sdev)=0.29 -Relstate unrelated: mean(mean)=1.60 sdev(mean)=0.23, mean(sdev)=0.54 sdev(sdev)=0.22 +Relstate parents: mean(mean)=1.63 sdev(mean)=0.20, mean(sdev)=0.54 sdev(sdev)=0.22 +Relstate unrelated: mean(mean)=1.55 sdev(mean)=0.24, mean(sdev)=0.59 sdev(sdev)=0.24 Relstate unknown: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 780 pairs are available of 780 Outliers: 0 diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgGRR/rgGRRtest1.html --- a/test-data/rgtestouts/rgGRR/rgGRRtest1.html Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgGRR/rgGRRtest1.html Mon May 10 10:17:11 2010 -0400 @@ -9,34 +9,34 @@ </head> <body> <div class="document"> -<h4><div>Output from rgGRR.py run at 15/04/2010 13:12:45<br> +<h4><div>Output from rgGRR.py run at 09/05/2010 21:23:42<br> </h4> If you need to rerun this analysis, the command line was -<pre>'/opt/galaxy/tools/rgenetics/rgGRR.py' '/opt/galaxy/test-data/tinywga' 'tinywga' '/opt/galaxy/test-data/rgtestouts/rgGRR/rgGRRtest1.html' '/opt/galaxy/test-data/rgtestouts/rgGRR' 'rgGRRtest1' '100' '6'</pre> +<pre>'/share/shared/galaxy/tools/rgenetics/rgGRR.py' '/share/shared/galaxy/test-data/tinywga' 'tinywga' '/share/shared/galaxy/test-data/rgtestouts/rgGRR/rgGRRtest1.html' '/share/shared/galaxy/test-data/rgtestouts/rgGRR' 'rgGRRtest1' '100' '6' 'true'</pre> </div> <embed src="rgGRRtest1.svg" type="image/svg+xml" width="1150" height="600" /><div><h4>Click the links below to save output files and plots</h4><br><ol> <li><a href="rgGRRtest1.svg" type="image/svg+xml" >rgGRR Plot (requires SVG)</a></li> <li><a href="rgGRRtest1_table.xls">Mean by SD alleles shared - 780 rows</a></li> +<li><a href="Log_rgGRRtest1.txt">Log_rgGRRtest1.txt</a></li> <li><a href="rgGRRtest1.html">rgGRRtest1.html</a></li> -<li><a href="Log_rgGRRtest1.txt">Log_rgGRRtest1.txt</a></li> </ol></div><div><h2>Outliers in tab delimited files linked above are also listed below</h2></div><div><hr><h3>Log from this job (also stored in Log_rgGRRtest1.txt)</h3><pre>Reading genotypes for 40 subjects and 5 markers Calculating 780 pairs... Estimated time is 0.00 to 0.00 seconds ... -T1: 0.00229454040527 T2: 0.0166795253754 T3: 0.000442743301392 TOT: 0.0201091766357 0 pairs with no (or not enough) comparable genotypes (0.0%) +T1: 0.00482821464539 T2: 0.0623338222504 T3: 0.000771522521973 TOT: 0.0691449642181 0 pairs with no (or not enough) comparable genotypes (0.0%) Relstate dupe: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 -Relstate parentchild: mean(mean)=1.82 sdev(mean)=0.14, mean(sdev)=0.33 sdev(sdev)=0.22 +Relstate parentchild: mean(mean)=1.73 sdev(mean)=0.20, mean(sdev)=0.38 sdev(sdev)=0.23 Relstate sibpairs: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 Relstate halfsibs: mean(mean)=nan sdev(mean)=0.00, mean(sdev)=nan sdev(sdev)=0.00 -Relstate parents: mean(mean)=1.62 sdev(mean)=0.21, mean(sdev)=0.53 sdev(sdev)=0.29 +Relstate parents: mean(mean)=1.63 sdev(mean)=0.20, mean(sdev)=0.54 sdev(sdev)=0.22 -Relstate unrelated: mean(mean)=1.60 sdev(mean)=0.23, mean(sdev)=0.54 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1.023277 5 5 +1340_9 1344_13 1.400000 0.894427 -1.469163 1.023277 5 5 +1340_9 1345_12 1.400000 0.894427 1.029902 -0.619941 5 5 +1341_1 1341_11 1.400000 0.894427 -0.642422 0.715736 5 5 +1341_1 1341_12 1.400000 0.894427 0.354770 0.285726 5 5 +1341_1 1341_13 1.400000 0.894427 0.875635 -0.416708 5 5 +1341_1 1341_14 1.400000 0.894427 0.875635 -0.416708 5 5 +1341_1 1341_2 1.400000 0.894427 0.875635 -0.416708 5 5 +1341_1 1344_1 1.400000 0.894427 -1.469163 1.023277 5 5 +1341_1 1344_12 1.400000 0.894427 0.196880 -0.195857 5 5 +1341_1 1344_13 1.400000 0.894427 0.196880 -0.195857 5 5 +1341_1 1345_12 1.400000 0.894427 1.029902 -0.619941 5 5 +1341_11 1341_12 1.400000 0.894427 -1.140216 1.652064 5 5 +1341_11 1341_13 1.400000 0.894427 0.875635 -0.416708 5 5 +1341_11 1341_14 1.400000 0.894427 0.875635 -0.416708 5 5 +1341_11 1341_2 1.400000 0.894427 0.875635 -0.416708 5 5 +1341_11 1344_1 1.400000 0.894427 -1.469163 2.115187 5 5 +1341_11 1344_12 1.400000 0.894427 0.196880 -0.195857 5 5 +1341_11 1344_13 1.400000 0.894427 0.196880 -0.195857 5 5 +1341_11 1345_12 1.400000 0.894427 -0.636142 1.267018 5 5 +1341_12 1341_13 1.400000 0.894427 -0.132290 0.048238 5 5 +1341_12 1341_14 1.400000 0.894427 -0.132290 0.048238 5 5 +1341_12 1341_2 1.400000 0.894427 -0.132290 0.048238 5 5 +1341_12 1344_1 1.400000 0.894427 -2.302185 1.712469 5 5 +1341_12 1344_12 1.400000 0.894427 -0.636142 1.267018 5 5 +1341_12 1344_13 1.400000 0.894427 -0.636142 1.267018 5 5 +1341_12 1345_12 1.400000 0.894427 1.862924 -2.506901 5 5 +1341_13 1341_14 1.400000 0.894427 1.883560 -2.485480 5 5 +1341_13 1341_2 1.400000 0.894427 1.351962 -1.627597 5 5 +1341_13 1344_1 1.400000 0.894427 -2.302185 1.712469 5 5 +1341_13 1344_12 1.400000 0.894427 -0.636142 -0.195857 5 5 +1341_13 1344_13 1.400000 0.894427 -0.636142 -0.195857 5 5 +1341_13 1345_12 1.400000 0.894427 0.196880 -0.195857 5 5 +1341_14 1341_2 1.400000 0.894427 1.351962 -1.627597 5 5 +1341_14 1344_1 1.400000 0.894427 -2.302185 1.712469 5 5 +1341_14 1344_12 1.400000 0.894427 -0.636142 -0.195857 5 5 +1341_14 1344_13 1.400000 0.894427 -0.636142 -0.195857 5 5 +1341_14 1345_12 1.400000 0.894427 0.196880 -0.195857 5 5 +1341_2 1344_1 1.400000 0.894427 -2.302185 1.712469 5 5 +1341_2 1344_12 1.400000 0.894427 -0.636142 -0.195857 5 5 +1341_2 1344_13 1.400000 0.894427 -0.636142 -0.195857 5 5 +1341_2 1345_12 1.400000 0.894427 0.196880 -0.195857 5 5 +1344_1 1344_12 1.400000 0.894427 -0.642422 0.715735 5 5 +1344_1 1344_13 1.400000 0.894427 -0.642422 0.715735 5 5 +1344_1 1345_12 1.400000 0.894427 -2.302185 1.712469 5 5 +1344_12 1344_13 1.400000 0.894427 1.883560 -2.485480 5 5 +1344_12 1345_12 1.400000 0.894427 -0.636142 1.267018 5 5 +1344_13 1345_12 1.400000 0.894427 -0.636142 1.267018 5 5 diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/1_rgHaploViewtest1.pdf Binary file test-data/rgtestouts/rgHaploView/1_rgHaploViewtest1.pdf has changed diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/1_rgHaploViewtest1.png Binary file test-data/rgtestouts/rgHaploView/1_rgHaploViewtest1.png has changed diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/2_HapMap_YRI_22.pdf Binary file test-data/rgtestouts/rgHaploView/2_HapMap_YRI_22.pdf has changed diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/2_HapMap_YRI_22.png Binary file test-data/rgtestouts/rgHaploView/2_HapMap_YRI_22.png has changed diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/Chromosome22YRI.LD.PNG Binary file test-data/rgtestouts/rgHaploView/Chromosome22YRI.LD.PNG has changed diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/Log_rgHaploViewtest1.txt --- a/test-data/rgtestouts/rgHaploView/Log_rgHaploViewtest1.txt Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgHaploView/Log_rgHaploViewtest1.txt Mon May 10 10:17:11 2010 -0400 @@ -1,7 +1,7 @@ -PATH=/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/home/rerla/bin +PATH=/share/apps:/share/shared/lx26-amd64/bin:/udd/rerla/bin:/share/shared/lx26-amd64/bin:/opt/gridengine/bin/lx26-amd64:/opt/gridengine/bin/lx26-amd64:/usr/kerberos/bin:/usr/java/latest/bin:/usr/local/bin:/bin:/usr/bin:/opt/eclipse:/opt/ganglia/bin:/opt/ganglia/sbin:/opt/maven/bin:/opt/openmpi/bin/:/opt/rocks/bin:/opt/rocks/sbin:/opt/gridengine/bin:/opt/gridengine:/bin/lx26-amd64:/usr/X11R6/bin ## rgHaploView.py looking for 10 rs (['rs2283802', 'rs2267000', 'rs16997606', 'rs4820537', 'rs3788347'])## rgHaploView.py: wrote 10 markers, 40 subjects for region -## executing java -jar /opt/galaxy/tool-data/rg/bin/haploview.jar -n -memory 2048 -pairwiseTagging -pedfile /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -log /opt/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng -chromosome 22 returned 0 +## executing java -jar /share/shared/galaxy/tool-data/rg/bin/haploview.jar -n -memory 2048 -pairwiseTagging -pedfile /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -log /share/shared/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng -chromosome 22 returned 0 ## executing mogrify -resize 800x400! *.PNG returned 0 ## executing convert -resize 800x400! rgHaploViewtest1.ped.LD.PNG rgHaploViewtest1.tmp.png returned 0 ## executing convert -pointsize 25 -fill maroon -draw "text 10,300 'rgHaploViewtest1'" rgHaploViewtest1.tmp.png 1_rgHaploViewtest1.png returned 0 @@ -12,16 +12,16 @@ ## executing pdfjoin "*.pdf" --fitpaper true --outfile alljoin.pdf returned 0 ## executing pdfnup alljoin.pdf --nup 1x2 --outfile allnup.pdf returned 0 ***************************************************** -Haploview 4.2 Java Version: 1.6.0_03 +Haploview 4.2 Java Version: 1.6.0_13 ***************************************************** -Arguments: -n -pairwiseTagging -pedfile /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -log /opt/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng -chromosome 22 +Arguments: -n -pairwiseTagging -pedfile /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -log /share/shared/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng -chromosome 22 Max LD comparison distance = 200000kb -Using data file: /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -Using marker information file: /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info +Using data file: /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped +Using marker information file: /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info 10 out of 10 markers passed the MAF threshold. 10 out of 10 markers passed the Mendel threshold. 10 out of 10 markers passed the genotyping threshold. @@ -33,11 +33,11 @@ Writing output to rgHaploViewtest1.ped.TESTS Writing output to rgHaploViewtest1.ped.CHAPS ***************************************************** -Haploview 4.2 Java Version: 1.6.0_03 +Haploview 4.2 Java Version: 1.6.0_13 ***************************************************** -Arguments: -n -chromosome 22 -panel YRI -hapmapDownload -startpos 21784 -endpos 21905 -ldcolorscheme RSQ -log /opt/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng +Arguments: -n -chromosome 22 -panel YRI -hapmapDownload -startpos 21784 -endpos 21905 -ldcolorscheme RSQ -log /share/shared/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng Max LD comparison distance = 200000kb diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/alljoin.pdf Binary file test-data/rgtestouts/rgHaploView/alljoin.pdf has changed diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/allnup.pdf Binary file test-data/rgtestouts/rgHaploView/allnup.pdf has changed diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/rgHaploViewtest1.html --- a/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.html Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.html Mon May 10 10:17:11 2010 -0400 @@ -23,13 +23,13 @@ <li><a href="rgHaploViewtest1.ped.LD.PNG">rgHaploViewtest1.ped.LD.PNG - rgHaploViewtest1.ped.LD.PNG</a></li> <li><a href="rgHaploViewtest1.ped.TAGS">rgHaploViewtest1.ped.TAGS - rgHaploViewtest1.ped.TAGS Tagger output</a></li> <li><a href="rgHaploViewtest1.ped.TESTS">rgHaploViewtest1.ped.TESTS - rgHaploViewtest1.ped.TESTS Tagger output</a></li> -</ol><br></div><div><hr>Job Log follows below (see Log_rgHaploViewtest1.txt)<pre>PATH=/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/home/rerla/bin +</ol><br></div><div><hr>Job Log follows below (see Log_rgHaploViewtest1.txt)<pre>PATH=/share/apps:/share/shared/lx26-amd64/bin:/udd/rerla/bin:/share/shared/lx26-amd64/bin:/opt/gridengine/bin/lx26-amd64:/opt/gridengine/bin/lx26-amd64:/usr/kerberos/bin:/usr/java/latest/bin:/usr/local/bin:/bin:/usr/bin:/opt/eclipse:/opt/ganglia/bin:/opt/ganglia/sbin:/opt/maven/bin:/opt/openmpi/bin/:/opt/rocks/bin:/opt/rocks/sbin:/opt/gridengine/bin:/opt/gridengine:/bin/lx26-amd64:/usr/X11R6/bin ## rgHaploView.py looking for 10 rs (['rs2283802', 'rs2267000', 'rs16997606', 'rs4820537', 'rs3788347'])## rgHaploView.py: wrote 10 markers, 40 subjects for region -## executing java -jar /opt/galaxy/tool-data/rg/bin/haploview.jar -n -memory 2048 -pairwiseTagging -pedfile /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -log /opt/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng -chromosome 22 returned 0 +## executing java -jar /share/shared/galaxy/tool-data/rg/bin/haploview.jar -n -memory 2048 -pairwiseTagging -pedfile /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -log /share/shared/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng -chromosome 22 returned 0 ## executing mogrify -resize 800x400! *.PNG returned 0 @@ -51,7 +51,7 @@ ***************************************************** -Haploview 4.2 Java Version: 1.6.0_03 +Haploview 4.2 Java Version: 1.6.0_13 ***************************************************** @@ -59,7 +59,7 @@ -Arguments: -n -pairwiseTagging -pedfile /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -log /opt/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng -chromosome 22 +Arguments: -n -pairwiseTagging -pedfile /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -info /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info -tagrsqcounts -tagrsqcutoff 0.8 -ldcolorscheme RSQ -log /share/shared/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng -chromosome 22 @@ -67,9 +67,9 @@ Max LD comparison distance = 200000kb -Using data file: /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped +Using data file: /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped -Using marker information file: /opt/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info +Using marker information file: /share/shared/galaxy/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.info 10 out of 10 markers passed the MAF threshold. @@ -93,7 +93,7 @@ ***************************************************** -Haploview 4.2 Java Version: 1.6.0_03 +Haploview 4.2 Java Version: 1.6.0_13 ***************************************************** @@ -101,7 +101,7 @@ -Arguments: -n -chromosome 22 -panel YRI -hapmapDownload -startpos 21784 -endpos 21905 -ldcolorscheme RSQ -log /opt/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng +Arguments: -n -chromosome 22 -panel YRI -hapmapDownload -startpos 21784 -endpos 21905 -ldcolorscheme RSQ -log /share/shared/galaxy/test-data/tinywga.log -maxDistance 200000 -compressedpng diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.LD.PNG Binary file test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.LD.PNG has changed diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TAGS --- a/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TAGS Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TAGS Mon May 10 10:17:11 2010 -0400 @@ -9,17 +9,17 @@ rs3788347 rs3788347 1.0 rs756632 rs756632 1.0 rs4820539 rs4820539 1.0 -rs2283804 rs2267006 1.0 -rs2267006 rs2267006 1.0 +rs2283804 rs2283804 1.0 +rs2267006 rs2283804 1.0 rs4822363 rs4822363 1.0 Test Alleles Captured -rs2267006 rs2267006,rs2283804 -rs4820539 rs4820539 -rs3788347 rs3788347 +rs2283804 rs2267006,rs2283804 rs756632 rs756632 +rs2283802 rs2283802 +rs4820537 rs4820537 rs2267000 rs2267000 rs4822363 rs4822363 -rs2283802 rs2283802 -rs4820537 rs4820537 rs16997606 rs16997606 +rs3788347 rs3788347 +rs4820539 rs4820539 diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TESTS --- a/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TESTS Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgHaploView/rgHaploViewtest1.ped.TESTS Mon May 10 10:17:11 2010 -0400 @@ -1,9 +1,9 @@ -rs2267006 -rs4820539 -rs3788347 +rs2283804 rs756632 +rs2283802 +rs4820537 rs2267000 rs4822363 -rs2283802 -rs4820537 rs16997606 +rs3788347 +rs4820539 diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bed --- a/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bed Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bed Mon May 10 10:17:11 2010 -0400 @@ -1,1 +1,1 @@ -lÿÿÿÿûÿúÿÿÿmÿÿÿýÿÿÿÿÿ:ú¢ÿ¿«¯ü( \ No newline at end of file +lú £ïªîþ¨:*»ïêìª,«Àÿÿÿÿûÿúÿÿÿ \ No newline at end of file diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim --- a/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim Mon May 10 10:17:11 2010 -0400 @@ -1,3 +1,3 @@ +22 rs3788347 0 21797804 3 1 +22 rs5759608 0 21832708 2 4 22 rs2267010 0 21864366 3 1 -22 rs12160770 0 21892925 1 3 -22 rs4822375 0 21905642 1 3 diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log --- a/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log Mon May 10 10:17:11 2010 -0400 @@ -1,9 +1,9 @@ -## Rgenetics: http://rgenetics.org Galaxy Tools rgLDIndep.py started 25/03/2010 21:01:24 +## Rgenetics: http://rgenetics.org Galaxy Tools rgLDIndep.py started 09/05/2010 21:23:42 ## Rgenetics January 4 2010: http://rgenetics.org Galaxy Tools rgLDIndep.py Plink pruneLD runner -## ldindep now executing plink --noweb --bfile /opt/galaxy/test-data/tinywga --indep-pairwise 10000 5000 0.1 --out /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 --mind 1 --geno 1 --maf 0 --hwe 0 --me 1 1 +## ldindep now executing plink --noweb --bfile /share/shared/galaxy/test-data/tinywga --indep-pairwise 10000 5000 0.1 --out /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 --mind 1 --geno 1 --maf 0 --hwe 0 --me 1 1 @----------------------------------------------------------@ -| PLINK! | v1.06 | 24/Apr/2009 | +| PLINK! | v1.07 | 10/Aug/2009 | |----------------------------------------------------------| | (C) 2009 Shaun Purcell, GNU General Public License, v2 | |----------------------------------------------------------| @@ -12,30 +12,30 @@ @----------------------------------------------------------@ Skipping web check... [ --noweb ] -Writing this text to log file [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log ] -Analysis started: Thu Mar 25 21:01:24 2010 +Writing this text to log file [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log ] +Analysis started: Sun May 9 21:23:42 2010 Options in effect: --noweb - --bfile /opt/galaxy/test-data/tinywga + --bfile /share/shared/galaxy/test-data/tinywga --indep-pairwise 10000 5000 0.1 - --out /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 + --out /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 --mind 1 --geno 1 --maf 0 --hwe 0 --me 1 1 -Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] -25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ] -Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] -40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] +Reading map (extended format) from [ /share/shared/galaxy/test-data/tinywga.bim ] +25 markers to be included from [ /share/shared/galaxy/test-data/tinywga.bim ] +Reading pedigree information from [ /share/shared/galaxy/test-data/tinywga.fam ] +40 individuals read from [ /share/shared/galaxy/test-data/tinywga.fam ] 40 individuals with nonmissing phenotypes Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) Missing phenotype value is also -9 10 cases, 30 controls and 0 missing 21 males, 19 females, and 0 of unspecified sex -Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] +Reading genotype bitfile from [ /share/shared/galaxy/test-data/tinywga.bed ] Detected that binary PED file is v1.00 SNP-major mode Before frequency and genotyping pruning, there are 25 SNPs 27 founders and 13 non-founders found @@ -60,20 +60,20 @@ 0 markers removed due to Mendel errors, 25 remaining Converting data to SNP-major format Performing LD-based pruning... -Writing pruned-in SNPs to [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in ] -Writing pruned-out SNPs to [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.out ] +Writing pruned-in SNPs to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in ] +Writing pruned-out SNPs to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.out ] Scanning from chromosome 22 to 22 Scan region on chromosome 22 from [ rs2283802 ] to [ rs4822375 ] For chromosome 22, 22 SNPs pruned out, 3 remaining -Analysis finished: Thu Mar 25 21:01:24 2010 +Analysis finished: Sun May 9 21:23:42 2010 -## ldindep now executing plink --noweb --bfile /opt/galaxy/test-data/tinywga --extract /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in --make-bed --out /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 +## ldindep now executing plink --noweb --bfile /share/shared/galaxy/test-data/tinywga --extract /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in --make-bed --out /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 @----------------------------------------------------------@ -| PLINK! | v1.06 | 24/Apr/2009 | +| PLINK! | v1.07 | 10/Aug/2009 | |----------------------------------------------------------| | (C) 2009 Shaun Purcell, GNU General Public License, v2 | |----------------------------------------------------------| @@ -82,48 +82,48 @@ @----------------------------------------------------------@ Skipping web check... [ --noweb ] -Writing this text to log file [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log ] -Analysis started: Thu Mar 25 21:01:24 2010 +Writing this text to log file [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log ] +Analysis started: Sun May 9 21:23:42 2010 Options in effect: --noweb - --bfile /opt/galaxy/test-data/tinywga - --extract /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in + --bfile /share/shared/galaxy/test-data/tinywga + --extract /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in --make-bed - --out /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 + --out /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 -Reading map (extended format) from [ /opt/galaxy/test-data/tinywga.bim ] -25 markers to be included from [ /opt/galaxy/test-data/tinywga.bim ] -Reading pedigree information from [ /opt/galaxy/test-data/tinywga.fam ] -40 individuals read from [ /opt/galaxy/test-data/tinywga.fam ] +Reading map (extended format) from [ /share/shared/galaxy/test-data/tinywga.bim ] +25 markers to be included from [ /share/shared/galaxy/test-data/tinywga.bim ] +Reading pedigree information from [ /share/shared/galaxy/test-data/tinywga.fam ] +40 individuals read from [ /share/shared/galaxy/test-data/tinywga.fam ] 40 individuals with nonmissing phenotypes Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) Missing phenotype value is also -9 10 cases, 30 controls and 0 missing 21 males, 19 females, and 0 of unspecified sex -Reading genotype bitfile from [ /opt/galaxy/test-data/tinywga.bed ] +Reading genotype bitfile from [ /share/shared/galaxy/test-data/tinywga.bed ] Detected that binary PED file is v1.00 SNP-major mode -Reading list of SNPs to extract [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in ] ... 3 read +Reading list of SNPs to extract [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in ] ... 3 read Before frequency and genotyping pruning, there are 3 SNPs 27 founders and 13 non-founders found -Total genotyping rate in remaining individuals is 0.975 +Total genotyping rate in remaining individuals is 1 0 SNPs failed missingness test ( GENO > 1 ) 0 SNPs failed frequency test ( MAF < 0 ) After frequency and genotyping pruning, there are 3 SNPs After filtering, 10 cases, 30 controls and 0 missing After filtering, 21 males, 19 females, and 0 of unspecified sex -Writing pedigree information to [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.fam ] -Writing map (extended format) information to [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim ] -Writing genotype bitfile to [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bed ] +Writing pedigree information to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.fam ] +Writing map (extended format) information to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim ] +Writing genotype bitfile to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bed ] Using (default) SNP-major mode -Analysis finished: Thu Mar 25 21:01:24 2010 +Analysis finished: Sun May 9 21:23:42 2010 -## ldindep now executing plink --noweb --bfile /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 --recode --out /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 +## ldindep now executing plink --noweb --bfile /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 --recode --out /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 @----------------------------------------------------------@ -| PLINK! | v1.06 | 24/Apr/2009 | +| PLINK! | v1.07 | 10/Aug/2009 | |----------------------------------------------------------| | (C) 2009 Shaun Purcell, GNU General Public License, v2 | |----------------------------------------------------------| @@ -132,38 +132,38 @@ @----------------------------------------------------------@ Skipping web check... [ --noweb ] -Writing this text to log file [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log ] -Analysis started: Thu Mar 25 21:01:24 2010 +Writing this text to log file [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.log ] +Analysis started: Sun May 9 21:23:42 2010 Options in effect: --noweb - --bfile /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 + --bfile /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 --recode - --out /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 + --out /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1 -Reading map (extended format) from [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim ] -3 markers to be included from [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim ] -Reading pedigree information from [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.fam ] -40 individuals read from [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.fam ] +Reading map (extended format) from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim ] +3 markers to be included from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bim ] +Reading pedigree information from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.fam ] +40 individuals read from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.fam ] 40 individuals with nonmissing phenotypes Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) Missing phenotype value is also -9 10 cases, 30 controls and 0 missing 21 males, 19 females, and 0 of unspecified sex -Reading genotype bitfile from [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bed ] +Reading genotype bitfile from [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.bed ] Detected that binary PED file is v1.00 SNP-major mode Before frequency and genotyping pruning, there are 3 SNPs 27 founders and 13 non-founders found -Total genotyping rate in remaining individuals is 0.975 +Total genotyping rate in remaining individuals is 1 0 SNPs failed missingness test ( GENO > 1 ) 0 SNPs failed frequency test ( MAF < 0 ) After frequency and genotyping pruning, there are 3 SNPs After filtering, 10 cases, 30 controls and 0 missing After filtering, 21 males, 19 females, and 0 of unspecified sex -Writing recoded ped file to [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.ped ] -Writing new map file to [ /opt/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.map ] +Writing recoded ped file to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.ped ] +Writing new map file to [ /share/shared/galaxy/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.map ] -Analysis finished: Thu Mar 25 21:01:24 2010 +Analysis finished: Sun May 9 21:23:42 2010 diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.map --- a/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.map Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.map Mon May 10 10:17:11 2010 -0400 @@ -1,3 +1,3 @@ +22 rs3788347 0 21797804 +22 rs5759608 0 21832708 22 rs2267010 0 21864366 -22 rs12160770 0 21892925 -22 rs4822375 0 21905642 diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.ped --- a/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.ped Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.ped Mon May 10 10:17:11 2010 -0400 @@ -1,40 +1,40 @@ -101 1 3 2 2 2 1 1 0 0 1 3 -101 2 0 0 2 1 1 1 3 3 1 3 -101 3 0 0 1 1 1 1 1 3 3 3 -105 1 3 2 2 2 1 1 0 0 1 1 -105 2 0 0 2 1 1 1 3 3 1 3 -105 3 0 0 1 1 1 1 3 3 1 3 -112 1 3 2 1 2 1 1 3 3 3 3 -112 2 0 0 2 1 1 1 3 3 3 3 -112 3 0 0 1 1 1 1 3 3 1 3 -117 1 3 2 2 2 1 1 3 3 1 1 -117 2 0 0 2 1 1 1 3 3 1 3 -117 3 0 0 1 1 1 1 3 3 1 3 -12 1 3 2 1 2 1 1 3 3 3 3 -12 2 0 0 2 1 1 1 3 3 3 3 -12 3 0 0 1 1 1 1 3 3 3 3 -13 1 3 2 1 2 1 1 3 3 3 3 -13 2 0 0 2 1 1 1 0 0 3 3 -13 3 0 0 1 1 3 1 3 3 3 3 -1334 1 10 11 1 2 1 1 3 3 3 3 -1334 10 0 0 1 1 1 1 3 3 1 3 -1334 11 0 0 2 1 1 1 3 3 3 3 -1334 12 0 0 1 1 1 1 3 3 1 3 -1334 13 0 0 2 1 1 1 3 3 1 3 -1334 2 12 13 2 2 1 1 3 3 1 3 -1340 1 9 10 1 2 3 1 3 3 3 3 -1340 10 0 0 2 1 3 1 3 3 3 3 -1340 11 0 0 1 1 1 1 3 3 1 3 -1340 12 0 0 2 1 1 1 3 3 1 3 -1340 2 11 12 2 2 1 1 3 3 1 3 -1340 9 0 0 1 1 1 1 3 3 3 3 -1341 1 11 12 1 1 1 1 3 3 1 1 -1341 11 0 0 1 1 1 1 3 3 1 3 -1341 12 0 0 2 1 1 1 3 3 1 1 -1341 13 0 0 1 1 1 1 3 3 3 3 -1341 14 0 0 2 1 1 1 3 3 3 3 -1341 2 13 14 2 1 1 1 3 3 3 3 -1344 1 12 13 1 1 1 1 3 3 1 1 -1344 12 0 0 1 1 1 1 3 3 1 3 -1344 13 0 0 2 1 1 1 3 3 1 3 -1345 12 0 0 1 1 1 1 3 3 1 1 +101 1 3 2 2 2 3 3 2 4 1 1 +101 2 0 0 2 1 3 3 2 4 1 1 +101 3 0 0 1 1 3 3 4 4 1 1 +105 1 3 2 2 2 3 1 2 2 1 1 +105 2 0 0 2 1 3 1 2 4 1 1 +105 3 0 0 1 1 3 1 2 4 1 1 +112 1 3 2 1 2 1 1 2 4 1 1 +112 2 0 0 2 1 1 1 2 2 1 1 +112 3 0 0 1 1 3 1 4 4 1 1 +117 1 3 2 2 2 3 3 2 4 1 1 +117 2 0 0 2 1 3 3 4 4 1 1 +117 3 0 0 1 1 3 3 2 4 1 1 +12 1 3 2 1 2 3 3 4 4 1 1 +12 2 0 0 2 1 3 3 4 4 1 1 +12 3 0 0 1 1 3 1 2 4 1 1 +13 1 3 2 1 2 3 1 4 4 1 1 +13 2 0 0 2 1 1 1 2 4 1 1 +13 3 0 0 1 1 3 3 2 4 3 1 +1334 1 10 11 1 2 3 1 2 4 1 1 +1334 10 0 0 1 1 3 1 4 4 1 1 +1334 11 0 0 2 1 1 1 2 2 1 1 +1334 12 0 0 1 1 1 1 4 4 1 1 +1334 13 0 0 2 1 3 1 2 4 1 1 +1334 2 12 13 2 2 1 1 4 4 1 1 +1340 1 9 10 1 2 3 1 2 4 3 1 +1340 10 0 0 2 1 3 1 2 4 3 1 +1340 11 0 0 1 1 3 1 2 4 1 1 +1340 12 0 0 2 1 3 1 2 4 1 1 +1340 2 11 12 2 2 3 1 2 2 1 1 +1340 9 0 0 1 1 1 1 4 4 1 1 +1341 1 11 12 1 1 3 1 2 4 1 1 +1341 11 0 0 1 1 1 1 2 2 1 1 +1341 12 0 0 2 1 3 1 4 4 1 1 +1341 13 0 0 1 1 1 1 2 4 1 1 +1341 14 0 0 2 1 1 1 2 4 1 1 +1341 2 13 14 2 1 1 1 2 4 1 1 +1344 1 12 13 1 1 3 3 2 2 1 1 +1344 12 0 0 1 1 3 1 2 2 1 1 +1344 13 0 0 2 1 3 1 2 2 1 1 +1345 12 0 0 1 1 3 1 4 4 1 1 diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in --- a/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.in Mon May 10 10:17:11 2010 -0400 @@ -1,3 +1,3 @@ +rs3788347 +rs5759608 rs2267010 -rs12160770 -rs4822375 diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.out --- a/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.out Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgLDIndep/rgLDIndeptest1.prune.out Mon May 10 10:17:11 2010 -0400 @@ -2,14 +2,12 @@ rs2267000 rs16997606 rs4820537 -rs3788347 rs756632 rs4820539 rs2283804 rs2267006 rs4822363 rs5751592 -rs5759608 rs5759612 rs2267009 rs5759636 @@ -17,6 +15,8 @@ rs2267013 rs6003566 rs2256725 +rs12160770 rs5751611 rs762601 rs2156921 +rs4822375 diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgManQQ/Allelep_manhattan.png Binary file test-data/rgtestouts/rgManQQ/Allelep_manhattan.png has changed diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgManQQ/Allelep_qqplot.png Binary file test-data/rgtestouts/rgManQQ/Allelep_qqplot.png has changed diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgManQQ/Armitagep_manhattan.png Binary file test-data/rgtestouts/rgManQQ/Armitagep_manhattan.png has changed diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgManQQ/Armitagep_qqplot.png Binary file test-data/rgtestouts/rgManQQ/Armitagep_qqplot.png has changed diff -r acaf971320bd -r 6aa1379d35e0 test-data/rgtestouts/rgManQQ/rgManQQtest1.R --- a/test-data/rgtestouts/rgManQQ/rgManQQtest1.R Mon May 10 10:03:00 2010 -0400 +++ b/test-data/rgtestouts/rgManQQ/rgManQQtest1.R Mon May 10 10:17:11 2010 -0400 @@ -108,7 +108,7 @@ if (spartan) plot=plot+opts(panel.background=theme_rect(col="grey50"), panel.grid.minor=theme_blank()) plot } -rgqqMan = function(infile="/opt/galaxy/test-data/smallwgaP.xls",chromcolumn=2, offsetcolumn=3, pvalscolumns=c(6,8), +rgqqMan = function(infile="/share/shared/galaxy/test-data/smallwgaP.xls",chromcolumn=2, offsetcolumn=3, pvalscolumns=c(6,8), title="rgManQQtest1",grey=0) { rawd = read.table(infile,head=T,sep=' ')

1 0

[hg] galaxy 3757: Clean up annotation display for workflow steps.
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/42de27d4215f changeset: 3757:42de27d4215f user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Sun May 09 22:37:50 2010 -0400 description: Clean up annotation display for workflow steps. diffstat: templates/workflow/display.mako | 6 +++++- 1 files changed, 5 insertions(+), 1 deletions(-) diffs (16 lines): diff -r 8094d8531fb2 -r 42de27d4215f templates/workflow/display.mako --- a/templates/workflow/display.mako Fri May 07 18:25:29 2010 -0400 +++ b/templates/workflow/display.mako Sun May 09 22:37:50 2010 -0400 @@ -108,7 +108,11 @@ </div> %endif </td> - <td class="annotation">${step.annotation}</td> + <td class="annotation"> + %if hasattr( step, "annotation") and step.annotation is not None: + ${step.annotation} + %endif + </td> </tr> %endfor </table>

1 0

[hg] galaxy 3758: lims:
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/acaf971320bd changeset: 3758:acaf971320bd user: rc date: Mon May 10 10:03:00 2010 -0400 description: lims: default view of requests page now shows requests belonging to any state diffstat: lib/galaxy/web/controllers/requests.py | 2 +- lib/galaxy/web/controllers/requests_admin.py | 8 +++++--- 2 files changed, 6 insertions(+), 4 deletions(-) diffs (44 lines): diff -r 42de27d4215f -r acaf971320bd lib/galaxy/web/controllers/requests.py --- a/lib/galaxy/web/controllers/requests.py Sun May 09 22:37:50 2010 -0400 +++ b/lib/galaxy/web/controllers/requests.py Mon May 10 10:03:00 2010 -0400 @@ -79,7 +79,7 @@ num_rows_per_page = 50 preserve_state = True use_paging = True - default_filter = dict( deleted="False", state=model.Request.states.NEW) + default_filter = dict( deleted="False") columns = [ NameColumn( "Name", key="name", diff -r 42de27d4215f -r acaf971320bd lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py Sun May 09 22:37:50 2010 -0400 +++ b/lib/galaxy/web/controllers/requests_admin.py Mon May 10 10:03:00 2010 -0400 @@ -90,7 +90,7 @@ num_rows_per_page = 50 preserve_state = True use_paging = True - default_filter = dict( deleted="False", state=model.Request.states.SUBMITTED) + default_filter = dict( deleted="False") columns = [ NameColumn( "Name", key="name", @@ -259,7 +259,7 @@ ''' List all request made by the current user ''' - #self.__sample_datasets(trans, **kwd) + self.__sample_datasets(trans, **kwd) if 'operation' in kwd: operation = kwd['operation'].lower() if not kwd.get( 'id', None ): @@ -1774,7 +1774,9 @@ status=status) def __sample_datasets(self, trans, **kwd): - samples = trans.sa_session.query( trans.app.model.Sample ).all() + samples = trans.sa_session.query( trans.app.model.Sample )\ + .filter( trans.app.model.Sample.table.c.deleted==False)\ + .all() for s in samples: if s.dataset_files: newdf = []

1 0

[hg] galaxy 3756: trackster: fix track saving
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/8094d8531fb2 changeset: 3756:8094d8531fb2 user: Kanwei Li <kanwei(a)gmail.com> date: Fri May 07 18:25:29 2010 -0400 description: trackster: fix track saving diffstat: static/scripts/packed/trackster.js | 2 +- static/scripts/trackster.js | 6 +++--- templates/tracks/browser.mako | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) diffs (50 lines): diff -r 4aec0992748e -r 8094d8531fb2 static/scripts/packed/trackster.js --- a/static/scripts/packed/trackster.js Fri May 07 10:28:28 2010 -0400 +++ b/static/scripts/packed/trackster.js Fri May 07 18:25:29 2010 -0400 @@ -1,1 +1,1 @@ -var DEBUG=false;var DENSITY=200,FEATURE_LEVELS=10,DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=5,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="/static/images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="/static/images/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src="/static/images/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern! (right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src="/static/images/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},clear:function(){this.obj_cache={};this.key_ary=[]}});var Drawer=function(){};$.extend(Drawer.prototype,{intensity:function(b,a,c){},});drawer=new Drawer();var View=function(b,d,c,a){this.vis_id=c;this.dbkey=a;this.title=d;this.chrom=b;this.tracks=[];this.label_tracks=[];this.! max_low=0;this.max_high=0;this.center=(this.max_high-this.max_low)/2;t his.zoom_factor=3;this.zoom_level=0;this.track_id_counter=0};$.extend(View.prototype,{add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);this.track_id_counter+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks.splice(this.tracks.indexOf(a))},update_options:function(){var b=$("ul#sortable-ul").sortable("toArray");for(var c in b){var e=b[c].split("_li")[0].split("track_")[1];$("#viewport").append($("#track_"+e))}for(var d in view.tracks){var a=view.tracks[d];if(a.update_options){a.update_options(d)}}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.center=this.center=(this.max_high-this.max_low)/2;this.zoom_level=0;$(".yaxislabel").remove()},redraw:function(f){this.span=this.max_high-this.max_low;var d=this.span/Math.pow(this.zoom_fa! ctor,this.zoom_level),b=this.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){e=this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));$("#overview-box").css({left:(this.low/this.span)*$("#overview-viewport").width(),width:Math.max(12,((this.high-this.low)/this.span)*$("#overview-viewport").width())}).show();$("#low").val(commatize(this.low));$("#high").val(commatize(this.high));if(!f){for(var c=0,a=this.tracks.length;c<a;c++){if(this.tracks[c].enabled){this.tracks[c].draw()}}for(var c=0,a=this.label_tracks.length;c<a;c++){this.label_tracks[c].draw()}}},zoom_in:function(a,b){if(this.max_high===0||this.high-this.low<30){return}if(a){this.center=a/b.width()*(this.high-this.low)+this.low}! this.zoom_level+=1;this.redraw()},zoom_out:function(){if(this.max_high ===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1;this.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.init_global()};$.extend(Track.prototype,{init_global:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div></div>").addClass("track").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)},init_each:function(c,b){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.content_div.css("height","30px");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.getJSON(data_url,c,function(d){if(!d||d==="error"||d.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(d.message){var f=a.view.tracks.indexOf(a);var e=$("<a href='javascript:void(0);'></a>").a! ttr("id",f+"_error");e.text("Click to view error");$("#"+f+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+d.message+"</pre>",{Close:hide_modal})});a.content_div.append(e)}}else{if(d==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(d.data!==undefined&&(d.data===null||d.data.length===0)){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;b(d);a.draw()}}}}})}else{a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}}});var TiledTrack=function(){};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var i=this.view.low,e=this.view.high,f=e-i,d=this.view.resolution;if(DEBUG){$("#debug").text(d+" "+this.view.zoom_res)}var k=$("<div style='position: relative;'>! </div>"),l=this.content_div.width()/f,h;this.content_div.children(":fi rst").remove();this.content_div.append(k),this.max_height=0;var a=Math.floor(i/d/DENSITY);while((a*DENSITY*d)<e){var j=this.content_div.width()+"_"+this.view.zoom_level+"_"+a;var c=this.tile_cache.get(j);if(c){var g=a*DENSITY*d;var b=(g-i)*l;if(this.left_offset){b-=this.left_offset}c.css({left:b});k.append(c);this.max_height=Math.max(this.max_height,c.height());this.content_div.css("height",this.max_height+"px")}else{this.delayed_draw(this,j,i,e,a,d,k,l)}a+=1}},delayed_draw:function(c,e,a,f,b,d,g,h){setTimeout(function(){if(!(a>c.view.high||f<c.view.low)){tile_element=c.draw_tile(d,b,g,h);if(tile_element){c.tile_cache.set(e,tile_element);c.max_height=Math.max(c.max_height,tile_element.height());c.content_div.css("height",c.max_height+"px")}}},50)}});var LabelTrack=function(a){Track.call(this,null,a);this.track_type="LabelTrack";this.hidden=true;this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-! c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,a,b){this.track_type="LineTrack";Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.height_px=100;this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={min_value:undefined,max_value:undefined,mode:"Line"};if(b.min_value!==undefined){this.prefs.min_value=b.min_value}if(b.max_value!==undefined){this.prefs.max_value=b.max_value}if(b.mode!==undefined){this.prefs.mode=b.mode}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=unde! fined;this.init_each({stats:true,chrom:a.view.chrom,low:null,high:null ,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");data=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=data.min;a.prefs.max_value=data.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=data.total_frequency;$("#linetrack_"+b+"_minval").remove();$("#linetrack_"+b+"_maxval").remove();var e=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(a.prefs.min_value);var d=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(a.prefs.max_value);d.css({position:"relative",top:"25px",left:"10px"});d.prependTo(a.container_div);e.css({position:"relative",top:a.height_px+55+"px",left:"10px"});e.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=! true;$.ajax({url:data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){data=g.data;c.data_cache.set(e,data);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(p,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*p,a=DENSITY*p,b=$("<canvas class='tile'></canvas>"),v=p+"_"+r;if(this.data_cache.get(v)===undefined){this.get_data(p,r);return}var j=this.data_cache.get(v);if(j===null){return}b.css({position:"absolute",top:0,left:(s-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var o=b.get(0).getContext("2d"),k=false,l=this.prefs.min_value,g=this.prefs.max_value,n=this.vertical_range,t=this.total_frequency,d=this.height_px,m=this.prefs.mode;o.beginPath();if(data.length>1){var f=Math.ceil((data[1][0]-data[0][0])*e)}else{var f=10}var u,h;for(var q=0;q<data.length;q++){u=(data[q][0]-s)*e;h=data[q][1]! ;if(m=="Intensity"){if(h===null){continue}if(h<=l){h=l}else{if(h>=g){h =g}}h=255-Math.floor((h-l)/n*255);o.fillStyle="rgb("+h+","+h+","+h+")";o.fillRect(u,0,f,this.height_px)}else{if(h===null){if(k&&m==="Filled"){o.lineTo(u,d)}k=false;continue}else{if(h<=l){h=l}else{if(h>=g){h=g}}h=Math.round(d-(h-l)/n*d);if(k){o.lineTo(u,h)}else{k=true;if(m==="Filled"){o.moveTo(u,d);o.lineTo(u,h)}else{o.moveTo(u,h)}}}}}if(m==="Filled"){if(k){o.lineTo(u,d)}o.fill()}else{o.stroke()}c.append(b);return b},gen_options:function(n){var a=$("<div></div>").addClass("form-row");var h="track_"+n+"_minval",k="track_"+n+"_maxval",e="track_"+n+"_mode",l=$("<label></label>").attr("for",h).text("Min value:"),b=(this.prefs.min_value===undefined?"":this.prefs.min_value),m=$("<input></input>").attr("id",h).val(b),g=$("<label></label>").attr("for",k).text("Max value:"),j=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",k).val(j),d=$("<label></label>").attr("for",e).text("Display mode:"),i=(this.prefs.mode===undefined?"Line":this.prefs.mo! de),c=$('<select id="'+e+'"><option value="Line" id="mode_Line">Line</option><option value="Filled" id="mode_Filled">Filled</option><option value="Intensity" id="mode_Intensity">Intensity</option></select>');c.children("#mode_"+i).attr("selected","selected");return a.append(l).append(m).append(g).append(f).append(d).append(c)},update_options:function(d){var a=$("#track_"+d+"_minval").val(),c=$("#track_"+d+"_maxval").val(),b=$("#track_"+d+"_mode option:selected").val();if(a!==this.prefs.min_value||c!==this.prefs.max_value||b!=this.prefs.mode){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(c);this.prefs.mode=b;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+d+"_minval").text(this.prefs.min_value);$("#linetrack_"+d+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(c,a,b){this.track_type="FeatureTrack";Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.height_px=100! ;this.container_div.addClass("feature-track");this.dataset_id=a;this.z o_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.default_font="9px Monaco, Lucida Console, monospace";this.left_offset=200;this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new Cache(20);this.prefs={block_color:"black",label_color:"black",show_counts:false};if(b.block_color!==undefined){this.prefs.block_color=b.block_color}if(b.label_color!==undefined){this.prefs.label_color=b.label_color}if(b.show_counts!==undefined){this.prefs.show_counts=b.show_counts}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.max_low+"_"+a.view.max_high;this.init_each({low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom,resolution:this.view.resolution},function(c){a.data_cache.set(b,c);a.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=tr! ue;$.getJSON(data_url,{chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,resolution:this.view.resolution},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,g,c){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=1/a;this.s_e_by_tile[a]={}}var m=this.inc_slots[a].w_scale,v=[],h=0,b=$("<canvas></canvas>").get(0).getContext("2d"),n=this.view.max_low;var d,f,x=[];for(var s=0,t=g.length;s<t;s++){var e=g[s],l=e[0];if(this.inc_slots[a][l]!==undefined){h=Math.max(h,this.inc_slots[a][l]);x.push(this.inc_slots[a][l])}else{v.push(s)}}for(var s=0,t=v.length;s<t;s++){var e=g[v[s]];l=e[0],feature_start=e[1],feature_end=e[2],feature_name=e[3];d=Math.floor((feature_start-n)*m);f=Math.ceil((feature_end-n)*m);if(!c){var p=b.measureText(feature_name).width;if(d-p<0){f+=p}else{d-=p}}var r=0;while(true){var o=true;if(this.s_e_by_tile[a][r]!==undefined){for(var q=0,w=this.s_e_by_tile[a][r].length;q<w;q++){var u=this.s_e_by! _tile[a][r][q];if(f>u[0]&&d<u[1]){o=false;break}}}if(o){if(this.s_e_by _tile[a][r]===undefined){this.s_e_by_tile[a][r]=[]}this.s_e_by_tile[a][r].push([d,f]);this.inc_slots[a][l]=r;h=Math.max(h,r);break}r++}}return h},rect_or_text:function(n,o,g,f,m,b,d,k,e,i){n.textAlign="center";var j=Math.round(o/2);if(d!==undefined&&o>g){n.fillStyle="#555";n.fillRect(k,i+1,e,9);n.fillStyle="#eee";for(var h=0,l=d.length;h<l;h++){if(b+h>=f&&b+h<=m){var a=Math.floor(Math.max(0,(b+h-f)*o));n.fillText(d[h],a+this.left_offset+j,i+9)}}}else{n.fillStyle="#555";n.fillRect(k,i+4,e,3)}},draw_tile:function(W,h,m,ak){var D=h*DENSITY*W,ac=(h+1)*DENSITY*W,C=DENSITY*W;var aj,r;var ad=D+"_"+ac;var w=this.data_cache.get(ad);if(w===undefined){this.data_queue[[D,ac]]=true;this.get_data(D,ac);return}if(w.dataset_type==="summary_tree"){r=30}else{var U=(w.extra_info==="no_detail");var al=(U?this.vertical_nodetail_px:this.vertical_detail_px);r=this.incremental_slots(this.view.zoom_res,w.data,U)*al+15;m.parent().css("height",Math.max(this.height_px,r)+"px");aj=this.inc_slots[this.vi! ew.zoom_res]}var a=Math.ceil(C*ak),K=$("<canvas class='tile'></canvas>"),Y=this.prefs.label_color,f=this.prefs.block_color,O=this.left_offset;K.css({position:"absolute",top:0,left:(D-this.view.low)*ak-O});K.get(0).width=a+O;K.get(0).height=r;var z=K.get(0).getContext("2d"),ah=z.measureText("A").width;z.fillStyle=this.prefs.block_color;z.font=this.default_font;z.textAlign="right";if(w.dataset_type=="summary_tree"){var J,G=55,ab=255-G,g=ab*2/3,Q=w.data,B=w.max,l=w.avg;if(Q.length>2){var b=Math.ceil((Q[1][0]-Q[0][0])*ak)}else{var b=50}for(var af=0,v=Q.length;af<v;af++){var S=Math.ceil((Q[af][0]-D)*ak);var R=Q[af][1];if(!R){continue}J=Math.floor(ab-(R/B)*ab);z.fillStyle="rgb("+J+","+J+","+J+")";z.fillRect(S+O,0,b,20);if(this.prefs.show_counts){if(J>g){z.fillStyle="black"}else{z.fillStyle="#ddd"}z.textAlign="center";z.fillText(Q[af][1],S+O+(b/2),12)}}m.append(K);return K}var ai=w.data;var ae=0;for(var af=0,v=ai.length;af<v;af++){var L=ai[af],I=L[0],ag=L[1],T=L[2],E=L[3];if(ag<=a! c&&T>=D){var V=Math.floor(Math.max(0,(ag-D)*ak)),A=Math.ceil(Math.min( a,Math.max(0,(T-D)*ak))),P=aj[I]*al;if(w.dataset_type==="bai"){z.fillStyle="#555";if(L[4] instanceof Array){var s=Math.floor(Math.max(0,(L[4][0]-D)*ak)),H=Math.ceil(Math.min(a,Math.max(0,(L[4][1]-D)*ak))),q=Math.floor(Math.max(0,(L[5][0]-D)*ak)),o=Math.ceil(Math.min(a,Math.max(0,(L[5][1]-D)*ak)));if(L[4][1]>=D&&L[4][0]<=ac){this.rect_or_text(z,ak,ah,D,ac,L[4][0],L[4][2],s+O,H-s,P)}if(L[5][1]>=D&&L[5][0]<=ac){this.rect_or_text(z,ak,ah,D,ac,L[5][0],L[5][2],q+O,o-q,P)}if(q>H){z.fillStyle="#999";z.fillRect(H+O,P+5,q-H,1)}}else{z.fillStyle="#555";this.rect_or_text(z,ak,ah,D,ac,ag,E,V+O,A-V,P)}if(!U&&ag>D){z.fillStyle=this.prefs.label_color;if(h===0&&V-z.measureText(E).width<0){z.textAlign="left";z.fillText(I,A+2+O,P+8)}else{z.textAlign="right";z.fillText(I,V-2+O,P+8)}z.fillStyle="#555"}}else{if(w.dataset_type==="interval_index"){if(U){z.fillRect(V+O,P+5,A-V,1)}else{var u=L[4],N=L[5],X=L[6],e=L[7];var t,Z,F=null,am=null;if(N&&X){F=Math.floor(Math.max(0,(N-D)*ak));am=Math.ceil(Math! .min(a,Math.max(0,(X-D)*ak)))}if(E!==undefined&&ag>D){z.fillStyle=Y;if(h===0&&V-z.measureText(E).width<0){z.textAlign="left";z.fillText(E,A+2+O,P+8)}else{z.textAlign="right";z.fillText(E,V-2+O,P+8)}z.fillStyle=f}if(e){if(u){if(u=="+"){z.fillStyle=RIGHT_STRAND}else{if(u=="-"){z.fillStyle=LEFT_STRAND}}z.fillRect(V+O,P,A-V,10);z.fillStyle=f}for(var ad=0,d=e.length;ad<d;ad++){var n=e[ad],c=Math.floor(Math.max(0,(n[0]-D)*ak)),M=Math.ceil(Math.min(a,Math.max((n[1]-D)*ak)));if(c>M){continue}t=5;Z=3;z.fillRect(c+O,P+Z,M-c,t);if(F!==undefined&&!(c>am||M<F)){t=9;Z=1;var aa=Math.max(c,F),p=Math.min(M,am);z.fillRect(aa+O,P+Z,p-aa,t)}}}else{t=9;Z=1;z.fillRect(V+O,P+Z,A-V,t);if(L.strand){if(L.strand=="+"){z.fillStyle=RIGHT_STRAND_INV}else{if(L.strand=="-"){z.fillStyle=LEFT_STRAND_INV}}z.fillRect(V+O,P,A-V,10);z.fillStyle=prefs.block_color}}}}}ae++}}m.append(K);return K},gen_options:function(i){var a=$("<div></div>").addClass("form-row");var e="track_"+i+"_block_color",k=$("<label></label! >").attr("for",e).text("Block color:"),l=$("<input></input>").attr("id ",e).attr("name",e).val(this.prefs.block_color),j="track_"+i+"_label_color",g=$("<label></label>").attr("for",j).text("Text color:"),h=$("<input></input>").attr("id",j).attr("name",j).val(this.prefs.label_color),f="track_"+i+"_show_count",c=$("<label></label>").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div></div>").append(b).append(c);return a.append(k).append(l).append(g).append(h).append(d)},update_options:function(d){var b=$("#track_"+d+"_block_color").val(),c=$("#track_"+d+"_label_color").val(),a=$("#track_"+d+"_show_count").attr("checked");if(b!==this.prefs.block_color||c!==this.prefs.label_color||a!=this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=c;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(c,a,b){FeatureTrack.call(this,c,a,b);this.track_type="ReadTrack";this.vertical_det! ail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{}); \ No newline at end of file +var DEBUG=false;var DENSITY=200,FEATURE_LEVELS=10,DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=5,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="/static/images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="/static/images/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src="/static/images/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern! (right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src="/static/images/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},clear:function(){this.obj_cache={};this.key_ary=[]}});var Drawer=function(){};$.extend(Drawer.prototype,{intensity:function(b,a,c){},});drawer=new Drawer();var View=function(b,d,c,a){this.vis_id=c;this.dbkey=a;this.title=d;this.chrom=b;this.tracks=[];this.label_tracks=[];this.! max_low=0;this.max_high=0;this.center=(this.max_high-this.max_low)/2;t his.zoom_factor=3;this.zoom_level=0;this.track_id_counter=0};$.extend(View.prototype,{add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);this.track_id_counter+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[this.tracks.indexOf(a)]},update_options:function(){var b=$("ul#sortable-ul").sortable("toArray");for(var c in b){var e=b[c].split("_li")[0].split("track_")[1];$("#viewport").append($("#track_"+e))}for(var d in view.tracks){var a=view.tracks[d];if(a&&a.update_options){a.update_options(d)}}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.center=this.center=(this.max_high-this.max_low)/2;this.zoom_level=0;$(".yaxislabel").remove()},redraw:function(f){this.span=this.max_high-this.max_low;var d=this.span/Math.pow(this.zoom_factor! ,this.zoom_level),b=this.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){e=this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));$("#overview-box").css({left:(this.low/this.span)*$("#overview-viewport").width(),width:Math.max(12,((this.high-this.low)/this.span)*$("#overview-viewport").width())}).show();$("#low").val(commatize(this.low));$("#high").val(commatize(this.high));if(!f){for(var c=0,a=this.tracks.length;c<a;c++){if(this.tracks[c]&&this.tracks[c].enabled){this.tracks[c].draw()}}for(var c=0,a=this.label_tracks.length;c<a;c++){this.label_tracks[c].draw()}}},zoom_in:function(a,b){if(this.max_high===0||this.high-this.low<30){return}if(a){this.center=a/b.width()*(this.high-this.lo! w)+this.low}this.zoom_level+=1;this.redraw()},zoom_out:function(){if(t his.max_high===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1;this.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.init_global()};$.extend(Track.prototype,{init_global:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div></div>").addClass("track").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)},init_each:function(c,b){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.content_div.css("height","30px");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.getJSON(data_url,c,function(d){if(!d||d==="error"||d.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(d.message){var f=a.view.tracks.indexOf(a);var e=$("<a href='javascript:void(0! );'></a>").attr("id",f+"_error");e.text("Click to view error");$("#"+f+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+d.message+"</pre>",{Close:hide_modal})});a.content_div.append(e)}}else{if(d==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(d.data!==undefined&&(d.data===null||d.data.length===0)){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;b(d);a.draw()}}}}})}else{a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}}});var TiledTrack=function(){};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var i=this.view.low,e=this.view.high,f=e-i,d=this.view.resolution;if(DEBUG){$("#debug").text(d+" "+this.view.zoom_res)}var k=$("<div style='position:! relative;'></div>"),l=this.content_div.width()/f,h;this.content_div.c hildren(":first").remove();this.content_div.append(k),this.max_height=0;var a=Math.floor(i/d/DENSITY);while((a*DENSITY*d)<e){var j=this.content_div.width()+"_"+this.view.zoom_level+"_"+a;var c=this.tile_cache.get(j);if(c){var g=a*DENSITY*d;var b=(g-i)*l;if(this.left_offset){b-=this.left_offset}c.css({left:b});k.append(c);this.max_height=Math.max(this.max_height,c.height());this.content_div.css("height",this.max_height+"px")}else{this.delayed_draw(this,j,i,e,a,d,k,l)}a+=1}},delayed_draw:function(c,e,a,f,b,d,g,h){setTimeout(function(){if(!(a>c.view.high||f<c.view.low)){tile_element=c.draw_tile(d,b,g,h);if(tile_element){c.tile_cache.set(e,tile_element);c.max_height=Math.max(c.max_height,tile_element.height());c.content_div.css("height",c.max_height+"px")}}},50)}});var LabelTrack=function(a){Track.call(this,null,a);this.track_type="LabelTrack";this.hidden=true;this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.vi! ew,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,a,b){this.track_type="LineTrack";Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.height_px=100;this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={min_value:undefined,max_value:undefined,mode:"Line"};if(b.min_value!==undefined){this.prefs.min_value=b.min_value}if(b.max_value!==undefined){this.prefs.max_value=b.max_value}if(b.mode!==undefined){this.prefs.mode=b.mode}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertica! l_range=undefined;this.init_each({stats:true,chrom:a.view.chrom,low:nu ll,high:null,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");data=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=data.min;a.prefs.max_value=data.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=data.total_frequency;$("#linetrack_"+b+"_minval").remove();$("#linetrack_"+b+"_maxval").remove();var e=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(a.prefs.min_value);var d=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(a.prefs.max_value);d.css({position:"relative",top:"25px",left:"10px"});d.prependTo(a.container_div);e.css({position:"relative",top:a.height_px+55+"px",left:"10px"});e.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.da! ta_queue[e]=true;$.ajax({url:data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){data=g.data;c.data_cache.set(e,data);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(p,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*p,a=DENSITY*p,b=$("<canvas class='tile'></canvas>"),v=p+"_"+r;if(this.data_cache.get(v)===undefined){this.get_data(p,r);return}var j=this.data_cache.get(v);if(j===null){return}b.css({position:"absolute",top:0,left:(s-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var o=b.get(0).getContext("2d"),k=false,l=this.prefs.min_value,g=this.prefs.max_value,n=this.vertical_range,t=this.total_frequency,d=this.height_px,m=this.prefs.mode;o.beginPath();if(data.length>1){var f=Math.ceil((data[1][0]-data[0][0])*e)}else{var f=10}var u,h;for(var q=0;q<data.length;q++){u=(data[q][0]-s)*e;! h=data[q][1];if(m=="Intensity"){if(h===null){continue}if(h<=l){h=l}els e{if(h>=g){h=g}}h=255-Math.floor((h-l)/n*255);o.fillStyle="rgb("+h+","+h+","+h+")";o.fillRect(u,0,f,this.height_px)}else{if(h===null){if(k&&m==="Filled"){o.lineTo(u,d)}k=false;continue}else{if(h<=l){h=l}else{if(h>=g){h=g}}h=Math.round(d-(h-l)/n*d);if(k){o.lineTo(u,h)}else{k=true;if(m==="Filled"){o.moveTo(u,d);o.lineTo(u,h)}else{o.moveTo(u,h)}}}}}if(m==="Filled"){if(k){o.lineTo(u,d)}o.fill()}else{o.stroke()}c.append(b);return b},gen_options:function(n){var a=$("<div></div>").addClass("form-row");var h="track_"+n+"_minval",k="track_"+n+"_maxval",e="track_"+n+"_mode",l=$("<label></label>").attr("for",h).text("Min value:"),b=(this.prefs.min_value===undefined?"":this.prefs.min_value),m=$("<input></input>").attr("id",h).val(b),g=$("<label></label>").attr("for",k).text("Max value:"),j=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",k).val(j),d=$("<label></label>").attr("for",e).text("Display mode:"),i=(this.prefs.mode===undefined?"Line":t! his.prefs.mode),c=$('<select id="'+e+'"><option value="Line" id="mode_Line">Line</option><option value="Filled" id="mode_Filled">Filled</option><option value="Intensity" id="mode_Intensity">Intensity</option></select>');c.children("#mode_"+i).attr("selected","selected");return a.append(l).append(m).append(g).append(f).append(d).append(c)},update_options:function(d){var a=$("#track_"+d+"_minval").val(),c=$("#track_"+d+"_maxval").val(),b=$("#track_"+d+"_mode option:selected").val();if(a!==this.prefs.min_value||c!==this.prefs.max_value||b!=this.prefs.mode){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(c);this.prefs.mode=b;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+d+"_minval").text(this.prefs.min_value);$("#linetrack_"+d+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(c,a,b){this.track_type="FeatureTrack";Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.h! eight_px=100;this.container_div.addClass("feature-track");this.dataset _id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.default_font="9px Monaco, Lucida Console, monospace";this.left_offset=200;this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new Cache(20);this.prefs={block_color:"black",label_color:"black",show_counts:false};if(b.block_color!==undefined){this.prefs.block_color=b.block_color}if(b.label_color!==undefined){this.prefs.label_color=b.label_color}if(b.show_counts!==undefined){this.prefs.show_counts=b.show_counts}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.max_low+"_"+a.view.max_high;this.init_each({low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom,resolution:this.view.resolution},function(c){a.data_cache.set(b,c);a.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data! _queue[c]=true;$.getJSON(data_url,{chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,resolution:this.view.resolution},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,g,c){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=1/a;this.s_e_by_tile[a]={}}var m=this.inc_slots[a].w_scale,v=[],h=0,b=$("<canvas></canvas>").get(0).getContext("2d"),n=this.view.max_low;var d,f,x=[];for(var s=0,t=g.length;s<t;s++){var e=g[s],l=e[0];if(this.inc_slots[a][l]!==undefined){h=Math.max(h,this.inc_slots[a][l]);x.push(this.inc_slots[a][l])}else{v.push(s)}}for(var s=0,t=v.length;s<t;s++){var e=g[v[s]];l=e[0],feature_start=e[1],feature_end=e[2],feature_name=e[3];d=Math.floor((feature_start-n)*m);f=Math.ceil((feature_end-n)*m);if(!c){var p=b.measureText(feature_name).width;if(d-p<0){f+=p}else{d-=p}}var r=0;while(true){var o=true;if(this.s_e_by_tile[a][r]!==undefined){for(var q=0,w=this.s_e_by_tile[a][r].length;q<w;q++){var u! =this.s_e_by_tile[a][r][q];if(f>u[0]&&d<u[1]){o=false;break}}}if(o){if (this.s_e_by_tile[a][r]===undefined){this.s_e_by_tile[a][r]=[]}this.s_e_by_tile[a][r].push([d,f]);this.inc_slots[a][l]=r;h=Math.max(h,r);break}r++}}return h},rect_or_text:function(n,o,g,f,m,b,d,k,e,i){n.textAlign="center";var j=Math.round(o/2);if(d!==undefined&&o>g){n.fillStyle="#555";n.fillRect(k,i+1,e,9);n.fillStyle="#eee";for(var h=0,l=d.length;h<l;h++){if(b+h>=f&&b+h<=m){var a=Math.floor(Math.max(0,(b+h-f)*o));n.fillText(d[h],a+this.left_offset+j,i+9)}}}else{n.fillStyle="#555";n.fillRect(k,i+4,e,3)}},draw_tile:function(W,h,m,ak){var D=h*DENSITY*W,ac=(h+1)*DENSITY*W,C=DENSITY*W;var aj,r;var ad=D+"_"+ac;var w=this.data_cache.get(ad);if(w===undefined){this.data_queue[[D,ac]]=true;this.get_data(D,ac);return}if(w.dataset_type==="summary_tree"){r=30}else{var U=(w.extra_info==="no_detail");var al=(U?this.vertical_nodetail_px:this.vertical_detail_px);r=this.incremental_slots(this.view.zoom_res,w.data,U)*al+15;m.parent().css("height",Math.max(this.height_px,r)+"px");aj=this.inc_s! lots[this.view.zoom_res]}var a=Math.ceil(C*ak),K=$("<canvas class='tile'></canvas>"),Y=this.prefs.label_color,f=this.prefs.block_color,O=this.left_offset;K.css({position:"absolute",top:0,left:(D-this.view.low)*ak-O});K.get(0).width=a+O;K.get(0).height=r;var z=K.get(0).getContext("2d"),ah=z.measureText("A").width;z.fillStyle=this.prefs.block_color;z.font=this.default_font;z.textAlign="right";if(w.dataset_type=="summary_tree"){var J,G=55,ab=255-G,g=ab*2/3,Q=w.data,B=w.max,l=w.avg;if(Q.length>2){var b=Math.ceil((Q[1][0]-Q[0][0])*ak)}else{var b=50}for(var af=0,v=Q.length;af<v;af++){var S=Math.ceil((Q[af][0]-D)*ak);var R=Q[af][1];if(!R){continue}J=Math.floor(ab-(R/B)*ab);z.fillStyle="rgb("+J+","+J+","+J+")";z.fillRect(S+O,0,b,20);if(this.prefs.show_counts){if(J>g){z.fillStyle="black"}else{z.fillStyle="#ddd"}z.textAlign="center";z.fillText(Q[af][1],S+O+(b/2),12)}}m.append(K);return K}var ai=w.data;var ae=0;for(var af=0,v=ai.length;af<v;af++){var L=ai[af],I=L[0],ag=L[1],T=L[2],E=L! [3];if(ag<=ac&&T>=D){var V=Math.floor(Math.max(0,(ag-D)*ak)),A=Math.ce il(Math.min(a,Math.max(0,(T-D)*ak))),P=aj[I]*al;if(w.dataset_type==="bai"){z.fillStyle="#555";if(L[4] instanceof Array){var s=Math.floor(Math.max(0,(L[4][0]-D)*ak)),H=Math.ceil(Math.min(a,Math.max(0,(L[4][1]-D)*ak))),q=Math.floor(Math.max(0,(L[5][0]-D)*ak)),o=Math.ceil(Math.min(a,Math.max(0,(L[5][1]-D)*ak)));if(L[4][1]>=D&&L[4][0]<=ac){this.rect_or_text(z,ak,ah,D,ac,L[4][0],L[4][2],s+O,H-s,P)}if(L[5][1]>=D&&L[5][0]<=ac){this.rect_or_text(z,ak,ah,D,ac,L[5][0],L[5][2],q+O,o-q,P)}if(q>H){z.fillStyle="#999";z.fillRect(H+O,P+5,q-H,1)}}else{z.fillStyle="#555";this.rect_or_text(z,ak,ah,D,ac,ag,E,V+O,A-V,P)}if(!U&&ag>D){z.fillStyle=this.prefs.label_color;if(h===0&&V-z.measureText(E).width<0){z.textAlign="left";z.fillText(I,A+2+O,P+8)}else{z.textAlign="right";z.fillText(I,V-2+O,P+8)}z.fillStyle="#555"}}else{if(w.dataset_type==="interval_index"){if(U){z.fillRect(V+O,P+5,A-V,1)}else{var u=L[4],N=L[5],X=L[6],e=L[7];var t,Z,F=null,am=null;if(N&&X){F=Math.floor(Math.max(0,(N-D)*ak));am=Ma! th.ceil(Math.min(a,Math.max(0,(X-D)*ak)))}if(E!==undefined&&ag>D){z.fillStyle=Y;if(h===0&&V-z.measureText(E).width<0){z.textAlign="left";z.fillText(E,A+2+O,P+8)}else{z.textAlign="right";z.fillText(E,V-2+O,P+8)}z.fillStyle=f}if(e){if(u){if(u=="+"){z.fillStyle=RIGHT_STRAND}else{if(u=="-"){z.fillStyle=LEFT_STRAND}}z.fillRect(V+O,P,A-V,10);z.fillStyle=f}for(var ad=0,d=e.length;ad<d;ad++){var n=e[ad],c=Math.floor(Math.max(0,(n[0]-D)*ak)),M=Math.ceil(Math.min(a,Math.max((n[1]-D)*ak)));if(c>M){continue}t=5;Z=3;z.fillRect(c+O,P+Z,M-c,t);if(F!==undefined&&!(c>am||M<F)){t=9;Z=1;var aa=Math.max(c,F),p=Math.min(M,am);z.fillRect(aa+O,P+Z,p-aa,t)}}}else{t=9;Z=1;z.fillRect(V+O,P+Z,A-V,t);if(L.strand){if(L.strand=="+"){z.fillStyle=RIGHT_STRAND_INV}else{if(L.strand=="-"){z.fillStyle=LEFT_STRAND_INV}}z.fillRect(V+O,P,A-V,10);z.fillStyle=prefs.block_color}}}}}ae++}}m.append(K);return K},gen_options:function(i){var a=$("<div></div>").addClass("form-row");var e="track_"+i+"_block_color",k=$("<l! abel></label>").attr("for",e).text("Block color:"),l=$("<input></input >").attr("id",e).attr("name",e).val(this.prefs.block_color),j="track_"+i+"_label_color",g=$("<label></label>").attr("for",j).text("Text color:"),h=$("<input></input>").attr("id",j).attr("name",j).val(this.prefs.label_color),f="track_"+i+"_show_count",c=$("<label></label>").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div></div>").append(b).append(c);return a.append(k).append(l).append(g).append(h).append(d)},update_options:function(d){var b=$("#track_"+d+"_block_color").val(),c=$("#track_"+d+"_label_color").val(),a=$("#track_"+d+"_show_count").attr("checked");if(b!==this.prefs.block_color||c!==this.prefs.label_color||a!=this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=c;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(c,a,b){FeatureTrack.call(this,c,a,b);this.track_type="ReadTrack";this.! vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{}); \ No newline at end of file diff -r 4aec0992748e -r 8094d8531fb2 static/scripts/trackster.js --- a/static/scripts/trackster.js Fri May 07 10:28:28 2010 -0400 +++ b/static/scripts/trackster.js Fri May 07 18:25:29 2010 -0400 @@ -118,7 +118,7 @@ }, remove_track: function( track ) { track.container_div.fadeOut('slow', function() { $(this).remove(); }); - delete this.tracks.splice(this.tracks.indexOf(track)); + delete this.tracks[this.tracks.indexOf(track)]; }, update_options: function() { var sorted = $("ul#sortable-ul").sortable('toArray'); @@ -129,7 +129,7 @@ for (var track_id in view.tracks) { var track = view.tracks[track_id]; - if (track.update_options) { + if (track && track.update_options) { track.update_options(track_id); } } @@ -173,7 +173,7 @@ $("#high").val( commatize(this.high) ); if (!nodraw) { for ( var i = 0, len = this.tracks.length; i < len; i++ ) { - if (this.tracks[i].enabled) { + if (this.tracks[i] && this.tracks[i].enabled) { this.tracks[i].draw(); } } diff -r 4aec0992748e -r 8094d8531fb2 templates/tracks/browser.mako --- a/templates/tracks/browser.mako Fri May 07 10:28:28 2010 -0400 +++ b/templates/tracks/browser.mako Fri May 07 18:25:29 2010 -0400 @@ -239,7 +239,7 @@ var sorted = $("ul#sortable-ul").sortable('toArray'); var payload = []; for (var i in sorted) { - var track_id = parseInt(sorted[i].split("track_")[1]), + var track_id = parseInt(sorted[i].split("track_")[1].split("_li")[0]), track = view.tracks[track_id]; payload.push( {

1 0

[hg] galaxy 3755: Another update to search+select: pack script a...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/4aec0992748e changeset: 3755:4aec0992748e user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Fri May 07 10:28:28 2010 -0400 description: Another update to search+select: pack script and replace icon. diffstat: static/images/fugue/control-270.png | 0 static/images/fugue/plus-white.png | 0 static/june_2007_style/blue/base.css | 2 +- static/scripts/packed/galaxy.base.js | 2 +- 4 files changed, 2 insertions(+), 2 deletions(-) diffs (21 lines): diff -r f550290ed5ad -r 4aec0992748e static/images/fugue/control-270.png Binary file static/images/fugue/control-270.png has changed diff -r f550290ed5ad -r 4aec0992748e static/images/fugue/plus-white.png Binary file static/images/fugue/plus-white.png has changed diff -r f550290ed5ad -r 4aec0992748e static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css Fri May 07 09:16:51 2010 -0400 +++ b/static/june_2007_style/blue/base.css Fri May 07 10:28:28 2010 -0400 @@ -147,4 +147,4 @@ .tipsy-west{background-position:left center;} .editable-text{cursor:pointer;} .editable-text:hover{cursor: text;border: dotted #999999 1px;} -.text-and-autocomplete-select{background-image:url(/static/images/fugue/plus-white.png);background-repeat: no-repeat;background-position:top right;} +.text-and-autocomplete-select{background-image:url(/static/images/fugue/control-270.png);background-repeat: no-repeat;background-position:right;} diff -r f550290ed5ad -r 4aec0992748e static/scripts/packed/galaxy.base.js --- a/static/scripts/packed/galaxy.base.js Fri May 07 09:16:51 2010 -0400 +++ b/static/scripts/packed/galaxy.base.js Fri May 07 10:28:28 2010 -0400 @@ -1,1 +1,1 @@ -$(document).ready(function(){replace_big_select_inputs()});$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};function ensure_popup_helper(){if($("#popup-helper").length===0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function attach_popupmenu(b,d){var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var c=function(g){$("#popup-helper").bind("click.popupmenu",a).show();d.click(a).css({left:0,top:-1000}).show();var f=g.pageX-d.width()/2;f=Math.min(f,$(document).scrollLeft()+$(window).width()-$(d).width()-20);f=Math.max(f,$(document).scrollLeft()+20);d.css({top:g.pageY-5,left:f});return false};$(b).click(c)}function make_popupmen! u(c,b){ensure_popup_helper();var a=$("<ul id='"+c.attr("id")+"-menu'></ul>");$.each(b,function(f,e){if(e){$("<li/>").html(f).click(e).appendTo(a)}else{$("<li class='head'/>").html(f).appendTo(a)}});var d=$("<div class='popmenu-wrapper'>");d.append(a).append("<div class='overlay-border'>").css("position","absolute").appendTo("body").hide();attach_popupmenu(c,d)}function make_popup_menus(){jQuery("div[popupmenu]").each(function(){var c={};$(this).find("a").each(function(){var b=$(this).attr("confirm"),d=$(this).attr("href"),e=$(this).attr("target");c[$(this).text()]=function(){if(!b||confirm(b)){var g=window;if(e=="_parent"){g=window.parent}else{if(e=="_top"){g=window.top}}g.location=d}}});var a=$("#"+$(this).attr("popupmenu"));make_popupmenu(a,c);$(this).remove();a.addClass("popup").show()})}function array_length(b){if(b.length){return b.length}var c=0;for(var a in b){c++}return c}function naturalSort(i,g){var n=/(-?[0-9\.]+)/g,j=i.toString().toLowerCase()||"",f=g.toString()! .toLowerCase()||"",k=String.fromCharCode(0),l=j.replace(n,k+"$1"+k).sp lit(k),e=f.replace(n,k+"$1"+k).split(k),d=(new Date(j)).getTime(),m=d?(new Date(f)).getTime():null;if(m){if(d<m){return -1}else{if(d>m){return 1}}}for(var h=0,c=Math.max(l.length,e.length);h<c;h++){oFxNcL=parseFloat(l[h])||l[h];oFyNcL=parseFloat(e[h])||e[h];if(oFxNcL<oFyNcL){return -1}else{if(oFxNcL>oFyNcL){return 1}}}return 0}function replace_big_select_inputs(a){$("select[name=dbkey]").each(function(){var b=$(this);if(a!==undefined&&b.find("option").length<a){return}var c=b.attr("value");var d=$("<input type='text' class='text-and-autocomplete-select'></input>");d.attr("size",40);d.attr("name",b.attr("name"));d.attr("id",b.attr("id"));d.click(function(){var i=$(this).attr("value");$(this).attr("value","Loading...");$(this).showAllInCache();$(this).attr("value",i);$(this).select()});var h=[];var g={};b.children("option").each(function(){var j=$(this).text();var i=$(this).attr("value");if(i=="?"){return}h.push(j);g[j]=i;g[i]=i;if(i==c){d.attr("value",j)}});h.push("unspecifie! d (?)");g["unspecified (?)"]="?";g["?"]="?";if(d.attr("value")==""){d.attr("value","Click to Search or Select")}h=h.sort(naturalSort);var f={selectFirst:false,autoFill:false,mustMatch:false,matchContains:true,max:1000,minChars:0,hideForLessThanMinChars:false};d.autocomplete(h,f);b.replaceWith(d);var e=function(){var j=d.attr("value");var i=g[j];if(i!==null&&i!==undefined){d.attr("value",i)}else{if(c!=""){d.attr("value",c)}else{d.attr("value","?")}}};d.parents("form").submit(function(){e()});$(document).bind("convert_dbkeys",function(){e()})})}function async_save_text(d,f,e,a,c,h,i,g,b){if(c===undefined){c=30}if(i===undefined){i=4}$("#"+d).live("click",function(){if($("#renaming-active").length>0){return}var l=$("#"+f),k=l.text(),j;if(h){j=$("<textarea></textarea>").attr({rows:i,cols:c}).text(k)}else{j=$("<input type='text'></input>").attr({value:k,size:c})}j.attr("id","renaming-active");j.blur(function(){$(this).remove();l.show();if(b){b(j)}});j.keyup(function(n){if(n.keyCo! de===27){$(this).trigger("blur")}else{if(n.keyCode===13){var m={};m[a] =$(this).val();$(this).trigger("blur");$.ajax({url:e,data:m,error:function(){alert("Text editing for elt "+f+" failed")},success:function(o){l.text(o);if(b){b(j)}}})}}});if(g){g(j)}l.hide();j.insertAfter(l);j.focus();j.select();return})}function init_history_items(d,a,c){var b=function(){try{var e=$.jStore.store("history_expand_state");if(e){for(var g in e){$("#"+g+" div.historyItemBody").show()}}}catch(f){$.jStore.remove("history_expand_state")}if($.browser.mozilla){$("div.historyItemBody").each(function(){if(!$(this).is(":visible")){$(this).find("pre.peek").css("overflow","hidden")}})}d.each(function(){var j=this.id;var h=$(this).children("div.historyItemBody");var i=h.find("pre.peek");$(this).find(".historyItemTitleBar > .historyItemTitle").wrap("<a href='javascript:void(0);'></a>").click(function(){if(h.is(":visible")){if($.browser.mozilla){i.css("overflow","hidden")}h.slideUp("fast");if(!c){var k=$.jStore.store("history_expand_state");if(k){delete k[j];$.jStore.store("h! 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u(c,b){ensure_popup_helper();var a=$("<ul id='"+c.attr("id")+"-menu'></ul>");$.each(b,function(f,e){if(e){$("<li/>").html(f).click(e).appendTo(a)}else{$("<li class='head'/>").html(f).appendTo(a)}});var d=$("<div class='popmenu-wrapper'>");d.append(a).append("<div class='overlay-border'>").css("position","absolute").appendTo("body").hide();attach_popupmenu(c,d)}function make_popup_menus(){jQuery("div[popupmenu]").each(function(){var c={};$(this).find("a").each(function(){var b=$(this).attr("confirm"),d=$(this).attr("href"),e=$(this).attr("target");c[$(this).text()]=function(){if(!b||confirm(b)){var g=window;if(e=="_parent"){g=window.parent}else{if(e=="_top"){g=window.top}}g.location=d}}});var a=$("#"+$(this).attr("popupmenu"));make_popupmenu(a,c);$(this).remove();a.addClass("popup").show()})}function array_length(b){if(b.length){return b.length}var c=0;for(var a in b){c++}return c}function naturalSort(i,g){var n=/(-?[0-9\.]+)/g,j=i.toString().toLowerCase()||"",f=g.toString()! .toLowerCase()||"",k=String.fromCharCode(0),l=j.replace(n,k+"$1"+k).sp lit(k),e=f.replace(n,k+"$1"+k).split(k),d=(new Date(j)).getTime(),m=d?(new Date(f)).getTime():null;if(m){if(d<m){return -1}else{if(d>m){return 1}}}for(var h=0,c=Math.max(l.length,e.length);h<c;h++){oFxNcL=parseFloat(l[h])||l[h];oFyNcL=parseFloat(e[h])||e[h];if(oFxNcL<oFyNcL){return -1}else{if(oFxNcL>oFyNcL){return 1}}}return 0}function replace_big_select_inputs(a){if(a===undefined){a=20}$('select[refresh_on_change!="true"]').each(function(){var b=$(this);if(b.find("option").length<a){return}var c=b.attr("value");var d=$("<input type='text' class='text-and-autocomplete-select'></input>");d.attr("size",40);d.attr("name",b.attr("name"));d.attr("id",b.attr("id"));d.click(function(){var i=$(this).attr("value");$(this).attr("value","Loading...");$(this).showAllInCache();$(this).attr("value",i);$(this).select()});var h=[];var g={};b.children("option").each(function(){var j=$(this).text();var i=$(this).attr("value");if(i=="?"){return}h.push(j);g[j]=i;g[i]=i;if(i==c){d.attr("value",j! )}});h.push("unspecified (?)");g["unspecified (?)"]="?";g["?"]="?";if(d.attr("value")==""){d.attr("value","Click to Search or Select")}h=h.sort(naturalSort);var f={selectFirst:false,autoFill:false,mustMatch:false,matchContains:true,max:1000,minChars:0,hideForLessThanMinChars:false};d.autocomplete(h,f);b.replaceWith(d);var e=function(){var j=d.attr("value");var i=g[j];if(i!==null&&i!==undefined){d.attr("value",i)}else{if(c!=""){d.attr("value",c)}else{d.attr("value","?")}}};d.parents("form").submit(function(){e()});$(document).bind("convert_dbkeys",function(){e()})})}function async_save_text(d,f,e,a,c,h,i,g,b){if(c===undefined){c=30}if(i===undefined){i=4}$("#"+d).live("click",function(){if($("#renaming-active").length>0){return}var l=$("#"+f),k=l.text(),j;if(h){j=$("<textarea></textarea>").attr({rows:i,cols:c}).text(k)}else{j=$("<input type='text'></input>").attr({value:k,size:c})}j.attr("id","renaming-active");j.blur(function(){$(this).remove();l.show();if(b){b(j)}});j.keyup! 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1 0

[hg] galaxy 3754: Replace large selects w/o refresh_on_change wi...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/f550290ed5ad changeset: 3754:f550290ed5ad user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Fri May 07 09:16:51 2010 -0400 description: Replace large selects w/o refresh_on_change with search+select. diffstat: static/scripts/galaxy.base.js | 12 ++++++++---- 1 files changed, 8 insertions(+), 4 deletions(-) diffs (24 lines): diff -r e42d0ae7b789 -r f550290ed5ad static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js Fri May 07 08:52:43 2010 -0400 +++ b/static/scripts/galaxy.base.js Fri May 07 09:16:51 2010 -0400 @@ -145,12 +145,16 @@ } // Replace select box with a text input box + autocomplete. -// TODO: make work with dynamic tool inputs and then can replace all big selects. +// TODO: make work with selects where refresh_on_change=True and refresh_on_change_values="..." function replace_big_select_inputs(min_length) { - $('select[name=dbkey]').each( function() { + // Set default for min_length. + if (min_length === undefined) + min_length = 20; + + $('select[refresh_on_change!="true"]').each( function() { var select_elt = $(this); - // Skip if # of options < threshold - if (min_length !== undefined && select_elt.find('option').length < min_length) + // Skip if # of options < min length. + if (select_elt.find('option').length < min_length) return; // Replace select with text + autocomplete.

1 0

[hg] galaxy 3753: Fix grid filtering bug.
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/e42d0ae7b789 changeset: 3753:e42d0ae7b789 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Fri May 07 08:52:43 2010 -0400 description: Fix grid filtering bug. diffstat: templates/grid_base.mako | 9 ++++++--- 1 files changed, 6 insertions(+), 3 deletions(-) diffs (19 lines): diff -r 8fdcfecfe856 -r e42d0ae7b789 templates/grid_base.mako --- a/templates/grid_base.mako Thu May 06 19:39:27 2010 -0400 +++ b/templates/grid_base.mako Fri May 07 08:52:43 2010 -0400 @@ -248,9 +248,12 @@ var url_args = ${h.to_json_string( cur_filter_dict )}; // Place "f-" in front of all filter arguments. - $.map(url_args, function(arg) { - return "f-" + arg; - }); + for (arg in url_args) + { + value = url_args[arg]; + delete url_args[arg]; + url_args["f-" + arg] = value; + } // Add sort argument to URL args. url_args['sort'] = "${encoded_sort_key}";

1 0

[hg] galaxy 3752: Add the modENCODEfly and modENCODEworm data so...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/8fdcfecfe856 changeset: 3752:8fdcfecfe856 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Thu May 06 19:39:27 2010 -0400 description: Add the modENCODEfly and modENCODEworm data source tools. diffstat: tools/data_source/fly_modencode.xml | 27 +++++++++++++++++++++++++++ tools/data_source/worm_modencode.xml | 27 +++++++++++++++++++++++++++ 2 files changed, 54 insertions(+), 0 deletions(-) diffs (62 lines): diff -r d3268bb6e48a -r 8fdcfecfe856 tools/data_source/fly_modencode.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/data_source/fly_modencode.xml Thu May 06 19:39:27 2010 -0400 @@ -0,0 +1,27 @@ +<?xml version="1.0"?> +<tool name="modENCODE fly" id="modENCODEfly" tool_type="data_source"> + <description>server</description> + <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> + <inputs action="http://modencode.oicr.on.ca/fgb2/gbrowse/fly" check_values="false" target="_top"> + <display>go to modENCODE fly server $GALAXY_URL</display> + <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=modENCODEfly" /> + </inputs> + <request_param_translation> + <request_param galaxy_name="URL" remote_name="URL" missing=""> + <append_param separator="&" first_separator="?" join="="> + <value name="d" missing="" /> + <value name="dbkey" missing="" /> + <value name="q" missing="" /> + <value name="s" missing="" /> + <value name="t" missing="" /> + </append_param> + </request_param> + <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" /> + <request_param galaxy_name="data_type" remote_name="data_type" missing="txt" /> + </request_param_translation> + <uihints minwidth="800"/> + <outputs> + <data name="output" format="txt" /> + </outputs> + <options sanitize="False" refresh="True"/> +</tool> diff -r d3268bb6e48a -r 8fdcfecfe856 tools/data_source/worm_modencode.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/data_source/worm_modencode.xml Thu May 06 19:39:27 2010 -0400 @@ -0,0 +1,27 @@ +<?xml version="1.0"?> +<tool name="modENCODE worm" id="modENCODEworm" tool_type="data_source"> + <description>server</description> + <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command> + <inputs action="http://modencode.oicr.on.ca/fgb2/gbrowse/worm" check_values="false" target="_top"> + <display>go to modENCODE worm server $GALAXY_URL</display> + <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=modENCODEworm" /> + </inputs> + <request_param_translation> + <request_param galaxy_name="URL" remote_name="URL" missing=""> + <append_param separator="&" first_separator="?" join="="> + <value name="d" missing="" /> + <value name="dbkey" missing="" /> + <value name="q" missing="" /> + <value name="s" missing="" /> + <value name="t" missing="" /> + </append_param> + </request_param> + <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" /> + <request_param galaxy_name="data_type" remote_name="data_type" missing="txt" /> + </request_param_translation> + <uihints minwidth="800"/> + <outputs> + <data name="output" format="txt" /> + </outputs> + <options sanitize="False" refresh="True"/> +</tool>

1 0

[hg] galaxy 3751: Fix bug that was preventing annotation of work...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/d3268bb6e48a changeset: 3751:d3268bb6e48a user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Thu May 06 17:52:49 2010 -0400 description: Fix bug that was preventing annotation of workflow input datasets. diffstat: templates/workflow/editor_generic_form.mako | 76 ++++++++++++++-------------- 1 files changed, 38 insertions(+), 38 deletions(-) diffs (84 lines): diff -r 370777a0693f -r d3268bb6e48a templates/workflow/editor_generic_form.mako --- a/templates/workflow/editor_generic_form.mako Thu May 06 12:30:54 2010 -0400 +++ b/templates/workflow/editor_generic_form.mako Thu May 06 17:52:49 2010 -0400 @@ -1,42 +1,42 @@ -<div class="toolForm"> - <div class="toolFormTitle">${form.title}</div> - <div class="toolFormBody"> - <form name="${form.name}" action="${h.url_for( action='editor_form_post' )}" method="post"> - <input type="hidden" name="type" value="${module.type}" /> - %if form.inputs: - %for input in form.inputs: - <% - cls = "form-row" - if input.error: - cls += " form-row-error" - %> - <div class="${cls}"> - <label> - ${input.label}: - </label> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="${input.type}" name="${input.name | h}" value="${input.value | h}" size="30"> - </div> - %if input.error: - <div style="float: left; color: red; font-weight: bold; padding-top: 1px; padding-bottom: 3px;"> - <div style="width: 300px;"><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}"> <span style="vertical-align: middle;">${input.error}</span></div> - </div> - %endif +<form name="${form.name}" action="${h.url_for( action='editor_form_post' )}" method="post"> + <div class="toolForm"> + <div class="toolFormTitle">${form.title}</div> + <div class="toolFormBody"> + <input type="hidden" name="type" value="${module.type}" /> + %if form.inputs: + %for input in form.inputs: + <% + cls = "form-row" + if input.error: + cls += " form-row-error" + %> + <div class="${cls}"> + <label> + ${input.label}: + </label> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="${input.type}" name="${input.name | h}" value="${input.value | h}" size="30"> + </div> + %if input.error: + <div style="float: left; color: red; font-weight: bold; padding-top: 1px; padding-bottom: 3px;"> + <div style="width: 300px;"><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}"> <span style="vertical-align: middle;">${input.error}</span></div> + </div> + %endif - %if input.help: - <div class="toolParamHelp" style="clear: both;"> - ${input.help} - </div> - %endif + %if input.help: + <div class="toolParamHelp" style="clear: both;"> + ${input.help} + </div> + %endif - <div style="clear: both"></div> + <div style="clear: both"></div> - </div> - %endfor - %else: - <div class="form-row"><i>No options</i></div> - %endif - </table> - </form> + </div> + %endfor + %else: + <div class="form-row"><i>No options</i></div> + %endif + </table> + </div> </div> -</div> +</form>

1 0

[hg] galaxy 3750: trackster:
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/370777a0693f changeset: 3750:370777a0693f user: Kanwei Li <kanwei(a)gmail.com> date: Thu May 06 12:30:54 2010 -0400 description: trackster: - Custom dbkeys now create new HDA and copies info in - Fix track reordering for all browsers - Fix track deletion - Fix BAM display diffstat: lib/galaxy/visualization/tracks/data/bam.py | 6 ++-- lib/galaxy/web/controllers/tracks.py | 35 ++++++++++++++++++---------- lib/galaxy/web/controllers/user.py | 19 +++++++++++++-- static/scripts/packed/trackster.js | 2 +- static/scripts/trackster.js | 28 ++++++++++++++--------- templates/tracks/browser.mako | 4 +-- templates/user/dbkeys.mako | 25 +++++++++++--------- tool_conf.xml.main | 1 + 8 files changed, 75 insertions(+), 45 deletions(-) diffs (294 lines): diff -r e7d91d58f4ad -r 370777a0693f lib/galaxy/visualization/tracks/data/bam.py --- a/lib/galaxy/visualization/tracks/data/bam.py Thu May 06 12:11:47 2010 -0400 +++ b/lib/galaxy/visualization/tracks/data/bam.py Thu May 06 12:30:54 2010 -0400 @@ -10,7 +10,7 @@ import logging log = logging.getLogger(__name__) -MAX_VALS = 50 # only display first MAX_VALS datapoints +MAX_VALS = 5000 # only display first MAX_VALS datapoints class BamDataProvider( object ): """ @@ -36,7 +36,7 @@ if chrom.startswith( 'chr' ): try: data = bamfile.fetch( start=start, end=end, reference=chrom[3:] ) - except: + except ValueError: return None else: return None @@ -74,4 +74,4 @@ results.append( [ qname, start, end, read['seq'], r1, r2 ] ) bamfile.close() - return results \ No newline at end of file + return { 'data': results, 'message': message } diff -r e7d91d58f4ad -r 370777a0693f lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py Thu May 06 12:11:47 2010 -0400 +++ b/lib/galaxy/web/controllers/tracks.py Thu May 06 12:30:54 2010 -0400 @@ -99,7 +99,7 @@ user = trans.get_user() if 'dbkeys' in user.preferences: user_keys = from_json_string( user.preferences['dbkeys'] ) - + dbkeys = [ (k, v) for k, v in trans.db_builds if k in self.len_files or k in user_keys ] return trans.fill_template( "tracks/new_browser.mako", dbkeys=dbkeys ) @@ -197,21 +197,24 @@ """ Helper method that returns chrom lengths for a given user and dbkey. """ + len_file = None + len_ds = None # If there is any dataset in the history of extension `len`, this will use it if 'dbkeys' in user.preferences: user_keys = from_json_string( user.preferences['dbkeys'] ) if dbkey in user_keys: - return user_keys[dbkey]['chroms'] + len_file = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( user_keys[dbkey]['len'] ).file_name - db_manifest = trans.db_dataset_for( dbkey ) - if not db_manifest: - db_manifest = os.path.join( trans.app.config.tool_data_path, 'shared','ucsc','chrom', "%s.len" % dbkey ) - else: - db_manifest = db_manifest.file_name + if not len_file: + len_ds = trans.db_dataset_for( dbkey ) + if not len_ds: + len_file = os.path.join( trans.app.config.tool_data_path, 'shared','ucsc','chrom', "%s.len" % dbkey ) + else: + len_file = len_ds.file_name manifest = {} - if not os.path.exists( db_manifest ): + if not os.path.exists( len_file ): return None - for line in open( db_manifest ): + for line in open( len_file ): if line.startswith("#"): continue line = line.rstrip("\r\n") fields = line.split("\t") @@ -240,7 +243,9 @@ # Need to check states again for the converted version if converted_dataset and converted_dataset.state == model.Dataset.states.ERROR: - return messages.ERROR + job_id = trans.sa_session.query( trans.app.model.JobToOutputDatasetAssociation ).filter_by( dataset_id=converted_dataset.id ).first().job_id + job = trans.sa_session.query( trans.app.model.Job ).get( job_id ) + return { 'kind': messages.ERROR, 'message': job.stderr } if not converted_dataset or converted_dataset.state != model.Dataset.states.OK: return messages.PENDING @@ -256,13 +261,17 @@ extra_info = "no_detail" else: frequencies, max_v, avg_v, delta = summary - return { "dataset_type": data_sources['index'], "data": frequencies, "max": max_v, "avg": avg_v, "delta": delta } + return { 'dataset_type': data_sources['index'], 'data': frequencies, 'max': max_v, 'avg': avg_v, 'delta': delta } dataset_type = data_sources['data'] data_provider = dataset_type_to_data_provider[ dataset_type ]( dataset.get_converted_dataset(trans, dataset_type), dataset ) - + data = data_provider.get_data( chrom, low, high, **kwargs ) - return { "dataset_type": dataset_type, "extra_info": extra_info, "data": data } + message = None + if isinstance(data, dict) and 'message' in data: + message = data['message'] + data = data['data'] + return { 'dataset_type': dataset_type, 'extra_info': extra_info, 'data': data, 'message': message } @web.expose def list_tracks( self, trans, hid ): diff -r e7d91d58f4ad -r 370777a0693f lib/galaxy/web/controllers/user.py --- a/lib/galaxy/web/controllers/user.py Thu May 06 12:11:47 2010 -0400 +++ b/lib/galaxy/web/controllers/user.py Thu May 06 12:30:54 2010 -0400 @@ -902,7 +902,18 @@ if not name or not key or not len_text: message = "You must specify values for all the fields." else: - chrom_dict = {} + # Create new len file + new_len = trans.app.model.HistoryDatasetAssociation( extension="len", create_dataset=True, sa_session=trans.sa_session ) + trans.sa_session.add( new_len ) + new_len.name = name + new_len.visible = False + new_len.history_id = trans.get_history().id + new_len.state = trans.app.model.Job.states.OK + new_len.info = "custom build .len file" + trans.sa_session.flush() + + counter = 0 + f = open(new_len.file_name, "w") for line in len_text.split("\n"): lst = line.strip().split() if not lst or len(lst) < 2: @@ -914,8 +925,10 @@ except ValueError: lines_skipped += 1 continue - chrom_dict[chrom] = length - dbkeys[key] = { "name": name, "chroms": chrom_dict } + counter += 1 + f.write("%s\t%s\n" % (chrom, length)) + f.close() + dbkeys[key] = { "name": name, "len": new_len.id, "count": counter } user.preferences['dbkeys'] = to_json_string(dbkeys) trans.sa_session.flush() diff -r e7d91d58f4ad -r 370777a0693f static/scripts/packed/trackster.js --- a/static/scripts/packed/trackster.js Thu May 06 12:11:47 2010 -0400 +++ b/static/scripts/packed/trackster.js Thu May 06 12:30:54 2010 -0400 @@ -1,1 +1,1 @@ -var DEBUG=false;var DENSITY=200,FEATURE_LEVELS=10,DATA_ERROR="There was an error in indexing this dataset.",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=5,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="/static/images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="/static/images/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src="/static/images/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern(! right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src="/static/images/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},clear:function(){this.obj_cache={};this.key_ary=[]}});var Drawer=function(){};$.extend(Drawer.prototype,{intensity:function(b,a,c){},});drawer=new Drawer();var View=function(b,d,c,a){this.vis_id=c;this.dbkey=a;this.title=d;this.chrom=b;this.tracks=[];this.label_tracks=[];this.m! ax_low=0;this.max_high=0;this.center=(this.max_high-this.max_low)/2;th is.zoom_factor=3;this.zoom_level=0;this.track_id_counter=0};$.extend(View.prototype,{add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);this.track_id_counter+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks[a]},update_options:function(){var b=$("ul#sortable-ul").sortable("toArray");var d=[];var c=$("#viewport > div").sort(function(g,f){return b.indexOf($(g).attr("id"))>b.indexOf($(f).attr("id"))});$("#viewport > div").remove();$("#viewport").html(c);for(var e in view.tracks){var a=view.tracks[e];if(a.update_options){a.update_options(e)}}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.center=this.center=(this.max_high-this.max_low)/2;this.zoom_level=0;$(".yaxislabel").remove()},redraw:function(f){this.span=this.max_high-this.max! _low;var d=this.span/Math.pow(this.zoom_factor,this.zoom_level),b=this.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){e=this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));$("#overview-box").css({left:(this.low/this.span)*$("#overview-viewport").width(),width:Math.max(12,((this.high-this.low)/this.span)*$("#overview-viewport").width())}).show();$("#low").val(commatize(this.low));$("#high").val(commatize(this.high));if(!f){for(var c=0,a=this.tracks.length;c<a;c++){if(this.tracks[c].enabled){this.tracks[c].draw()}}for(var c=0,a=this.label_tracks.length;c<a;c++){this.label_tracks[c].draw()}}},zoom_in:function(a,b){if(this.max_high===0||this.high-this.low<30){return}if(a){this.center=! a/b.width()*(this.high-this.low)+this.low}this.zoom_level+=1;this.redr aw()},zoom_out:function(){if(this.max_high===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1;this.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.init_global()};$.extend(Track.prototype,{init_global:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div></div>").addClass("track").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)},init_each:function(c,b){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.content_div.css("height","30px");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.getJSON(data_url,c,function(d){if(!d||d==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR)}else{if(d==="no converter"){a.container_div.addClass("error");a.cont! ent_div.text(DATA_NOCONVERTER)}else{if(d.data&&d.data.length===0||d.data===null){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;b(d);a.draw()}}}}})}else{a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}}});var TiledTrack=function(){};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var i=this.view.low,e=this.view.high,f=e-i,d=this.view.resolution;if(DEBUG){$("#debug").text(d+" "+this.view.zoom_res)}var k=$("<div style='position: relative;'></div>"),l=this.content_div.width()/f,h;this.content_div.children(":first").remove();this.content_div.append(k),this.max_height=0;var a=Math.floor(i/d/DENSITY);while((a*DENSITY*d)<e){var j=this.content_div.width()+"_"+this.view.zoom_level+"_"+a;var c=this.tile_cache.get(j);if(c! ){var g=a*DENSITY*d;var b=(g-i)*l;if(this.left_offset){b-=this.left_of fset}c.css({left:b});k.append(c);this.max_height=Math.max(this.max_height,c.height());this.content_div.css("height",this.max_height+"px")}else{this.delayed_draw(this,j,i,e,a,d,k,l)}a+=1}},delayed_draw:function(c,e,a,f,b,d,g,h){setTimeout(function(){if(!(a>c.view.high||f<c.view.low)){tile_element=c.draw_tile(d,b,g,h);if(tile_element){c.tile_cache.set(e,tile_element);c.max_height=Math.max(c.max_height,tile_element.height());c.content_div.css("height",c.max_height+"px")}}},50)}});var LabelTrack=function(a){Track.call(this,null,a);this.track_type="LabelTrack";this.hidden=true;this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css! ({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,a,b){this.track_type="LineTrack";Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.height_px=100;this.container_div.addClass("line-track");this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={min_value:undefined,max_value:undefined,mode:"Line"};if(b.min_value!==undefined){this.prefs.min_value=b.min_value}if(b.max_value!==undefined){this.prefs.max_value=b.max_value}if(b.mode!==undefined){this.prefs.mode=b.mode}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=undefined;this.init_each({stats:true,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(c){data=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=data.min;a.prefs.ma! x_value=data.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#t rack_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=data.total_frequency;$("#linetrack_"+b+"_minval").remove();$("#linetrack_"+b+"_maxval").remove();var e=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(a.prefs.min_value);var d=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(a.prefs.max_value);d.css({position:"relative",top:"25px"});d.prependTo(a.container_div);e.css({position:"relative",top:a.height_px+55+"px"});e.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=true;$.ajax({url:data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){data=g.data;c.data_cache.set(e,data);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(o! ,q,c,e){if(this.vertical_range===undefined){return}var r=q*DENSITY*o,a=DENSITY*o,b=$("<canvas class='tile'></canvas>"),u=o+"_"+q;if(this.data_cache.get(u)===undefined){this.get_data(o,q);return}var t=this.data_cache.get(u);if(t===null){return}b.css({position:"absolute",top:0,left:(r-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var n=b.get(0).getContext("2d"),k=false,l=this.prefs.min_value,g=this.prefs.max_value,m=this.vertical_range,s=this.total_frequency,d=this.height_px;n.beginPath();if(t.length>1){var f=Math.ceil((t[1][0]-t[0][0])*e)}else{var f=10}for(var p=0;p<t.length;p++){var j=t[p][0]-r;var h=t[p][1];if(this.prefs.mode=="Intensity"){if(h===null){continue}j=j*e;if(h<=l){h=l}else{if(h>=g){h=g}}h=255-Math.floor((h-l)/m*255);n.fillStyle="rgb("+h+","+h+","+h+")";n.fillRect(j,0,f,this.height_px)}else{if(h===null){k=false;continue}else{j=j*e;if(h<=l){h=l}else{if(h>=g){h=g}}h=Math.round(d-(h-l)/m*d);if(k){n.lineTo(j,h)}else{n.moveTo(j,h);k=! true}}}}n.stroke();c.append(b);return b},gen_options:function(n){var a =$("<div></div>").addClass("form-row");var h="track_"+n+"_minval",k="track_"+n+"_maxval",e="track_"+n+"_mode",l=$("<label></label>").attr("for",h).text("Min value:"),b=(this.prefs.min_value===undefined?"":this.prefs.min_value),m=$("<input></input>").attr("id",h).val(b),g=$("<label></label>").attr("for",k).text("Max value:"),j=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",k).val(j),d=$("<label></label>").attr("for",e).text("Display mode:"),i=(this.prefs.mode===undefined?"Line":this.prefs.mode),c=$('<select id="'+e+'"><option value="Line" id="mode_Line">Line</option><option value="Intensity" id="mode_Intensity">Intensity</option></select>');c.children("#mode_"+i).attr("selected","selected");return a.append(l).append(m).append(g).append(f).append(d).append(c)},update_options:function(d){var a=$("#track_"+d+"_minval").val(),c=$("#track_"+d+"_maxval").val(),b=$("#track_"+d+"_mode option:selected").val();if(a!==this.prefs.min_value||c!! ==this.prefs.max_value||b!=this.prefs.mode){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(c);this.prefs.mode=b;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+d+"_minval").text(this.prefs.min_value);$("#linetrack_"+d+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(c,a,b){this.track_type="FeatureTrack";Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.height_px=100;this.container_div.addClass("feature-track");this.dataset_id=a;this.zo_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.default_font="9px Monaco, Lucida Console, monospace";this.left_offset=200;this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new Cache(20);this.prefs={block_color:"black",label_color:"black",show_counts:false};if(b.block_color!==undefine! d){this.prefs.block_color=b.block_color}if(b.label_color!==undefined){ this.prefs.label_color=b.label_color}if(b.show_counts!==undefined){this.prefs.show_counts=b.show_counts}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.max_low+"_"+a.view.max_high;this.init_each({low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom,resolution:this.view.resolution},function(c){a.data_cache.set(b,c);a.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=true;$.getJSON(data_url,{chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,resolution:this.view.resolution},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,g,c){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=1/a;this.s_e_by_tile[a]={}}var m=this.inc_slots[a].w_scale,v=[],h=0,b=$("<canvas></canvas>").get(0).getContext("2d"),n=this.view.max_low;var d,f,x=[];for(var s=0,t=g.length;s<t;s++){var e=g[s],l=e[0];if(this.inc_slots[! a][l]!==undefined){h=Math.max(h,this.inc_slots[a][l]);x.push(this.inc_slots[a][l])}else{v.push(s)}}for(var s=0,t=v.length;s<t;s++){var e=g[v[s]];l=e[0],feature_start=e[1],feature_end=e[2],feature_name=e[3];d=Math.floor((feature_start-n)*m);f=Math.ceil((feature_end-n)*m);if(!c){var p=b.measureText(feature_name).width;if(d-p<0){f+=p}else{d-=p}}var r=0;while(true){var o=true;if(this.s_e_by_tile[a][r]!==undefined){for(var q=0,w=this.s_e_by_tile[a][r].length;q<w;q++){var u=this.s_e_by_tile[a][r][q];if(f>u[0]&&d<u[1]){o=false;break}}}if(o){if(this.s_e_by_tile[a][r]===undefined){this.s_e_by_tile[a][r]=[]}this.s_e_by_tile[a][r].push([d,f]);this.inc_slots[a][l]=r;h=Math.max(h,r);break}r++}}return h},rect_or_text:function(n,o,g,f,m,b,d,k,e,i){n.textAlign="center";var j=Math.round(o/2);if(d!==undefined&&o>g){n.fillStyle="#555";n.fillRect(k,i+1,e,9);n.fillStyle="#eee";for(var h=0,l=d.length;h<l;h++){if(b+h>=f&&b+h<=m){var a=Math.floor(Math.max(0,(b+h-f)*o));n.fillText(d[h],a+this.left_! offset+j,i+9)}}}else{n.fillStyle="#555";n.fillRect(k,i+4,e,3)}},draw_t ile:function(W,h,m,ak){var D=h*DENSITY*W,ac=(h+1)*DENSITY*W,C=DENSITY*W;var aj,r;var ad=D+"_"+ac;var w=this.data_cache.get(ad);if(w===undefined){this.data_queue[[D,ac]]=true;this.get_data(D,ac);return}if(w.dataset_type==="summary_tree"){r=30}else{var U=(w.extra_info==="no_detail");var al=(U?this.vertical_nodetail_px:this.vertical_detail_px);r=this.incremental_slots(this.view.zoom_res,w.data,U)*al+15;m.parent().css("height",Math.max(this.height_px,r)+"px");aj=this.inc_slots[this.view.zoom_res]}var a=Math.ceil(C*ak),K=$("<canvas class='tile'></canvas>"),Y=this.prefs.label_color,f=this.prefs.block_color,O=this.left_offset;K.css({position:"absolute",top:0,left:(D-this.view.low)*ak-O});K.get(0).width=a+O;K.get(0).height=r;var z=K.get(0).getContext("2d"),ah=z.measureText("A").width;z.fillStyle=this.prefs.block_color;z.font=this.default_font;z.textAlign="right";if(w.dataset_type=="summary_tree"){var J,G=55,ab=255-G,g=ab*2/3,Q=w.data,B=w.max,l=w.avg;if(Q.length>2){var b=Math.ceil((Q! [1][0]-Q[0][0])*ak)}else{var b=50}for(var af=0,v=Q.length;af<v;af++){var S=Math.ceil((Q[af][0]-D)*ak);var R=Q[af][1];if(!R){continue}J=Math.floor(ab-(R/B)*ab);z.fillStyle="rgb("+J+","+J+","+J+")";z.fillRect(S+O,0,b,20);if(this.prefs.show_counts){if(J>g){z.fillStyle="black"}else{z.fillStyle="#ddd"}z.textAlign="center";z.fillText(Q[af][1],S+O+(b/2),12)}}m.append(K);return K}var ai=w.data;var ae=0;for(var af=0,v=ai.length;af<v;af++){var L=ai[af],I=L[0],ag=L[1],T=L[2],E=L[3];if(ag<=ac&&T>=D){var V=Math.floor(Math.max(0,(ag-D)*ak)),A=Math.ceil(Math.min(a,Math.max(0,(T-D)*ak))),P=aj[I]*al;if(w.dataset_type==="bai"){z.fillStyle="#555";if(L[4] instanceof Array){var s=Math.floor(Math.max(0,(L[4][0]-D)*ak)),H=Math.ceil(Math.min(a,Math.max(0,(L[4][1]-D)*ak))),q=Math.floor(Math.max(0,(L[5][0]-D)*ak)),o=Math.ceil(Math.min(a,Math.max(0,(L[5][1]-D)*ak)));if(L[4][1]>=D&&L[4][0]<=ac){this.rect_or_text(z,ak,ah,D,ac,L[4][0],L[4][2],s+O,H-s,P)}if(L[5][1]>=D&&L[5][0]<=ac){this.rect_or_text(z,ak! ,ah,D,ac,L[5][0],L[5][2],q+O,o-q,P)}if(q>H){z.fillStyle="#999";z.fillR ect(H+O,P+5,q-H,1)}}else{z.fillStyle="#555";this.rect_or_text(z,ak,ah,D,ac,ag,E,V+O,A-V,P)}if(!U&&ag>D){z.fillStyle=this.prefs.label_color;if(h===0&&V-z.measureText(E).width<0){z.textAlign="left";z.fillText(I,A+2+O,P+8)}else{z.textAlign="right";z.fillText(I,V-2+O,P+8)}z.fillStyle="#555"}}else{if(w.dataset_type==="interval_index"){if(U){z.fillRect(V+O,P+5,A-V,1)}else{var u=L[4],N=L[5],X=L[6],e=L[7];var t,Z,F=null,am=null;if(N&&X){F=Math.floor(Math.max(0,(N-D)*ak));am=Math.ceil(Math.min(a,Math.max(0,(X-D)*ak)))}if(E!==undefined&&ag>D){z.fillStyle=Y;if(h===0&&V-z.measureText(E).width<0){z.textAlign="left";z.fillText(E,A+2+O,P+8)}else{z.textAlign="right";z.fillText(E,V-2+O,P+8)}z.fillStyle=f}if(e){if(u){if(u=="+"){z.fillStyle=RIGHT_STRAND}else{if(u=="-"){z.fillStyle=LEFT_STRAND}}z.fillRect(V+O,P,A-V,10);z.fillStyle=f}for(var ad=0,d=e.length;ad<d;ad++){var n=e[ad],c=Math.floor(Math.max(0,(n[0]-D)*ak)),M=Math.ceil(Math.min(a,Math.max((n[1]-D)*ak)));if(c>M){continue}t=5;Z=3;z.fillR! ect(c+O,P+Z,M-c,t);if(F!==undefined&&!(c>am||M<F)){t=9;Z=1;var aa=Math.max(c,F),p=Math.min(M,am);z.fillRect(aa+O,P+Z,p-aa,t)}}}else{t=9;Z=1;z.fillRect(V+O,P+Z,A-V,t);if(L.strand){if(L.strand=="+"){z.fillStyle=RIGHT_STRAND_INV}else{if(L.strand=="-"){z.fillStyle=LEFT_STRAND_INV}}z.fillRect(V+O,P,A-V,10);z.fillStyle=prefs.block_color}}}}}ae++}}m.append(K);return K},gen_options:function(i){var a=$("<div></div>").addClass("form-row");var e="track_"+i+"_block_color",k=$("<label></label>").attr("for",e).text("Block color:"),l=$("<input></input>").attr("id",e).attr("name",e).val(this.prefs.block_color),j="track_"+i+"_label_color",g=$("<label></label>").attr("for",j).text("Text color:"),h=$("<input></input>").attr("id",j).attr("name",j).val(this.prefs.label_color),f="track_"+i+"_show_count",c=$("<label></label>").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$(! "<div></div>").append(b).append(c);return a.append(k).append(l).append (g).append(h).append(d)},update_options:function(d){var b=$("#track_"+d+"_block_color").val(),c=$("#track_"+d+"_label_color").val(),a=$("#track_"+d+"_show_count").attr("checked");if(b!==this.prefs.block_color||c!==this.prefs.label_color||a!=this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=c;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(c,a,b){FeatureTrack.call(this,c,a,b);this.track_type="ReadTrack";this.vertical_detail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{}); \ No newline at end of file +var DEBUG=false;var DENSITY=200,FEATURE_LEVELS=10,DATA_ERROR="There was an error in indexing this dataset. ",DATA_NOCONVERTER="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",DATA_NONE="No data for this chrom/contig.",DATA_PENDING="Currently indexing... please wait",DATA_LOADING="Loading data...",CACHED_TILES_FEATURE=10,CACHED_TILES_LINE=30,CACHED_DATA=5,CONTEXT=$("<canvas></canvas>").get(0).getContext("2d"),RIGHT_STRAND,LEFT_STRAND;var right_img=new Image();right_img.src="/static/images/visualization/strand_right.png";right_img.onload=function(){RIGHT_STRAND=CONTEXT.createPattern(right_img,"repeat")};var left_img=new Image();left_img.src="/static/images/visualization/strand_left.png";left_img.onload=function(){LEFT_STRAND=CONTEXT.createPattern(left_img,"repeat")};var right_img_inv=new Image();right_img_inv.src="/static/images/visualization/strand_right_inv.png";right_img_inv.onload=function(){RIGHT_STRAND_INV=CONTEXT.createPattern! (right_img_inv,"repeat")};var left_img_inv=new Image();left_img_inv.src="/static/images/visualization/strand_left_inv.png";left_img_inv.onload=function(){LEFT_STRAND_INV=CONTEXT.createPattern(left_img_inv,"repeat")};function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}var Cache=function(a){this.num_elements=a;this.clear()};$.extend(Cache.prototype,{get:function(b){var a=this.key_ary.indexOf(b);if(a!=-1){this.key_ary.splice(a,1);this.key_ary.push(b)}return this.obj_cache[b]},set:function(b,c){if(!this.obj_cache[b]){if(this.key_ary.length>=this.num_elements){var a=this.key_ary.shift();delete this.obj_cache[a]}this.key_ary.push(b)}this.obj_cache[b]=c;return c},clear:function(){this.obj_cache={};this.key_ary=[]}});var Drawer=function(){};$.extend(Drawer.prototype,{intensity:function(b,a,c){},});drawer=new Drawer();var View=function(b,d,c,a){this.vis_id=c;this.dbkey=a;this.title=d;this.chrom=b;this.tracks=[];this.label_tracks=[];this.! max_low=0;this.max_high=0;this.center=(this.max_high-this.max_low)/2;t his.zoom_factor=3;this.zoom_level=0;this.track_id_counter=0};$.extend(View.prototype,{add_track:function(a){a.view=this;a.track_id=this.track_id_counter;this.tracks.push(a);if(a.init){a.init()}a.container_div.attr("id","track_"+a.track_id);this.track_id_counter+=1},add_label_track:function(a){a.view=this;this.label_tracks.push(a)},remove_track:function(a){a.container_div.fadeOut("slow",function(){$(this).remove()});delete this.tracks.splice(this.tracks.indexOf(a))},update_options:function(){var b=$("ul#sortable-ul").sortable("toArray");for(var c in b){var e=b[c].split("_li")[0].split("track_")[1];$("#viewport").append($("#track_"+e))}for(var d in view.tracks){var a=view.tracks[d];if(a.update_options){a.update_options(d)}}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.center=this.center=(this.max_high-this.max_low)/2;this.zoom_level=0;$(".yaxislabel").remove()},redraw:function(f){this.span=this.max_high-this.max_low;var d=this.span/Math.pow(this.zoom_fa! ctor,this.zoom_level),b=this.center-(d/2),e=b+d;if(b<0){b=0;e=b+d}else{if(e>this.max_high){e=this.max_high;b=e-d}}this.low=Math.floor(b);this.high=Math.ceil(e);this.center=Math.round(this.low+(this.high-this.low)/2);this.resolution=Math.pow(10,Math.ceil(Math.log((this.high-this.low)/200)/Math.LN10));this.zoom_res=Math.pow(FEATURE_LEVELS,Math.max(0,Math.ceil(Math.log(this.resolution,FEATURE_LEVELS)/Math.log(FEATURE_LEVELS))));$("#overview-box").css({left:(this.low/this.span)*$("#overview-viewport").width(),width:Math.max(12,((this.high-this.low)/this.span)*$("#overview-viewport").width())}).show();$("#low").val(commatize(this.low));$("#high").val(commatize(this.high));if(!f){for(var c=0,a=this.tracks.length;c<a;c++){if(this.tracks[c].enabled){this.tracks[c].draw()}}for(var c=0,a=this.label_tracks.length;c<a;c++){this.label_tracks[c].draw()}}},zoom_in:function(a,b){if(this.max_high===0||this.high-this.low<30){return}if(a){this.center=a/b.width()*(this.high-this.low)+this.low}! this.zoom_level+=1;this.redraw()},zoom_out:function(){if(this.max_high ===0){return}if(this.zoom_level<=0){this.zoom_level=0;return}this.zoom_level-=1;this.redraw()}});var Track=function(a,b){this.name=a;this.parent_element=b;this.init_global()};$.extend(Track.prototype,{init_global:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div></div>").addClass("track").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)},init_each:function(c,b){var a=this;a.enabled=false;a.data_queue={};a.tile_cache.clear();a.data_cache.clear();a.content_div.css("height","30px");if(!a.content_div.text()){a.content_div.text(DATA_LOADING)}a.container_div.removeClass("nodata error pending");if(a.view.chrom){$.getJSON(data_url,c,function(d){if(!d||d==="error"||d.kind==="error"){a.container_div.addClass("error");a.content_div.text(DATA_ERROR);if(d.message){var f=a.view.tracks.indexOf(a);var e=$("<a href='javascript:void(0);'></a>").a! ttr("id",f+"_error");e.text("Click to view error");$("#"+f+"_error").live("click",function(){show_modal("Trackster Error","<pre>"+d.message+"</pre>",{Close:hide_modal})});a.content_div.append(e)}}else{if(d==="no converter"){a.container_div.addClass("error");a.content_div.text(DATA_NOCONVERTER)}else{if(d.data!==undefined&&(d.data===null||d.data.length===0)){a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}else{if(d==="pending"){a.container_div.addClass("pending");a.content_div.text(DATA_PENDING);setTimeout(function(){a.init()},5000)}else{a.content_div.text("");a.content_div.css("height",a.height_px+"px");a.enabled=true;b(d);a.draw()}}}}})}else{a.container_div.addClass("nodata");a.content_div.text(DATA_NONE)}}});var TiledTrack=function(){};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var i=this.view.low,e=this.view.high,f=e-i,d=this.view.resolution;if(DEBUG){$("#debug").text(d+" "+this.view.zoom_res)}var k=$("<div style='position: relative;'>! </div>"),l=this.content_div.width()/f,h;this.content_div.children(":fi rst").remove();this.content_div.append(k),this.max_height=0;var a=Math.floor(i/d/DENSITY);while((a*DENSITY*d)<e){var j=this.content_div.width()+"_"+this.view.zoom_level+"_"+a;var c=this.tile_cache.get(j);if(c){var g=a*DENSITY*d;var b=(g-i)*l;if(this.left_offset){b-=this.left_offset}c.css({left:b});k.append(c);this.max_height=Math.max(this.max_height,c.height());this.content_div.css("height",this.max_height+"px")}else{this.delayed_draw(this,j,i,e,a,d,k,l)}a+=1}},delayed_draw:function(c,e,a,f,b,d,g,h){setTimeout(function(){if(!(a>c.view.high||f<c.view.low)){tile_element=c.draw_tile(d,b,g,h);if(tile_element){c.tile_cache.set(e,tile_element);c.max_height=Math.max(c.max_height,tile_element.height());c.content_div.css("height",c.max_height+"px")}}},50)}});var LabelTrack=function(a){Track.call(this,null,a);this.track_type="LabelTrack";this.hidden=true;this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-! c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+commatize(a)+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,a,b){this.track_type="LineTrack";Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.height_px=100;this.dataset_id=a;this.data_cache=new Cache(CACHED_DATA);this.tile_cache=new Cache(CACHED_TILES_LINE);this.prefs={min_value:undefined,max_value:undefined,mode:"Line"};if(b.min_value!==undefined){this.prefs.min_value=b.min_value}if(b.max_value!==undefined){this.prefs.max_value=b.max_value}if(b.mode!==undefined){this.prefs.mode=b.mode}};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.tracks.indexOf(a);a.vertical_range=unde! fined;this.init_each({stats:true,chrom:a.view.chrom,low:null,high:null ,dataset_id:a.dataset_id},function(c){a.container_div.addClass("line-track");data=c.data;if(isNaN(parseFloat(a.prefs.min_value))||isNaN(parseFloat(a.prefs.max_value))){a.prefs.min_value=data.min;a.prefs.max_value=data.max;$("#track_"+b+"_minval").val(a.prefs.min_value);$("#track_"+b+"_maxval").val(a.prefs.max_value)}a.vertical_range=a.prefs.max_value-a.prefs.min_value;a.total_frequency=data.total_frequency;$("#linetrack_"+b+"_minval").remove();$("#linetrack_"+b+"_maxval").remove();var e=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_minval").text(a.prefs.min_value);var d=$("<div></div>").addClass("yaxislabel").attr("id","linetrack_"+b+"_maxval").text(a.prefs.max_value);d.css({position:"relative",top:"25px",left:"10px"});d.prependTo(a.container_div);e.css({position:"relative",top:a.height_px+55+"px",left:"10px"});e.prependTo(a.container_div)})},get_data:function(d,b){var c=this,a=b*DENSITY*d,f=(b+1)*DENSITY*d,e=d+"_"+b;if(!c.data_queue[e]){c.data_queue[e]=! true;$.ajax({url:data_url,dataType:"json",data:{chrom:this.view.chrom,low:a,high:f,dataset_id:this.dataset_id,resolution:this.view.resolution},success:function(g){data=g.data;c.data_cache.set(e,data);delete c.data_queue[e];c.draw()},error:function(h,g,i){console.log(h,g,i)}})}},draw_tile:function(p,r,c,e){if(this.vertical_range===undefined){return}var s=r*DENSITY*p,a=DENSITY*p,b=$("<canvas class='tile'></canvas>"),v=p+"_"+r;if(this.data_cache.get(v)===undefined){this.get_data(p,r);return}var j=this.data_cache.get(v);if(j===null){return}b.css({position:"absolute",top:0,left:(s-this.view.low)*e});b.get(0).width=Math.ceil(a*e);b.get(0).height=this.height_px;var o=b.get(0).getContext("2d"),k=false,l=this.prefs.min_value,g=this.prefs.max_value,n=this.vertical_range,t=this.total_frequency,d=this.height_px,m=this.prefs.mode;o.beginPath();if(data.length>1){var f=Math.ceil((data[1][0]-data[0][0])*e)}else{var f=10}var u,h;for(var q=0;q<data.length;q++){u=(data[q][0]-s)*e;h=data[q][1]! ;if(m=="Intensity"){if(h===null){continue}if(h<=l){h=l}else{if(h>=g){h =g}}h=255-Math.floor((h-l)/n*255);o.fillStyle="rgb("+h+","+h+","+h+")";o.fillRect(u,0,f,this.height_px)}else{if(h===null){if(k&&m==="Filled"){o.lineTo(u,d)}k=false;continue}else{if(h<=l){h=l}else{if(h>=g){h=g}}h=Math.round(d-(h-l)/n*d);if(k){o.lineTo(u,h)}else{k=true;if(m==="Filled"){o.moveTo(u,d);o.lineTo(u,h)}else{o.moveTo(u,h)}}}}}if(m==="Filled"){if(k){o.lineTo(u,d)}o.fill()}else{o.stroke()}c.append(b);return b},gen_options:function(n){var a=$("<div></div>").addClass("form-row");var h="track_"+n+"_minval",k="track_"+n+"_maxval",e="track_"+n+"_mode",l=$("<label></label>").attr("for",h).text("Min value:"),b=(this.prefs.min_value===undefined?"":this.prefs.min_value),m=$("<input></input>").attr("id",h).val(b),g=$("<label></label>").attr("for",k).text("Max value:"),j=(this.prefs.max_value===undefined?"":this.prefs.max_value),f=$("<input></input>").attr("id",k).val(j),d=$("<label></label>").attr("for",e).text("Display mode:"),i=(this.prefs.mode===undefined?"Line":this.prefs.mo! de),c=$('<select id="'+e+'"><option value="Line" id="mode_Line">Line</option><option value="Filled" id="mode_Filled">Filled</option><option value="Intensity" id="mode_Intensity">Intensity</option></select>');c.children("#mode_"+i).attr("selected","selected");return a.append(l).append(m).append(g).append(f).append(d).append(c)},update_options:function(d){var a=$("#track_"+d+"_minval").val(),c=$("#track_"+d+"_maxval").val(),b=$("#track_"+d+"_mode option:selected").val();if(a!==this.prefs.min_value||c!==this.prefs.max_value||b!=this.prefs.mode){this.prefs.min_value=parseFloat(a);this.prefs.max_value=parseFloat(c);this.prefs.mode=b;this.vertical_range=this.prefs.max_value-this.prefs.min_value;$("#linetrack_"+d+"_minval").text(this.prefs.min_value);$("#linetrack_"+d+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.draw()}}});var FeatureTrack=function(c,a,b){this.track_type="FeatureTrack";Track.call(this,c,$("#viewport"));TiledTrack.call(this);this.height_px=100! ;this.container_div.addClass("feature-track");this.dataset_id=a;this.z o_slots={};this.show_labels_scale=0.001;this.showing_details=false;this.vertical_detail_px=10;this.vertical_nodetail_px=3;this.default_font="9px Monaco, Lucida Console, monospace";this.left_offset=200;this.inc_slots={};this.data_queue={};this.s_e_by_tile={};this.tile_cache=new Cache(CACHED_TILES_FEATURE);this.data_cache=new Cache(20);this.prefs={block_color:"black",label_color:"black",show_counts:false};if(b.block_color!==undefined){this.prefs.block_color=b.block_color}if(b.label_color!==undefined){this.prefs.label_color=b.label_color}if(b.show_counts!==undefined){this.prefs.show_counts=b.show_counts}};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{init:function(){var a=this,b=a.view.max_low+"_"+a.view.max_high;this.init_each({low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom,resolution:this.view.resolution},function(c){a.data_cache.set(b,c);a.draw()})},get_data:function(a,d){var b=this,c=a+"_"+d;if(!b.data_queue[c]){b.data_queue[c]=tr! ue;$.getJSON(data_url,{chrom:b.view.chrom,low:a,high:d,dataset_id:b.dataset_id,resolution:this.view.resolution},function(e){b.data_cache.set(c,e);delete b.data_queue[c];b.draw()})}},incremental_slots:function(a,g,c){if(!this.inc_slots[a]){this.inc_slots[a]={};this.inc_slots[a].w_scale=1/a;this.s_e_by_tile[a]={}}var m=this.inc_slots[a].w_scale,v=[],h=0,b=$("<canvas></canvas>").get(0).getContext("2d"),n=this.view.max_low;var d,f,x=[];for(var s=0,t=g.length;s<t;s++){var e=g[s],l=e[0];if(this.inc_slots[a][l]!==undefined){h=Math.max(h,this.inc_slots[a][l]);x.push(this.inc_slots[a][l])}else{v.push(s)}}for(var s=0,t=v.length;s<t;s++){var e=g[v[s]];l=e[0],feature_start=e[1],feature_end=e[2],feature_name=e[3];d=Math.floor((feature_start-n)*m);f=Math.ceil((feature_end-n)*m);if(!c){var p=b.measureText(feature_name).width;if(d-p<0){f+=p}else{d-=p}}var r=0;while(true){var o=true;if(this.s_e_by_tile[a][r]!==undefined){for(var q=0,w=this.s_e_by_tile[a][r].length;q<w;q++){var u=this.s_e_by! _tile[a][r][q];if(f>u[0]&&d<u[1]){o=false;break}}}if(o){if(this.s_e_by _tile[a][r]===undefined){this.s_e_by_tile[a][r]=[]}this.s_e_by_tile[a][r].push([d,f]);this.inc_slots[a][l]=r;h=Math.max(h,r);break}r++}}return h},rect_or_text:function(n,o,g,f,m,b,d,k,e,i){n.textAlign="center";var j=Math.round(o/2);if(d!==undefined&&o>g){n.fillStyle="#555";n.fillRect(k,i+1,e,9);n.fillStyle="#eee";for(var h=0,l=d.length;h<l;h++){if(b+h>=f&&b+h<=m){var a=Math.floor(Math.max(0,(b+h-f)*o));n.fillText(d[h],a+this.left_offset+j,i+9)}}}else{n.fillStyle="#555";n.fillRect(k,i+4,e,3)}},draw_tile:function(W,h,m,ak){var D=h*DENSITY*W,ac=(h+1)*DENSITY*W,C=DENSITY*W;var aj,r;var ad=D+"_"+ac;var w=this.data_cache.get(ad);if(w===undefined){this.data_queue[[D,ac]]=true;this.get_data(D,ac);return}if(w.dataset_type==="summary_tree"){r=30}else{var U=(w.extra_info==="no_detail");var al=(U?this.vertical_nodetail_px:this.vertical_detail_px);r=this.incremental_slots(this.view.zoom_res,w.data,U)*al+15;m.parent().css("height",Math.max(this.height_px,r)+"px");aj=this.inc_slots[this.vi! ew.zoom_res]}var a=Math.ceil(C*ak),K=$("<canvas class='tile'></canvas>"),Y=this.prefs.label_color,f=this.prefs.block_color,O=this.left_offset;K.css({position:"absolute",top:0,left:(D-this.view.low)*ak-O});K.get(0).width=a+O;K.get(0).height=r;var z=K.get(0).getContext("2d"),ah=z.measureText("A").width;z.fillStyle=this.prefs.block_color;z.font=this.default_font;z.textAlign="right";if(w.dataset_type=="summary_tree"){var J,G=55,ab=255-G,g=ab*2/3,Q=w.data,B=w.max,l=w.avg;if(Q.length>2){var b=Math.ceil((Q[1][0]-Q[0][0])*ak)}else{var b=50}for(var af=0,v=Q.length;af<v;af++){var S=Math.ceil((Q[af][0]-D)*ak);var R=Q[af][1];if(!R){continue}J=Math.floor(ab-(R/B)*ab);z.fillStyle="rgb("+J+","+J+","+J+")";z.fillRect(S+O,0,b,20);if(this.prefs.show_counts){if(J>g){z.fillStyle="black"}else{z.fillStyle="#ddd"}z.textAlign="center";z.fillText(Q[af][1],S+O+(b/2),12)}}m.append(K);return K}var ai=w.data;var ae=0;for(var af=0,v=ai.length;af<v;af++){var L=ai[af],I=L[0],ag=L[1],T=L[2],E=L[3];if(ag<=a! c&&T>=D){var V=Math.floor(Math.max(0,(ag-D)*ak)),A=Math.ceil(Math.min( a,Math.max(0,(T-D)*ak))),P=aj[I]*al;if(w.dataset_type==="bai"){z.fillStyle="#555";if(L[4] instanceof Array){var s=Math.floor(Math.max(0,(L[4][0]-D)*ak)),H=Math.ceil(Math.min(a,Math.max(0,(L[4][1]-D)*ak))),q=Math.floor(Math.max(0,(L[5][0]-D)*ak)),o=Math.ceil(Math.min(a,Math.max(0,(L[5][1]-D)*ak)));if(L[4][1]>=D&&L[4][0]<=ac){this.rect_or_text(z,ak,ah,D,ac,L[4][0],L[4][2],s+O,H-s,P)}if(L[5][1]>=D&&L[5][0]<=ac){this.rect_or_text(z,ak,ah,D,ac,L[5][0],L[5][2],q+O,o-q,P)}if(q>H){z.fillStyle="#999";z.fillRect(H+O,P+5,q-H,1)}}else{z.fillStyle="#555";this.rect_or_text(z,ak,ah,D,ac,ag,E,V+O,A-V,P)}if(!U&&ag>D){z.fillStyle=this.prefs.label_color;if(h===0&&V-z.measureText(E).width<0){z.textAlign="left";z.fillText(I,A+2+O,P+8)}else{z.textAlign="right";z.fillText(I,V-2+O,P+8)}z.fillStyle="#555"}}else{if(w.dataset_type==="interval_index"){if(U){z.fillRect(V+O,P+5,A-V,1)}else{var u=L[4],N=L[5],X=L[6],e=L[7];var t,Z,F=null,am=null;if(N&&X){F=Math.floor(Math.max(0,(N-D)*ak));am=Math.ceil(Math! .min(a,Math.max(0,(X-D)*ak)))}if(E!==undefined&&ag>D){z.fillStyle=Y;if(h===0&&V-z.measureText(E).width<0){z.textAlign="left";z.fillText(E,A+2+O,P+8)}else{z.textAlign="right";z.fillText(E,V-2+O,P+8)}z.fillStyle=f}if(e){if(u){if(u=="+"){z.fillStyle=RIGHT_STRAND}else{if(u=="-"){z.fillStyle=LEFT_STRAND}}z.fillRect(V+O,P,A-V,10);z.fillStyle=f}for(var ad=0,d=e.length;ad<d;ad++){var n=e[ad],c=Math.floor(Math.max(0,(n[0]-D)*ak)),M=Math.ceil(Math.min(a,Math.max((n[1]-D)*ak)));if(c>M){continue}t=5;Z=3;z.fillRect(c+O,P+Z,M-c,t);if(F!==undefined&&!(c>am||M<F)){t=9;Z=1;var aa=Math.max(c,F),p=Math.min(M,am);z.fillRect(aa+O,P+Z,p-aa,t)}}}else{t=9;Z=1;z.fillRect(V+O,P+Z,A-V,t);if(L.strand){if(L.strand=="+"){z.fillStyle=RIGHT_STRAND_INV}else{if(L.strand=="-"){z.fillStyle=LEFT_STRAND_INV}}z.fillRect(V+O,P,A-V,10);z.fillStyle=prefs.block_color}}}}}ae++}}m.append(K);return K},gen_options:function(i){var a=$("<div></div>").addClass("form-row");var e="track_"+i+"_block_color",k=$("<label></label! >").attr("for",e).text("Block color:"),l=$("<input></input>").attr("id ",e).attr("name",e).val(this.prefs.block_color),j="track_"+i+"_label_color",g=$("<label></label>").attr("for",j).text("Text color:"),h=$("<input></input>").attr("id",j).attr("name",j).val(this.prefs.label_color),f="track_"+i+"_show_count",c=$("<label></label>").attr("for",f).text("Show summary counts"),b=$('<input type="checkbox" style="float:left;"></input>').attr("id",f).attr("name",f).attr("checked",this.prefs.show_counts),d=$("<div></div>").append(b).append(c);return a.append(k).append(l).append(g).append(h).append(d)},update_options:function(d){var b=$("#track_"+d+"_block_color").val(),c=$("#track_"+d+"_label_color").val(),a=$("#track_"+d+"_show_count").attr("checked");if(b!==this.prefs.block_color||c!==this.prefs.label_color||a!=this.prefs.show_counts){this.prefs.block_color=b;this.prefs.label_color=c;this.prefs.show_counts=a;this.tile_cache.clear();this.draw()}}});var ReadTrack=function(c,a,b){FeatureTrack.call(this,c,a,b);this.track_type="ReadTrack";this.vertical_det! ail_px=10;this.vertical_nodetail_px=5};$.extend(ReadTrack.prototype,TiledTrack.prototype,FeatureTrack.prototype,{}); \ No newline at end of file diff -r e7d91d58f4ad -r 370777a0693f static/scripts/trackster.js --- a/static/scripts/trackster.js Thu May 06 12:11:47 2010 -0400 +++ b/static/scripts/trackster.js Thu May 06 12:30:54 2010 -0400 @@ -5,7 +5,7 @@ var DENSITY = 200, FEATURE_LEVELS = 10, - DATA_ERROR = "There was an error in indexing this dataset.", + DATA_ERROR = "There was an error in indexing this dataset. ", DATA_NOCONVERTER = "A converter for this dataset is not installed. Please check your datatypes_conf.xml file.", DATA_NONE = "No data for this chrom/contig.", DATA_PENDING = "Currently indexing... please wait", @@ -118,17 +118,15 @@ }, remove_track: function( track ) { track.container_div.fadeOut('slow', function() { $(this).remove(); }); - delete this.tracks[track]; + delete this.tracks.splice(this.tracks.indexOf(track)); }, update_options: function() { var sorted = $("ul#sortable-ul").sortable('toArray'); - var payload = []; + for (var id_i in sorted) { + var id = sorted[id_i].split("_li")[0].split("track_")[1]; + $("#viewport").append( $("#track_" + id) ); + } - var divs = $("#viewport > div").sort(function (a, b) { - return sorted.indexOf( $(a).attr('id') ) > sorted.indexOf( $(b).attr('id') ); - }); - $("#viewport > div").remove(); - $("#viewport").html(divs); for (var track_id in view.tracks) { var track = view.tracks[track_id]; if (track.update_options) { @@ -234,13 +232,22 @@ if (track.view.chrom) { $.getJSON( data_url, params, function (result) { - if (!result || result === "error") { + if (!result || result === "error" || result.kind === "error") { track.container_div.addClass("error"); track.content_div.text(DATA_ERROR); + if (result.message) { + var track_id = track.view.tracks.indexOf(track); + var error_link = $("<a href='javascript:void(0);'></a>").attr("id", track_id + "_error"); + error_link.text("Click to view error"); + $("#" + track_id + "_error").live("click", function() { + show_modal( "Trackster Error", "<pre>" + result.message + "</pre>", { "Close" : hide_modal } ); + }); + track.content_div.append(error_link); + } } else if (result === "no converter") { track.container_div.addClass("error"); track.content_div.text(DATA_NOCONVERTER); - } else if (result.data && result.data.length === 0 || result.data === null) { + } else if (result.data !== undefined && (result.data === null || result.data.length === 0)) { track.container_div.addClass("nodata"); track.content_div.text(DATA_NONE); } else if (result === "pending") { @@ -441,7 +448,6 @@ var result = this.data_cache.get(key); if (result === null) { return; } - console.log(result); canvas.css( { position: "absolute", diff -r e7d91d58f4ad -r 370777a0693f templates/tracks/browser.mako --- a/templates/tracks/browser.mako Thu May 06 12:11:47 2010 -0400 +++ b/templates/tracks/browser.mako Thu May 06 12:30:54 2010 -0400 @@ -272,7 +272,6 @@ $.ajax({ url: "${h.url_for( action='chroms' )}", - ## If vis is new, it doesn't have an id, so send the dbkey instead. %if config.get('vis_id'): data: { vis_id: view.vis_id }, %else: @@ -327,7 +326,7 @@ $("#track_" + track_id + "_editable").toggle(); }); del_icon.bind("click", function() { - $("#track_" + track_id + "_li").fadeOut('slow', function() { $("#track_" + track_id).remove(); }); + $("#track_" + track_id + "_li").fadeOut('slow', function() { $("#track_" + track_id + "_li").remove(); }); view.remove_track(track); view.update_options(); }); @@ -354,4 +353,3 @@ </script> </%def> - diff -r e7d91d58f4ad -r 370777a0693f templates/user/dbkeys.mako --- a/templates/user/dbkeys.mako Thu May 06 12:11:47 2010 -0400 +++ b/templates/user/dbkeys.mako Thu May 06 12:30:54 2010 -0400 @@ -41,23 +41,26 @@ <tr class="header"> <th>Name</th> <th>Key</th> - <th>Chroms/Lengths</th> + <th>Number of Chroms</th> <th></th> </tr> % for key, dct in dbkeys.iteritems(): <tr> - <td>${dct["name"] | h}</td> + <td>${dct['name'] | h}</td> <td>${key | h}</td> <td> - <span>${len(dct["chroms"])} entries</span> - <pre id="pre_${key}" class="db_hide"> - <table cellspacing="0" cellpadding="0"> - <tr><th>Chrom</th><th>Length</th></tr> - % for chrom, chrom_len in dct["chroms"].iteritems(): - <tr><td>${chrom | h}</td><td>${chrom_len | h}</td></tr> - % endfor - </table> - </pre> +## <span>${len(dct["chroms"])} entries</span> +## <pre id="pre_${key}" class="db_hide"> +## <table cellspacing="0" cellpadding="0"> +## <tr><th>Chrom</th><th>Length</th></tr> +## % for chrom, chrom_len in dct["chroms"].iteritems(): +## <tr><td>${chrom | h}</td><td>${chrom_len | h}</td></tr> +## % endfor +## </table> +## </pre> + % if 'count' in dct: + ${dct['count']} + % endif </td> <td><form action="dbkeys" method="post"><input type="hidden" name="key" value="${key}" /><input type="submit" name="delete" value="Delete" /></form></td> </tr> diff -r e7d91d58f4ad -r 370777a0693f tool_conf.xml.main --- a/tool_conf.xml.main Thu May 06 12:11:47 2010 -0400 +++ b/tool_conf.xml.main Thu May 06 12:30:54 2010 -0400 @@ -35,6 +35,7 @@ <tool file="filters/changeCase.xml" /> <tool file="filters/pasteWrapper.xml" /> <tool file="filters/remove_beginning.xml" /> + <tool file="filters/randomlines.xml" /> <tool file="filters/headWrapper.xml" /> <tool file="filters/tailWrapper.xml" /> <tool file="filters/trimmer.xml" />

1 0

[hg] galaxy 3749: Updated builds.txt (and manual_builds.txt) to ...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/e7d91d58f4ad changeset: 3749:e7d91d58f4ad user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Thu May 06 12:11:47 2010 -0400 description: Updated builds.txt (and manual_builds.txt) to newest version, corresponding to that on main. Includes hg19 and phiX correction. diffstat: tool-data/shared/ucsc/builds.txt | 291 +++++++++++++++++-------------- tool-data/shared/ucsc/manual_builds.txt | 2 +- 2 files changed, 160 insertions(+), 133 deletions(-) diffs (355 lines): diff -r 91bc27508c75 -r e7d91d58f4ad tool-data/shared/ucsc/builds.txt --- a/tool-data/shared/ucsc/builds.txt Thu May 06 10:58:23 2010 -0400 +++ b/tool-data/shared/ucsc/builds.txt Thu May 06 12:11:47 2010 -0400 @@ -1,133 +1,156 @@ #Harvested from http://genome-test.cse.ucsc.edu/cgi-bin/das/dsn ? unspecified (?) -hg18 Human Mar. 2006 (hg18) -hg17 Human May 2004 (hg17) -hg16 Human July 2003 (hg16) -hg15 Human Apr. 2003 (hg15) -hg13 Human Nov. 2002 (hg13) -venter1 J. Craig Venter Sep. 2007 (venter1) -panTro2 Chimp Mar. 2006 (panTro2) -panTro1 Chimp Nov. 2003 (panTro1) -ponAbe2 Orangutan July 2007 (ponAbe2) -rheMac2 Rhesus Jan. 2006 (rheMac2) -calJac1 Marmoset June 2007 (calJac1) -otoGar1 Bushbaby Dec. 2006 (otoGar1) -tupBel1 TreeShrew Dec. 2006 (tupBel1) -mm9 Mouse July 2007 (mm9) -mm8 Mouse Feb. 2006 (mm8) -mm7 Mouse Aug. 2005 (mm7) -mm6 Mouse Mar. 2005 (mm6) -mm5 Mouse May 2004 (mm5) -mm4 Mouse Oct. 2003 (mm4) -mm3 Mouse Feb. 2003 (mm3) -mm2 Mouse Feb. 2002 (mm2) -rn4 Rat Nov. 2004 (rn4) -rn3 Rat June 2003 (rn3) -rn2 Rat Jan. 2003 (rn2) -oryCun1 Rabbit May 2005 (oryCun1) -felCat3 Cat Mar. 2006 (felCat3) -canFam2 Dog May 2005 (canFam2) -canFam1 Dog July 2004 (canFam1) -equCab1 Horse Jan. 2007 (equCab1) -bosTau4 Cow Oct. 2007 (bosTau4) -bosTau3 Cow Aug. 2006 (bosTau3) -bosTau2 Cow Mar. 2005 (bosTau2) -bosTau1 Cow Sep. 2004 (bosTau1) -choHof1 Sloth Feb. 2008 (choHof1) -dasNov1 Armadillo May 2005 (dasNov1) -echTel1 Tenrec July 2005 (echTel1) -loxAfr1 Elephant May 2005 (loxAfr1) -monDom4 Opossum Jan. 2006 (monDom4) -monDom1 Opossum Oct. 2004 (monDom1) -ornAna1 Platypus Mar. 2007 (ornAna1) -galGal3 Chicken May 2006 (galGal3) -galGal2 Chicken Feb. 2004 (galGal2) -anoCar1 Lizard Feb. 2007 (anoCar1) -xenTro2 X. tropicalis Aug. 2005 (xenTro2) -xenTro1 X. tropicalis Oct. 2004 (xenTro1) -danRer5 Zebrafish July 2007 (danRer5) -danRer4 Zebrafish Mar. 2006 (danRer4) -danRer3 Zebrafish May 2005 (danRer3) -danRer2 Zebrafish June 2004 (danRer2) -danRer1 Zebrafish Nov. 2003 (danRer1) -tetNig1 Tetraodon Feb. 2004 (tetNig1) -fr2 Fugu Oct. 2004 (fr2) -fr1 Fugu Aug. 2002 (fr1) -gasAcu1 Stickleback Feb. 2006 (gasAcu1) -oryLat1 Medaka Apr. 2006 (oryLat1) -petMar1 Lamprey Mar. 2007 (petMar1) -borEut13 Boreoeutherian Apr. 24. 2006 (borEut13) -canHg12 Boreoeutherian Nov. 19. 2005 (canHg12) -rodEnt13 Rodent Apr. 24. 2006 (rodEnt13) -priMat13 Primate Apr. 24. 2006 (priMat13) -nonAfr13 Non-Afrotheria Apr. 24. 2006 (nonAfr13) -lauRas13 Laurasiatheria Apr. 24. 2006 (lauRas13) -homIni14 Hominidae Oct. 1. 2006 (homIni14) -homIni13 Hominidae Apr. 24. 2006 (homIni13) -gliRes13 Glires Apr. 24. 2006 (gliRes13) -eutHer13 Eutheria Apr. 24. 2006 (eutHer13) -euaGli13 Euarchontoglires Apr. 24. 2006 (euaGli13) -catArr1 Catarrhini June 13. 2006 (catArr1) -afrOth13 Afrotheria Apr. 24. 2006 (afrOth13) -braFlo1 Lancelet Mar. 2006 (braFlo1) -ci2 C. intestinalis Mar. 2005 (ci2) -ci1 C. intestinalis Dec. 2002 (ci1) -cioSav2 C. savignyi July 2005 (cioSav2) -cioSav1 C. savignyi Sept. 2001 (cioSav1) -strPur2 S. purpuratus Sep. 2006 (strPur2) -strPur1 S. purpuratus Apr. 2005 (strPur1) -ce4 C. elegans Jan. 2007 (ce4) -ce3 C. elegans March 2005 (ce3) -ce2 C. elegans Mar. 2004 (ce2) -ce1 C. elegans May 2003 (ce1) -caePb1 C. brenneri Jan. 2007 (caePb1) -cb3 C. briggsae Jan. 2007 (cb3) -cb2 C. briggsae Aug 2005 (cb2) -cb1 C. briggsae July 2002 (cb1) -caeRem2 C. remanei Mar. 2006 (caeRem2) -caeRem1 C. remanei March 2005 (caeRem1) -priPac1 P. pacificus Feb. 2007 (priPac1) -dm3 D. melanogaster Apr. 2006 (dm3) -dm2 D. melanogaster Apr. 2004 (dm2) -dm1 D. melanogaster Jan. 2003 (dm1) -droSim1 D. simulans Apr. 2005 (droSim1) -droSec1 D. sechellia Oct. 2005 (droSec1) -droYak2 D. yakuba Nov. 2005 (droYak2) -droYak1 D. yakuba Apr. 2004 (droYak1) -droEre1 D. erecta Aug. 2005 (droEre1) -droAna2 D. ananassae Aug. 2005 (droAna2) -droAna1 D. ananassae July 2004 (droAna1) -dp3 D. pseudoobscura Nov. 2004 (dp3) -dp2 D. pseudoobscura Aug. 2003 (dp2) -droPer1 D. persimilis Oct. 2005 (droPer1) -droVir2 D. virilis Aug. 2005 (droVir2) -droVir1 D. virilis July 2004 (droVir1) -droMoj2 D. mojavensis Aug. 2005 (droMoj2) -droMoj1 D. mojavensis Aug. 2004 (droMoj1) -droGri1 D. grimshawi Aug. 2005 (droGri1) -anoGam1 A. gambiae Feb. 2003 (anoGam1) -apiMel2 A. mellifera Jan. 2005 (apiMel2) -apiMel1 A. mellifera July 2004 (apiMel1) -triCas2 T. castaneum Sep. 2005 (triCas2) -falciparum P. falciparum Plasmodium falciparum (falciparum) -sacCer1 S. cerevisiae Oct. 2003 (sacCer1) -sc1 SARS coronavirus Apr. 2003 (sc1) -campJeju1 Campylobacter jejuni 02/25/2000 (campJeju1) -campJeju_RM1221_1 Campylobacter jejuni RM1221 01/07/2005 (campJeju_RM1221_1) -eschColi_CFT073_1 Escherichia coli CFT073 12/10/2002 (eschColi_CFT073_1) -eschColi_K12_1 Escherichia coli K12 09/05/1997 (eschColi_K12_1) -eschColi_O157H7_1 Escherichia coli O157H7 03/29/2000 (eschColi_O157H7_1) -eschColi_O157H7EDL933_1 Escherichia coli O157H7 EDL933 02/24/2001 (eschColi_O157H7EDL933_1) -vibrChol1 Vibrio cholerae O1 El Tor 08/22/2000 (vibrChol1) -vibrChol_MO10_1 Vibrio cholerae MO10 09/17/2005 (vibrChol_MO10_1) -vibrChol_O395_1 Vibrio cholerae O395 09/17/2005 (vibrChol_O395_1) -vibrFisc_ES114_1 Vibrio fischeri ES114 02/11/2005 (vibrFisc_ES114_1) -vibrPara1 Vibrio parahaemolyticus 06/02/2000 (vibrPara1) -vibrVuln_CMCP6_1 Vibrio vulnificus CMCP6 09/23/2003 (vibrVuln_CMCP6_1) -vibrVuln_YJ016_1 Vibrio vulnificus YJ016 12/06/2003 (vibrVuln_YJ016_1) -heliHepa1 Helicobacter hepaticus 06/18/2003 (heliHepa1) -heliPylo_26695_1 Helicobacter pylori 26695 08/07/1997 (heliPylo_26695_1) -heliPylo_J99_1 Helicobacter pylori J99 01/29/1999 (heliPylo_J99_1) +hg19Haps hg19Haplotypes Feb. 2009 (GRCh37/hg19Haps) (hg19Haps) +hg19 Human Feb. 2009 (GRCh37/hg19) (hg19) +hg18 Human Mar. 2006 (NCBI36/hg18) (hg18) +hg17 Human May 2004 (NCBI35/hg17) (hg17) +hg16 Human July 2003 (NCBI34/hg16) (hg16) +hg15 Human Apr. 2003 (NCBI33/hg15) (hg15) +venter1 J. Craig Venter Sep. 2007 (HuRef/venter1) (venter1) +panTro2 Chimp Mar. 2006 (CGSC 2.1/panTro2) (panTro2) +panTro1 Chimp Nov. 2003 (CGSC 1.1/panTro1) (panTro1) +gorGor2 Gorilla Aug. 2009 (Sanger 4/gorGor2) (gorGor2) +gorGor1 Gorilla Oct. 2008 (Sanger 0.1/gorGor1) (gorGor1) +ponAbe2 Orangutan July 2007 (WUGSC 2.0.2/ponAbe2) (ponAbe2) +rheMac2 Rhesus Jan. 2006 (MGSC Merged 1.0/rheMac2) (rheMac2) +papHam1 Baboon Nov. 2008 (Baylor 1.0/papHam1) (papHam1) +calJac3 Marmoset March 2009 (WUGSC 3.2/calJac3) (calJac3) +calJac1 Marmoset June 2007 (WUGSC 2.0.2/calJac1) (calJac1) +otoGar1 Bushbaby Dec. 2006 (Broad/otoGar1) (otoGar1) +micMur1 Mouse lemur Jun. 2003 (Broad/micMur1) (micMur1) +tupBel1 Tree shrew Dec. 2006 (Broad/tupBel1) (tupBel1) +mmtv MMTV Nov. 2009 (MMTV/mmtv) (mmtv) +homPan20 chimp/human Jun. 2008 (UCSC Recon/homPan20) (homPan20) +homIni20 orang/human Jun. 2008 (UCSC Recon/homIni20) (homIni20) +sorAra1 Shrew June 2006 (Broad/sorAra1) (sorAra1) +mm9 Mouse July 2007 (NCBI37/mm9) (mm9) +mm8 Mouse Feb. 2006 (NCBI36/mm8) (mm8) +mm7 Mouse Aug. 2005 (NCBI35/mm7) (mm7) +rn4 Rat Nov. 2004 (Baylor 3.4/rn4) (rn4) +rn3 Rat June 2003 (Baylor 3.1/rn3) (rn3) +speTri1 Squirrel Feb. 2008 (Broad/speTri1) (speTri1) +cavPor3 Guinea pig Feb. 2008 (Broad/cavPor3) (cavPor3) +oryCun2 Rabbit Apr. 2009 (Broad/oryCun2) (oryCun2) +oryCun1 Rabbit May 2005 (Broad/oryCun1) (oryCun1) +ochPri2 Pika Jul. 2008 (Broad/ochPri2) (ochPri2) +eriEur1 Hedgehog June 2006 (Broad/eriEur1) (eriEur1) +felCatV17e Cat Dec. 2008 (NHGRI/GTB V17e/felCatV17e) (felCatV17e) +felCat3 Cat Mar. 2006 (Broad/felCat3) (felCat3) +ailMel1 Panda Dec. 2009 (BGI-Shenzhen 1.0/ailMel1) (ailMel1) +nemVec1 Starlet sea anemone Jun. 2007 (JGI-PDF/nemVec1) (nemVec1) +canFam2 Dog May 2005 (Broad/canFam2) (canFam2) +canFam1 Dog July 2004 (Broad/canFam1) (canFam1) +canFamPoodle1 Dog May 2003 (TIGR Poodle/canFamPoodle1) (canFamPoodle1) +equCab2 Horse Sep. 2007 (Broad/equCab2) (equCab2) +equCab1 Horse Jan. 2007 (Broad/equCab1) (equCab1) +susScr2 Pig Nov. 2009 (SGSC Sscrofa9.2/susScr2) (susScr2) +pteVam1 Megabat Jul. 2008 (Broad/pteVam1) (pteVam1) +myoLuc1 Microbat Mar. 2006 (Broad/myoLuc1) (myoLuc1) +susScr1 Pig Apr. 2009 (SGSC 9.53/susScr1) (susScr1) +turTru1 Dolphin Feb. 2008 (Broad/turTru1) (turTru1) +tarSyr1 Tarsier Aug. 2008 (Broad/tarSyr1) (tarSyr1) +proCap1 Rock hyrax Jul. 2008 (Broad/proCap1) (proCap1) +oviAri1 Sheep Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1) (oviAri1) +dipOrd1 Kangaroo rat Jul. 2008 (Broad/dipOrd1) (dipOrd1) +choHof1 Sloth Jul. 2008 (Broad/choHof1) (choHof1) +bosTau4 Cow Oct. 2007 (Baylor 4.0/bosTau4) (bosTau4) +bosTau3 Cow Aug. 2006 (Baylor 3.1/bosTau3) (bosTau3) +bosTau2 Cow Mar. 2005 (Baylor 2.0/bosTau2) (bosTau2) +macEug1 Wallaby Nov. 2007 (Baylor 1.0/macEug1) (macEug1) +dasNov2 Armadillo Jul. 2008 (Broad/dasNov2) (dasNov2) +dasNov1 Armadillo May 2005 (Broad/dasNov1) (dasNov1) +echTel1 Tenrec July 2005 (Broad/echTel1) (echTel1) +loxAfr3 Elephant Jul. 2009 (Broad/loxAfr3) (loxAfr3) +loxAfr2 Elephant Jul. 2008 (Broad/loxAfr2) (loxAfr2) +loxAfr1 Elephant May 2005 (Broad/loxAfr1) (loxAfr1) +monDom5 Opossum Oct. 2006 (Broad/monDom5) (monDom5) +monDom4 Opossum Jan. 2006 (Broad/monDom4) (monDom4) +monDom1 Opossum Oct. 2004 (Broad prelim/monDom1) (monDom1) +ornAna1 Platypus Mar. 2007 (WUGSC 5.0.1/ornAna1) (ornAna1) +galGal3 Chicken May 2006 (WUGSC 2.1/galGal3) (galGal3) +galGal2 Chicken Feb. 2004 (WUGSC 1.0/galGal2) (galGal2) +taeGut1 Zebra finch Jul. 2008 (WUGSC 3.2.4/taeGut1) (taeGut1) +anoCar1 Lizard Feb. 2007 (Broad/anoCar1) (anoCar1) +xenTro2 X. tropicalis Aug. 2005 (JGI 4.1/xenTro2) (xenTro2) +xenTro1 X. tropicalis Oct. 2004 (JGI 3.0/xenTro1) (xenTro1) +danRer6 Zebrafish Dec. 2008 (Zv8/danRer6) (danRer6) +danRer5 Zebrafish July 2007 (Zv7/danRer5) (danRer5) +danRer4 Zebrafish Mar. 2006 (Zv6/danRer4) (danRer4) +danRer3 Zebrafish May 2005 (Zv5/danRer3) (danRer3) +tetNig2 Tetraodon Mar. 2007 (Genoscope 8.0/tetNig2) (tetNig2) +tetNig1 Tetraodon Feb. 2004 (Genoscope 7/tetNig1) (tetNig1) +fr2 Fugu Oct. 2004 (JGI 4.0/fr2) (fr2) +fr1 Fugu Aug. 2002 (JGI 3.0/fr1) (fr1) +gasAcu1 Stickleback Feb. 2006 (Broad/gasAcu1) (gasAcu1) +oryLat2 Medaka Oct. 2005 (NIG/UT MEDAKA1/oryLat2) (oryLat2) +oryLat1 Medaka Apr. 2006 (NIG/UT MEDAKA1/oryLat1) (oryLat1) +petMar1 Lamprey Mar. 2007 (WUGSC 3.0/petMar1) (petMar1) +borEut13 Boreoeutherian Apr. 24. 2006 (UCSC Recon/borEut13) (borEut13) +canHg12 Boreoeutherian Nov. 19. 2005 (UCSC Recon/canHg12) (canHg12) +rodEnt13 Rodent Apr. 24. 2006 (UCSC Recon/rodEnt13) (rodEnt13) +priMat13 Primate Apr. 24. 2006 (UCSC Recon/priMat13) (priMat13) +nonAfr13 Non-Afrotheria Apr. 24. 2006 (UCSC Recon/nonAfr13) (nonAfr13) +lauRas13 Laurasiatheria Apr. 24. 2006 (UCSC Recon/lauRas13) (lauRas13) +homIni14 Hominidae Oct. 1. 2006 (UCSC Recon/homIni14) (homIni14) +homIni13 Hominidae Apr. 24. 2006 (UCSC Recon/homIni13) (homIni13) +gliRes13 Glires Apr. 24. 2006 (UCSC Recon/gliRes13) (gliRes13) +eutHer13 Eutheria Apr. 24. 2006 (UCSC Recon/eutHer13) (eutHer13) +euaGli13 Euarchontoglires Apr. 24. 2006 (UCSC Recon/euaGli13) (euaGli13) +catArr1 Catarrhini June 13. 2006 (UCSC Recon/catArr1) (catArr1) +afrOth13 Afrotheria Apr. 24. 2006 (UCSC Recon/afrOth13) (afrOth13) +braFlo1 Lancelet Mar. 2006 (JGI 1.0/braFlo1) (braFlo1) +ci2 C. intestinalis Mar. 2005 (JGI 2.1/ci2) (ci2) +ci1 C. intestinalis Dec. 2002 (JGI 1.0/ci1) (ci1) +cioSav2 C. savignyi July 2005 (Sidow Lab 2.0/cioSav2) (cioSav2) +cioSav1 C. savignyi Apr. 2003 (Broad/cioSav1) (cioSav1) +strPur2 S. purpuratus Sep. 2006 (Baylor 2.1/strPur2) (strPur2) +strPur1 S. purpuratus Apr. 2005 (Baylor 1.1/strPur1) (strPur1) +ce8 C. elegans Jun 2009 (WS204/ce8) (ce8) +ce7 C. elegans Feb 2009 (WS200/ce7) (ce7) +aplCal1 Sea hare Sept. 2008 (Broad 2.0/aplCal1) (aplCal1) +ce6 C. elegans May 2008 (WS190/ce6) (ce6) +ce5 C. elegans Aug. 2007 (WS180/ce5) (ce5) +ce4 C. elegans Jan. 2007 (WS170/ce4) (ce4) +ce3 C. elegans March 2005 (WS140/ce3) (ce3) +ce2 C. elegans Mar. 2004 (WS120/ce2) (ce2) +caePb2 C. brenneri Feb. 2008 (WUGSC 6.0.1/caePb2) (caePb2) +caePb1 C. brenneri Jan. 2007 (WUGSC 4.0/caePb1) (caePb1) +cb3 C. briggsae Jan. 2007 (WUGSC 1.0/cb3) (cb3) +cb2 C. briggsae Aug 2005 (WUGSC prelim/cb2) (cb2) +cb1 C. briggsae July 2002 (WormBase cb25.agp8/cb1) (cb1) +caeRem3 C. remanei May 2007 (WUGSC 15.0.1/caeRem3) (caeRem3) +caeRem2 C. remanei Mar. 2006 (WUGSC 1.0/caeRem2) (caeRem2) +caeRem1 C. remanei March 2005 (WUGSC prelim/caeRem1) (caeRem1) +caeJap2 C. japonica Jan. 2009 (WUGSC 4.0.1/caeJap2) (caeJap2) +caeJap1 C. japonica Mar. 2008 (WUGSC 3.0.2/caeJap1) (caeJap1) +priPac1 P. pacificus Feb. 2007 (WUGSC 5.0/priPac1) (priPac1) +dm3 D. melanogaster Apr. 2006 (BDGP R5/dm3) (dm3) +dm2 D. melanogaster Apr. 2004 (BDGP R4/dm2) (dm2) +dm1 D. melanogaster Jan. 2003 (BDGP R3/dm1) (dm1) +droSim1 D. simulans Apr. 2005 (WUGSC mosaic 1.0/droSim1) (droSim1) +droSec1 D. sechellia Oct. 2005 (Broad/droSec1) (droSec1) +droYak2 D. yakuba Nov. 2005 (WUGSC 7.1/droYak2) (droYak2) +droYak1 D. yakuba Apr. 2004 (WUGSC 1.0/droYak1) (droYak1) +droEre1 D. erecta Aug. 2005 (Agencourt prelim/droEre1) (droEre1) +droAna2 D. ananassae Aug. 2005 (Agencourt prelim/droAna2) (droAna2) +droAna1 D. ananassae July 2004 (TIGR/droAna1) (droAna1) +dp3 D. pseudoobscura Nov. 2004 (FlyBase 1.03/dp3) (dp3) +dp2 D. pseudoobscura Aug. 2003 (Baylor freeze1/dp2) (dp2) +droPer1 D. persimilis Oct. 2005 (Broad/droPer1) (droPer1) +droVir2 D. virilis Aug. 2005 (Agencourt prelim/droVir2) (droVir2) +droVir1 D. virilis July 2004 (Agencourt prelim/droVir1) (droVir1) +droMoj2 D. mojavensis Aug. 2005 (Agencourt prelim/droMoj2) (droMoj2) +droMoj1 D. mojavensis Aug. 2004 (Agencourt prelim/droMoj1) (droMoj1) +droGri1 D. grimshawi Aug. 2005 (Agencourt prelim/droGri1) (droGri1) +anoGam1 A. gambiae Feb. 2003 (IAGEC MOZ2/anoGam1) (anoGam1) +apiMel2 A. mellifera Jan. 2005 (Baylor 2.0/apiMel2) (apiMel2) +apiMel1 A. mellifera July 2004 (Baylor 1.2/apiMel1) (apiMel1) +triCas2 T. castaneum Sep. 2005 (Baylor 2.0/triCas2) (triCas2) +falciparum P. falciparum Plasmodium falciparum (?/falciparum) (falciparum) +sacCer2 S. cerevisiae June 2008 (SGD/sacCer2) (sacCer2) +sacCer1 S. cerevisiae Oct. 2003 (SGD/sacCer1) (sacCer1) +sc1 SARS coronavirus Apr. 2003 (GenBank Apr. 14 '03/sc1) (sc1) +phiX phiX174 (phiX) 16079 Mycobacterium sp. JLS (16079) symbTher_IAM14863 Symbiobacterium thermophilum IAM 14863 (symbTher_IAM14863) 16070 Yersinia pseudotuberculosis IP 31758 (16070) @@ -356,6 +379,7 @@ 16062 Leuconostoc citreum KM20 (16062) 16148 Leptospira borgpetersenii serovar Hardjo-bovis JB197 (16148) 16146 Leptospira borgpetersenii serovar Hardjo-bovis L550 (16146) +vibrVuln_CMCP6_1 Vibrio vulnificus CMCP6 (vibrVuln_CMCP6_1) 10877 Bacillus thuringiensis serovar konkukian str. 97-27 (10877) 19517 Clostridium botulinum A str. ATCC 19397 (19517) nitrWino_NB_255 Nitrobacter winogradskyi Nb-255 (nitrWino_NB_255) @@ -500,6 +524,7 @@ 28507 Clostridium botulinum A3 str. Loch Maree (28507) colwPsyc_34H Colwellia psychrerythraea 34H (colwPsyc_34H) hyphNept_ATCC15444 Hyphomonas neptunium ATCC 15444 (hyphNept_ATCC15444) +vibrChol1 Vibrio cholerae O1 biovar eltor str. N16961 (vibrChol1) deinGeot_DSM11300 Deinococcus geothermalis DSM 11300 (deinGeot_DSM11300) 312 Buchnera aphidicola str. Sg (Schizaphis graminum) (312) 311 Streptococcus pyogenes MGAS315 (311) @@ -536,6 +561,7 @@ 12720 Enterobacter sakazakii ATCC BAA-894 (12720) therMari Thermotoga maritima MSB8 (therMari) mycoGeni Mycoplasma genitalium G37 (mycoGeni) +vibrFisc_ES114_1 Vibrio fischeri ES114 (vibrFisc_ES114_1) pyroIsla1 Pyrobaculum islandicum DSM 4184 (pyroIsla1) 17407 Burkholderia multivorans ATCC 17616 (17407) 13030 Salmonella enterica subsp. arizonae serovar 62:z4,z23:-- (13030) @@ -544,6 +570,7 @@ 19857 Vibrio harveyi ATCC BAA-1116 (19857) 17639 Parvibaculum lavamentivorans DS-1 (17639) 18059 Mycobacterium bovis BCG str. Pasteur 1173P2 (18059) +vibrPara1 Vibrio parahaemolyticus RIMD 2210633 (vibrPara1) 259 Escherichia coli O157:H7 EDL933 (259) 64 Staphylococcus epidermidis RP62A (64) neisGono_FA1090_1 Neisseria gonorrhoeae FA 1090 (neisGono_FA1090_1) @@ -598,6 +625,7 @@ vermEise_EF01_2 Verminephrobacter eiseniae EF01-2 (vermEise_EF01_2) granBeth_CGDNIH1 Granulibacter bethesdensis CGDNIH1 (granBeth_CGDNIH1) alcaBork_SK2 Alcanivorax borkumensis SK2 (alcaBork_SK2) +vibrChol_O395_1 Vibrio cholerae O395 (vibrChol_O395_1) nitrOcea_ATCC19707 Nitrosococcus oceani ATCC 19707 (nitrOcea_ATCC19707) campJeju_RM1221 Campylobacter jejuni RM1221 (campJeju_RM1221) 12468 Bacillus cereus E33L (12468) @@ -723,6 +751,7 @@ 12637 Clostridium beijerinckii NCIMB 8052 (12637) ehrlRumi_WELGEVONDEN Ehrlichia ruminantium str. Welgevonden (ehrlRumi_WELGEVONDEN) methLabrZ_1 Methanocorpusculum labreanum Z (methLabrZ_1) +vibrVuln_YJ016_1 Vibrio vulnificus YJ016 (vibrVuln_YJ016_1) 13773 Streptococcus thermophilus LMD-9 (13773) 20039 Leptothrix cholodnii SP-6 (20039) shewAmaz Shewanella amazonensis SB2B (shewAmaz) @@ -786,7 +815,5 @@ aeroHydr_ATCC7966 Aeromonas hydrophila subsp. hydrophila ATCC 7966 (aeroHydr_ATCC7966) baciAnth_AMES Bacillus anthracis str. Ames (baciAnth_AMES) shewOnei Shewanella oneidensis MR-1 (shewOnei) -equCab2 Horse Sep. 2007 (equCab2) -arabidopsis Arabidopsis thaliana TAIR9 -arabidopsis_tair8 Arabidopsis thaliana TAIR8 -araTha1 Arabidopsis thaliana TAIR7 +15217 Human herpesvirus 1 (15217) +lMaj5 Leishmania major 2005 (lMaj5) diff -r 91bc27508c75 -r e7d91d58f4ad tool-data/shared/ucsc/manual_builds.txt --- a/tool-data/shared/ucsc/manual_builds.txt Thu May 06 10:58:23 2010 -0400 +++ b/tool-data/shared/ucsc/manual_builds.txt Thu May 06 12:11:47 2010 -0400 @@ -1,4 +1,4 @@ -phix phiX174 phix=5386 +phiX phiX174 phiX=5386 16079 Mycobacterium sp. JLS NC_009077=6048425 symbTher_IAM14863 Symbiobacterium thermophilum IAM 14863 chr=3566135 16070 Yersinia pseudotuberculosis IP 31758 NC_009708=4723306,NC_009705=153140,NC_009704=58679

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[hg] galaxy 3748: Update documentation in cufftools wrappers.
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/91bc27508c75 changeset: 3748:91bc27508c75 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Thu May 06 10:58:23 2010 -0400 description: Update documentation in cufftools wrappers. diffstat: tools/ngs_rna/cuffcompare_wrapper.xml | 2 +- tools/ngs_rna/cuffdiff_wrapper.xml | 26 +++++++++++++++++++------- tools/ngs_rna/cufflinks_wrapper.xml | 2 +- 3 files changed, 21 insertions(+), 9 deletions(-) diffs (76 lines): diff -r e72342f71adc -r 91bc27508c75 tools/ngs_rna/cuffcompare_wrapper.xml --- a/tools/ngs_rna/cuffcompare_wrapper.xml Thu May 06 10:43:13 2010 -0400 +++ b/tools/ngs_rna/cuffcompare_wrapper.xml Thu May 06 10:58:23 2010 -0400 @@ -93,7 +93,7 @@ <help> **Cuffcompare Overview** -Cuffcompare is part of Cufflinks_. Cuffcompare helps you: (a) compare your assembled transcripts to a reference annotation and (b) track Cufflinks transcripts across multiple experiments (e.g. across a time course). Please cite: Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L. Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. (manuscript in press) +Cuffcompare is part of Cufflinks_. Cuffcompare helps you: (a) compare your assembled transcripts to a reference annotation and (b) track Cufflinks transcripts across multiple experiments (e.g. across a time course). Please cite: Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L. Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. Nature Biotechnology doi:10.1038/nbt.1621 .. _Cufflinks: http://cufflinks.cbcb.umd.edu/ diff -r e72342f71adc -r 91bc27508c75 tools/ngs_rna/cuffdiff_wrapper.xml --- a/tools/ngs_rna/cuffdiff_wrapper.xml Thu May 06 10:43:13 2010 -0400 +++ b/tools/ngs_rna/cuffdiff_wrapper.xml Thu May 06 10:58:23 2010 -0400 @@ -48,13 +48,13 @@ <data format="tabular" name="genes_exp" label="${tool.name} on ${on_string}: gene expression"/> <data format="tabular" name="tss_groups_exp" label="${tool.name} on ${on_string}: TSS groups expression"/> <data format="tabular" name="cds_exp_fpkm_tracking" label="${tool.name} on ${on_string}: CDS Expression FPKM Tracking"/> - <data format="tabular" name="splicing_diff" label="${tool.name} on ${on_string}: splicing diff"/> - <data format="tabular" name="cds_diff" label="${tool.name} on ${on_string}: CDS diff"/> - <data format="tabular" name="promoters_diff" label="${tool.name} on ${on_string}: promoters diff"/> + <data format="tabular" name="isoforms_fpkm_tracking" label="${tool.name} on ${on_string}: isoform FPKM tracking"/> + <data format="tabular" name="genes_fpkm_tracking" label="${tool.name} on ${on_string}: gene FPKM tracking"/> <data format="tabular" name="tss_groups_fpkm_tracking" label="${tool.name} on ${on_string}: TSS groups FPKM tracking" /> <data format="tabular" name="cds_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM tracking"/> - <data format="tabular" name="genes_fpkm_tracking" label="${tool.name} on ${on_string}: gene FPKM tracking"/> - <data format="tabular" name="isoforms_fpkm_tracking" label="${tool.name} on ${on_string}: isoform FPKM tracking"/> + <data format="tabular" name="splicing_diff" label="${tool.name} on ${on_string}: splicing diff"/> + <data format="tabular" name="promoters_diff" label="${tool.name} on ${on_string}: promoters diff"/> + <data format="tabular" name="cds_diff" label="${tool.name} on ${on_string}: CDS diff"/> </outputs> <tests> @@ -65,7 +65,7 @@ <help> **Cuffdiff Overview** -Cuffdiff is part of Cufflinks_. Cuffdiff find significant changes in transcript expression, splicing, and promoter use. Please cite: Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L. Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. (manuscript in press) +Cuffdiff is part of Cufflinks_. Cuffdiff find significant changes in transcript expression, splicing, and promoter use. Please cite: Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L. Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. Nature Biotechnology doi:10.1038/nbt.1621 .. _Cufflinks: http://cufflinks.cbcb.umd.edu/ @@ -91,7 +91,19 @@ **Outputs** -TODO +Cuffdiff produces many output files: + +1. Transcript FPKM expression tracking. +2. Gene FPKM expression tracking; tracks the summed FPKM of transcripts sharing each gene_id +3. Primary transcript FPKM tracking; tracks the summed FPKM of transcripts sharing each tss_id +4. Coding sequence FPKM tracking; tracks the summed FPKM of transcripts sharing each p_id, indepedent of tss_id +5. Transcript differential FPKM. +6. Gene differential FPKM. Tests difference sin the summed FPKM of transcripts sharing each gene_id +7. Primary transcript differential FPKM. Tests difference sin the summed FPKM of transcripts sharing each tss_id +8. Coding sequence differential FPKM. Tests difference sin the summed FPKM of transcripts sharing each p_id independent of tss_id +9. Differential splicing tests: this tab delimited file lists, for each primary transcript, the amount of overloading detected among its isoforms, i.e. how much differential splicing exists between isoforms processed from a single primary transcript. Only primary transcripts from which two or more isoforms are spliced are listed in this file. +10. Differential promoter tests: this tab delimited file lists, for each gene, the amount of overloading detected among its primary transcripts, i.e. how much differential promoter use exists between samples. Only genes producing two or more distinct primary transcripts (i.e. multi-promoter genes) are listed here. +11. Differential CDS tests: this tab delimited file lists, for each gene, the amount of overloading detected among its coding sequences, i.e. how much differential CDS output exists between samples. Only genes producing two or more distinct CDS (i.e. multi-protein genes) are listed here. ------- diff -r e72342f71adc -r 91bc27508c75 tools/ngs_rna/cufflinks_wrapper.xml --- a/tools/ngs_rna/cufflinks_wrapper.xml Thu May 06 10:43:13 2010 -0400 +++ b/tools/ngs_rna/cufflinks_wrapper.xml Thu May 06 10:58:23 2010 -0400 @@ -77,7 +77,7 @@ <help> **Cufflinks Overview** -Cufflinks_ assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one. Please cite: Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L. Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. (manuscript in press) +Cufflinks_ assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one. Please cite: Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L. Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. Nature Biotechnology doi:10.1038/nbt.1621 .. _Cufflinks: http://cufflinks.cbcb.umd.edu/

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[hg] galaxy 3747: lims: workflow selectbox in the samples page f...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/e72342f71adc changeset: 3747:e72342f71adc user: rc date: Thu May 06 10:43:13 2010 -0400 description: lims: workflow selectbox in the samples page fixed diffstat: lib/galaxy/web/controllers/requests_admin.py | 34 ++++++++++++++-------------- templates/admin/requests/show_request.mako | 11 +++++++- templates/requests/show_request.mako | 11 +++++++- 3 files changed, 35 insertions(+), 21 deletions(-) diffs (100 lines): diff -r e3d164679f80 -r e72342f71adc lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py Thu May 06 10:08:57 2010 -0400 +++ b/lib/galaxy/web/controllers/requests_admin.py Thu May 06 10:43:13 2010 -0400 @@ -1773,23 +1773,23 @@ message=message, status=status) -# def __sample_datasets(self, trans, **kwd): -# samples = trans.sa_session.query( trans.app.model.Sample ).all() -# for s in samples: -# if s.dataset_files: -# newdf = [] -# for df in s.dataset_files: -# if type(s.dataset_files[0]) == type([1,2]): -# filepath = df[0] -# status = df[1] -# newdf.append(dict(filepath=filepath, -# status=status, -# name=filepath.split('/')[-1], -# error_msg='', -# size='Unknown')) -# s.dataset_files = newdf -# trans.sa_session.add( s ) -# trans.sa_session.flush() + def __sample_datasets(self, trans, **kwd): + samples = trans.sa_session.query( trans.app.model.Sample ).all() + for s in samples: + if s.dataset_files: + newdf = [] + for df in s.dataset_files: + if type(s.dataset_files[0]) == type([1,2]): + filepath = df[0] + status = df[1] + newdf.append(dict(filepath=filepath, + status=status, + name=filepath.split('/')[-1], + error_msg='', + size='Unknown')) + s.dataset_files = newdf + trans.sa_session.add( s ) + trans.sa_session.flush() # ## #### Request Type Stuff ################################################### diff -r e3d164679f80 -r e72342f71adc templates/admin/requests/show_request.mako --- a/templates/admin/requests/show_request.mako Thu May 06 10:08:57 2010 -0400 +++ b/templates/admin/requests/show_request.mako Thu May 06 10:43:13 2010 -0400 @@ -292,6 +292,11 @@ </select> %elif field['type'] == 'WorkflowField': <select name="sample_${index}_field_${field_index}"> + %if str(sample_values[field_index]) == 'none': + <option value="none" selected>Select one</option> + %else: + <option value="none">Select one</option> + %endif %for option_index, option in enumerate(request.user.stored_workflows): %if not option.deleted: %if str(option.id) == str(sample_values[field_index]): @@ -320,8 +325,10 @@ <td> %if sample_values[field_index]: %if field['type'] == 'WorkflowField': - <% workflow = trans.sa_session.query( trans.app.model.StoredWorkflow ).get( int(sample_values[field_index]) ) %> - <a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id(workflow.id) )}">${workflow.name}</a> + %if str(sample_values[field_index]) != 'none': + <% workflow = trans.sa_session.query( trans.app.model.StoredWorkflow ).get( int(sample_values[field_index]) ) %> + <a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id(workflow.id) )}">${workflow.name}</a> + %endif %else: ${sample_values[field_index]} %endif diff -r e3d164679f80 -r e72342f71adc templates/requests/show_request.mako --- a/templates/requests/show_request.mako Thu May 06 10:08:57 2010 -0400 +++ b/templates/requests/show_request.mako Thu May 06 10:43:13 2010 -0400 @@ -214,6 +214,11 @@ </select> %elif field['type'] == 'WorkflowField': <select name="sample_${index}_field_${field_index}"> + %if str(sample_values[field_index]) == 'none': + <option value="none" selected>Select one</option> + %else: + <option value="none">Select one</option> + %endif %for option_index, option in enumerate(request.user.stored_workflows): %if not option.deleted: %if str(option.id) == str(sample_values[field_index]): @@ -242,8 +247,10 @@ <td> %if sample_values[field_index]: %if field['type'] == 'WorkflowField': - <% workflow = trans.sa_session.query( trans.app.model.StoredWorkflow ).get( int(sample_values[field_index]) ) %> - <a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id(workflow.id) )}">${workflow.name}</a> + %if str(sample_values[field_index]) != 'none': + <% workflow = trans.sa_session.query( trans.app.model.StoredWorkflow ).get( int(sample_values[field_index]) ) %> + <a href="${h.url_for( controller='workflow', action='run', id=trans.security.encode_id(workflow.id) )}">${workflow.name}</a> + %endif %else: ${sample_values[field_index]} %endif

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[hg] galaxy 3746: Fix for downloading a library dataset from the...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/e3d164679f80 changeset: 3746:e3d164679f80 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Thu May 06 10:08:57 2010 -0400 description: Fix for downloading a library dataset from the library dataset's info page. diffstat: templates/library/common/ldda_info.mako | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (12 lines): diff -r ab83e2ef8a99 -r e3d164679f80 templates/library/common/ldda_info.mako --- a/templates/library/common/ldda_info.mako Wed May 05 11:34:29 2010 -0400 +++ b/templates/library/common/ldda_info.mako Thu May 06 10:08:57 2010 -0400 @@ -58,7 +58,7 @@ %endif %if cntrller=='library' and ldda.has_data: <a class="action-button" href="${h.url_for( controller='library_common', action='act_on_multiple_datasets', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), ldda_ids=trans.security.encode_id( ldda.id ), do_action='import_to_history', use_panels=use_panels, show_deleted=show_deleted )}">Import this dataset into your current history</a> - <a class="action-button" href="${h.url_for( controller='library', action='download_dataset_from_folder', cntrller=cntrller, id=trans.security.encode_id( ldda.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Download this dataset</a> + <a class="action-button" href="${h.url_for( controller='library_common', action='download_dataset_from_folder', cntrller=cntrller, id=trans.security.encode_id( ldda.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Download this dataset</a> %endif </div> %endif

1 0

[hg] galaxy 3745: Enhanced column join to allow user to specify ...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/ab83e2ef8a99 changeset: 3745:ab83e2ef8a99 user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Wed May 05 11:34:29 2010 -0400 description: Enhanced column join to allow user to specify fill values for empty columns, either one value for all or by column diffstat: test-data/column_join_out1.pileup | 120 +++++++++++++++--------------- test-data/column_join_out2.pileup | 80 ++++++++++---------- test-data/column_join_out3.pileup | 140 +++++++++++++++++----------------- tools/new_operations/column_join.py | 120 +++++++++++++++++++++++------ tools/new_operations/column_join.xml | 86 ++++++++++++++++++--- 5 files changed, 337 insertions(+), 209 deletions(-) diffs (667 lines): diff -r 5f59c890ee8d -r ab83e2ef8a99 test-data/column_join_out1.pileup --- a/test-data/column_join_out1.pileup Tue May 04 22:27:05 2010 -0400 +++ b/test-data/column_join_out1.pileup Wed May 05 11:34:29 2010 -0400 @@ -1,60 +1,60 @@ -chr1 1 T T 87 25 G G 25 25 -chr1 2 A T 87 25 T T 25 25 -chr1 3 A G 87 25 T T 27 25 -chr1 4 A T 55 25 A A 36 25 -chr1 5 C A 54 25 A A 36 25 -chr1 6 G T 87 25 T T 36 25 -chr1 7 A C 87 25 G G 42 25 -chr1 8 G A 87 25 T T 45 25 -chr1 9 A T 87 25 A A 51 25 -chr1 10 G A 57 25 G G 54 25 -chr1 11 C A 57 25 C C 57 25 -chr1 12 T A 99 25 T T 60 25 -chr1 13 A C 99 25 T T 78 25 -chr1 14 G C 55 25 A A 56 25 -chr1 15 T G 68 25 A A 87 25 -chr4 1 T T 90 25 -chr4 2 A A 87 25 -chr4 3 A A 34 25 -chr4 4 T T 55 25 -chr4 5 A A 54 25 -chr4 6 T T 87 25 -chr4 7 A A 80 25 -chr4 8 A A 87 25 -chr4 9 A A 87 25 -chr4 10 G G 57 25 -chr4 11 C C 57 25 -chr4 12 A A 99 25 -chr4 13 A A 99 25 -chr4 14 G G 55 25 -chr4 15 G G 68 25 -chrM 1 A G 25 25 T G 25 25 -chrM 2 C T 25 25 C A 25 25 -chrM 3 T G 27 25 C A 25 25 -chrM 4 G C 36 25 G A 36 25 -chrM 5 T A 38 25 A T 36 25 -chrM 6 T A 39 25 A G 36 25 -chrM 7 G C 43 25 C G 42 25 -chrM 8 A C 46 25 T T 45 25 -chrM 9 T G 53 25 C A 51 25 -chrM 10 T G 56 25 G G 54 25 -chrM 11 C G 57 25 T C 57 25 -chrM 12 T C 61 25 A T 60 25 -chrM 13 T G 79 25 A T 78 25 -chrM 14 A C 58 25 G A 56 25 -chrM 15 G A 87 25 G A 87 25 -chrM 16 G C 88 25 -chrM 17 A C 88 25 -chrM 18 G A 89 25 -chrM 19 G T 58 25 -chrM 20 T C 55 25 -chrM 21 C T 87 25 -chrM 22 C A 87 25 -chrM 23 A G 87 25 -chrM 24 A T 89 25 -chrM 25 G A 57 25 -chrM 26 C G 58 25 -chrM 27 T A 99 25 -chrM 28 A C 99 25 -chrM 29 G C 58 25 -chrM 30 T T 65 25 +chr1 1 ? ? ? ? T T 87 25 G G 25 25 +chr1 2 ? ? ? ? A T 87 25 T T 25 25 +chr1 3 ? ? ? ? A G 87 25 T T 27 25 +chr1 4 ? ? ? ? A T 55 25 A A 36 25 +chr1 5 ? ? ? ? C A 54 25 A A 36 25 +chr1 6 ? ? ? ? G T 87 25 T T 36 25 +chr1 7 ? ? ? ? A C 87 25 G G 42 25 +chr1 8 ? ? ? ? G A 87 25 T T 45 25 +chr1 9 ? ? ? ? A T 87 25 A A 51 25 +chr1 10 ? ? ? ? G A 57 25 G G 54 25 +chr1 11 ? ? ? ? C A 57 25 C C 57 25 +chr1 12 ? ? ? ? T A 99 25 T T 60 25 +chr1 13 ? ? ? ? A C 99 25 T T 78 25 +chr1 14 ? ? ? ? G C 55 25 A A 56 25 +chr1 15 ? ? ? ? T G 68 25 A A 87 25 +chr4 1 ? ? ? ? ? ? ? ? T T 90 25 +chr4 2 ? ? ? ? ? ? ? ? A A 87 25 +chr4 3 ? ? ? ? ? ? ? ? A A 34 25 +chr4 4 ? ? ? ? ? ? ? ? T T 55 25 +chr4 5 ? ? ? ? ? ? ? ? A A 54 25 +chr4 6 ? ? ? ? ? ? ? ? T T 87 25 +chr4 7 ? ? ? ? ? ? ? ? A A 80 25 +chr4 8 ? ? ? ? ? ? ? ? A A 87 25 +chr4 9 ? ? ? ? ? ? ? ? A A 87 25 +chr4 10 ? ? ? ? ? ? ? ? G G 57 25 +chr4 11 ? ? ? ? ? ? ? ? C C 57 25 +chr4 12 ? ? ? ? ? ? ? ? A A 99 25 +chr4 13 ? ? ? ? ? ? ? ? A A 99 25 +chr4 14 ? ? ? ? ? ? ? ? G G 55 25 +chr4 15 ? ? ? ? ? ? ? ? G G 68 25 +chrM 1 A G 25 25 T G 25 25 ? ? ? ? +chrM 2 C T 25 25 C A 25 25 ? ? ? ? +chrM 3 T G 27 25 C A 25 25 ? ? ? ? +chrM 4 G C 36 25 G A 36 25 ? ? ? ? +chrM 5 T A 38 25 A T 36 25 ? ? ? ? +chrM 6 T A 39 25 A G 36 25 ? ? ? ? +chrM 7 G C 43 25 C G 42 25 ? ? ? ? +chrM 8 A C 46 25 T T 45 25 ? ? ? ? +chrM 9 T G 53 25 C A 51 25 ? ? ? ? +chrM 10 T G 56 25 G G 54 25 ? ? ? ? +chrM 11 C G 57 25 T C 57 25 ? ? ? ? +chrM 12 T C 61 25 A T 60 25 ? ? ? ? +chrM 13 T G 79 25 A T 78 25 ? ? ? ? +chrM 14 A C 58 25 G A 56 25 ? ? ? ? +chrM 15 G A 87 25 G A 87 25 ? ? ? ? +chrM 16 G C 88 25 ? ? ? ? ? ? ? ? +chrM 17 A C 88 25 ? ? ? ? ? ? ? ? +chrM 18 G A 89 25 ? ? ? ? ? ? ? ? +chrM 19 G T 58 25 ? ? ? ? ? ? ? ? +chrM 20 T C 55 25 ? ? ? ? ? ? ? ? +chrM 21 C T 87 25 ? ? ? ? ? ? ? ? +chrM 22 C A 87 25 ? ? ? ? ? ? ? ? +chrM 23 A G 87 25 ? ? ? ? ? ? ? ? +chrM 24 A T 89 25 ? ? ? ? ? ? ? ? +chrM 25 G A 57 25 ? ? ? ? ? ? ? ? +chrM 26 C G 58 25 ? ? ? ? ? ? ? ? +chrM 27 T A 99 25 ? ? ? ? ? ? ? ? +chrM 28 A C 99 25 ? ? ? ? ? ? ? ? +chrM 29 G C 58 25 ? ? ? ? ? ? ? ? +chrM 30 T T 65 25 ? ? ? ? ? ? ? ? diff -r 5f59c890ee8d -r ab83e2ef8a99 test-data/column_join_out2.pileup --- a/test-data/column_join_out2.pileup Tue May 04 22:27:05 2010 -0400 +++ b/test-data/column_join_out2.pileup Wed May 05 11:34:29 2010 -0400 @@ -1,15 +1,15 @@ -chr1 1 C 1 -chr1 2 G 2 -chr1 3 A 2 -chr1 4 C 2 -chr1 5 T 3 -chr1 6 G 3 -chr1 7 C 4 -chr1 8 A 4 -chr1 9 T 5 -chr1 10 G 5 -chr1 11 A 5 -chr1 12 C 5 +chr1 1 C 1 +chr1 2 G 2 +chr1 3 A 2 +chr1 4 C 2 +chr1 5 T 3 +chr1 6 G 3 +chr1 7 C 4 +chr1 8 A 4 +chr1 9 T 5 +chr1 10 G 5 +chr1 11 A 5 +chr1 12 C 5 chr1 42 T 1 C 1 chr1 43 G 2 C 2 chr1 44 T 2 T 2 @@ -20,21 +20,21 @@ chr1 49 C 5 G 5 chr1 50 A 5 A 5 chr1 51 A 5 G 5 -chr1 52 A 5 -chr1 53 G 5 -chr2 1 T 6 -chr2 2 G 6 -chr2 3 C 7 -chr2 4 G 7 -chr2 5 G 7 -chr2 6 A 7 -chr2 7 T 8 -chr2 8 A 8 -chr2 9 C 9 -chr2 10 T 9 -chr2 11 C 10 -chr2 12 G 10 -chr2 13 A 11 +chr1 52 A 5 +chr1 53 G 5 +chr2 1 T 6 +chr2 2 G 6 +chr2 3 C 7 +chr2 4 G 7 +chr2 5 G 7 +chr2 6 A 7 +chr2 7 T 8 +chr2 8 A 8 +chr2 9 C 9 +chr2 10 T 9 +chr2 11 C 10 +chr2 12 G 10 +chr2 13 A 11 chr2 52 T 5 chr2 53 A 5 chr2 54 T 5 @@ -43,19 +43,19 @@ chr2 57 T 5 chr2 58 T 6 chr2 59 A 6 -chr2 77 C 6 -chr2 78 G 6 -chr2 79 T 7 -chr2 80 C 7 -chr2 81 G 7 -chr2 82 A 8 -chr2 83 A 8 -chr2 84 T 8 -chr2 85 G 8 -chr2 86 C 9 -chr2 87 G 9 -chr2 88 G 10 -chr2 89 G 10 +chr2 77 C 6 +chr2 78 G 6 +chr2 79 T 7 +chr2 80 C 7 +chr2 81 G 7 +chr2 82 A 8 +chr2 83 A 8 +chr2 84 T 8 +chr2 85 G 8 +chr2 86 C 9 +chr2 87 G 9 +chr2 88 G 10 +chr2 89 G 10 chr3 60 C 6 chr3 61 T 6 chr3 62 C 6 diff -r 5f59c890ee8d -r ab83e2ef8a99 test-data/column_join_out3.pileup --- a/test-data/column_join_out3.pileup Tue May 04 22:27:05 2010 -0400 +++ b/test-data/column_join_out3.pileup Wed May 05 11:34:29 2010 -0400 @@ -1,70 +1,70 @@ -chr1 1 C 1 ^:. -chr1 2 G 2 .^:. -chr1 3 A 2 .. -chr1 4 C 2 .. -chr1 5 T 3 ..^:. -chr1 6 G 3 ..^:, -chr1 7 C 4 .N., -chr1 8 A 4 ..., -chr1 9 T 5 ..C., -chr1 10 G 5 N..., -chr1 11 A 5 .C.., -chr1 12 C 5 ..N., -chr1 42 T 1 ^:. C 1 ^:. -chr1 43 G 2 .^:. C 2 .^:. -chr1 44 T 2 .. T 2 .. -chr1 45 C 3 ..^:. A 3 ..^:. -chr1 46 G 3 ..^:. G 4 ...^:. -chr1 47 T 4 ...^:, A 5 ....^:, -chr1 48 A 4 .N., T 5 ...N, -chr1 49 C 5 ...., G 5 ...., -chr1 50 A 5 ..G., A 5 .G.., -chr1 51 A 5 A..., G 5 ...., -chr1 52 A 5 ...., -chr1 53 G 5 ..N., -chr2 1 T 6 .C..., -chr2 2 G 6 ..N.., -chr2 3 C 7 ..C..., -chr2 4 G 7 .G...., -chr2 5 G 7 ...N.., -chr2 6 A 7 ..T..., -chr2 7 T 8 ...C..., -chr2 8 A 8 ..A...., -chr2 9 C 9 .GA..N.., -chr2 10 T 9 ........, -chr2 11 C 10 .>>..T..., -chr2 12 G 10 .N..G...., -chr2 13 A 11 ....A..T.., -chr2 14 G 11 ..N....... -chr2 15 C 11 A.....NG.. -chr2 16 T 11 ...C.....G -chr2 17 C 12 G......TN.. -chr2 18 A 12 N......G..A -chr2 19 A 13 .......NN... -chr2 20 C 13 ..GT.......N -chr2 52 T 5 .N.., -chr2 53 A 5 ...., -chr2 54 T 5 ...., -chr2 55 T 5 ...., -chr2 56 C 5 ...., -chr2 57 T 5 ...., -chr2 58 T 6 .N..., -chr2 59 A 6 ....., -chr2 77 C 6 .G..., -chr2 78 G 6 ..N.., -chr2 79 T 7 ..N..., -chr2 80 C 7 .G...., -chr2 81 G 7 ...A.., -chr2 82 A 8 ...G..., -chr2 83 A 8 ...T..., -chr2 84 T 8 ..A...., -chr2 85 G 8 .GA...., -chr2 86 C 9 ........, -chr2 87 G 9 ....T..., -chr3 60 C 6 ...G., -chr3 61 T 6 ..N.., -chr3 62 C 6 ...A., -chr3 63 C 7 .N...., -chr3 64 A 7 ...G.., -chr3 65 T 7 ...AA., -chr3 66 A 7 ....N., +chr1 1 C 1 ^:. X X +chr1 2 G 2 .^:. X X +chr1 3 A 2 .. X X +chr1 4 C 2 .. X X +chr1 5 T 3 ..^:. X X +chr1 6 G 3 ..^:, X X +chr1 7 C 4 .N., X X +chr1 8 A 4 ..., X X +chr1 9 T 5 ..C., X X +chr1 10 G 5 N..., X X +chr1 11 A 5 .C.., X X +chr1 12 C 5 ..N., X X +chr1 42 X T 1 ^:. C 1 ^:. +chr1 43 X G 2 .^:. C 2 .^:. +chr1 44 X T 2 .. T 2 .. +chr1 45 X C 3 ..^:. A 3 ..^:. +chr1 46 X G 3 ..^:. G 4 ...^:. +chr1 47 X T 4 ...^:, A 5 ....^:, +chr1 48 X A 4 .N., T 5 ...N, +chr1 49 X C 5 ...., G 5 ...., +chr1 50 X A 5 ..G., A 5 .G.., +chr1 51 X A 5 A..., G 5 ...., +chr1 52 X A 5 ...., X +chr1 53 X G 5 ..N., X +chr2 1 T 6 .C..., X X +chr2 2 G 6 ..N.., X X +chr2 3 C 7 ..C..., X X +chr2 4 G 7 .G...., X X +chr2 5 G 7 ...N.., X X +chr2 6 A 7 ..T..., X X +chr2 7 T 8 ...C..., X X +chr2 8 A 8 ..A...., X X +chr2 9 C 9 .GA..N.., X X +chr2 10 T 9 ........, X X +chr2 11 C 10 .>>..T..., X X +chr2 12 G 10 .N..G...., X X +chr2 13 A 11 ....A..T.., X X +chr2 14 G 11 ..N....... X X +chr2 15 C 11 A.....NG.. X X +chr2 16 T 11 ...C.....G X X +chr2 17 C 12 G......TN.. X X +chr2 18 A 12 N......G..A X X +chr2 19 A 13 .......NN... X X +chr2 20 C 13 ..GT.......N X X +chr2 52 X X T 5 .N.., +chr2 53 X X A 5 ...., +chr2 54 X X T 5 ...., +chr2 55 X X T 5 ...., +chr2 56 X X C 5 ...., +chr2 57 X X T 5 ...., +chr2 58 X X T 6 .N..., +chr2 59 X X A 6 ....., +chr2 77 X C 6 .G..., X +chr2 78 X G 6 ..N.., X +chr2 79 X T 7 ..N..., X +chr2 80 X C 7 .G...., X +chr2 81 X G 7 ...A.., X +chr2 82 X A 8 ...G..., X +chr2 83 X A 8 ...T..., X +chr2 84 X T 8 ..A...., X +chr2 85 X G 8 .GA...., X +chr2 86 X C 9 ........, X +chr2 87 X G 9 ....T..., X +chr3 60 X X C 6 ...G., +chr3 61 X X T 6 ..N.., +chr3 62 X X C 6 ...A., +chr3 63 X X C 7 .N...., +chr3 64 X X A 7 ...G.., +chr3 65 X X T 7 ...AA., +chr3 66 X X A 7 ....N., diff -r 5f59c890ee8d -r ab83e2ef8a99 tools/new_operations/column_join.py --- a/tools/new_operations/column_join.py Tue May 04 22:27:05 2010 -0400 +++ b/tools/new_operations/column_join.py Wed May 05 11:34:29 2010 -0400 @@ -13,7 +13,19 @@ """ -import os, re, sys, tempfile +import optparse, os, re, struct, sys, tempfile + +try: + simple_json_exception = None + from galaxy import eggs + from galaxy.util.bunch import Bunch + from galaxy.util import stringify_dictionary_keys + import pkg_resources + pkg_resources.require("simplejson") + import simplejson +except Exception, e: + simplejson_exception = e + simplejson = None def stop_err( msg ): sys.stderr.write( msg ) @@ -136,17 +148,50 @@ return '%s\t%s' % tuple( min_ref_pos ), min_loc def __main__(): - output = sys.argv[1] - input1 = sys.argv[2] - input2 = sys.argv[3] - hinge = int( sys.argv[4] ) - cols = [ int( c ) for c in sys.argv[5].split( ',' ) ] - inputs = sys.argv[6:] - assert len( cols ) > 2, 'You need to select at least one column in addition to the first two' + parser = optparse.OptionParser() + parser.add_option( '', '--output', dest='output', help='' ) + parser.add_option( '', '--input1', dest='input1', help='' ) + parser.add_option( '', '--input2', dest='input2', help='' ) + parser.add_option( '', '--hinge', dest='hinge', help='' ) + parser.add_option( '', '--columns', dest='columns', help='' ) + parser.add_option( '', '--fill_options_file', dest='fill_options_file', default=None, help='' ) + (options, args) = parser.parse_args() + output = options.output + input1 = options.input1 + input2 = options.input2 + hinge = int( options.hinge ) + cols = [ int( c ) for c in str( options.columns ).split( ',' ) if int( c ) > hinge ] + inputs = [ input1, input2 ] + if options.fill_options_file == "None": + inputs.extend( args ) + else: + try: + col = int( args[0] ) + except ValueError: + inputs.extend( args ) + fill_options = None + if options.fill_options_file != "None" and options.fill_options_file is not None: + try: + if simplejson is None: + raise simplejson_exception + fill_options = Bunch( **stringify_dictionary_keys( simplejson.load( open( options.fill_options_file ) ) ) ) + except Exception, e: + print "Warning: Ignoring fill options due to simplejson error (%s)." % e + if fill_options is None: + fill_options = Bunch() + if 'file1_columns' not in fill_options: + fill_options.file1_columns = None + if fill_options and fill_options.file1_columns: + fill_empty = {} + for col in cols: + fill_empty[ col ] = fill_options.file1_columns[ col - 1 ] + else: + fill_empty = None + assert len( cols ) > 0, 'You need to select at least one column in addition to the hinge' + delimiter = '\t' # make sure all files are sorted in same way, ascending tmp_input_files = [] - input_files = [ input1, input2 ] - input_files.extend( inputs ) + input_files = inputs[:] for in_file in input_files: tmp_file = tempfile.NamedTemporaryFile() tmp_file_name = tmp_file.name @@ -162,10 +207,9 @@ current_lines = [ f.readline() for f in tmp_input_files ] last_lines = ''.join( current_lines ).strip() last_loc = -1 - i = 0 while last_lines: # get the "minimum" hinge, which should come first, and the file location in list - hinges = [ '\t'.join( line.split( '\t' )[ :hinge ] ) for line in current_lines ] + hinges = [ delimiter.join( line.split( delimiter )[ :hinge ] ) for line in current_lines ] hinge_dict = {} for i in range( len( hinges ) ): if not hinge_dict.has_key( hinges[ i ] ): @@ -174,33 +218,59 @@ hinges = [ h for h in hinges if h ] current, loc = hinges[0], hinge_dict[ hinges[0] ] # first output empty columns for vertical alignment (account for "missing" files) + # write output if trailing empty columns + current_data = [] if current != old_current: - last_loc = -1 - if loc - last_loc > 1: - current_data = [ '' for col in range( ( loc - last_loc - 1 ) * len( [ col for col in cols if col > hinge ] ) ) ] + # fill trailing empty columns with appropriate fill value + if not first_line: + if last_loc < len( inputs ) - 1: + if not fill_empty: + filler = [ '' for col in range( ( len( inputs ) - last_loc - 1 ) * len( cols ) ) ] + else: + filler = [ fill_empty[ cols[ col % len( cols ) ] ] for col in range( ( len( inputs ) - last_loc - 1 ) * len( cols ) ) ] + fout.write( '%s%s' % ( delimiter, delimiter.join( filler ) ) ) + # insert line break before current line + fout.write( '\n' ) + # fill leading empty columns with appropriate fill value + if loc > 0: + if not fill_empty: + current_data = [ '' for col in range( loc * len( cols ) ) ] + else: + current_data = [ fill_empty[ cols[ col % len( cols ) ] ] for col in range( loc * len( cols ) ) ] else: - current_data = [] + if loc - last_loc > 1: + if not fill_empty: + current_data = [ '' for col in range( ( loc - last_loc - 1 ) * len( cols ) ) ] + else: + current_data = [ fill_empty[ cols[ col % len( cols ) ] ] for col in range( ( loc - last_loc - 1 ) * len( cols ) ) ] # now output actual data - split_line = current_lines[ loc ].strip().split( '\t' ) + split_line = current_lines[ loc ].strip().split( delimiter ) if ''.join( split_line ): + # add actual data to be output below for col in cols: if col > hinge: current_data.append( split_line[ col - 1 ] ) + # grab next line for selected file current_lines[ loc ] = tmp_input_files[ loc ].readline() + # write relevant data to file if current == old_current: - if current_data: - fout.write( '\t%s' % '\t'.join( current_data ) ) + fout.write( '%s%s' % ( delimiter, delimiter.join( current_data ) ) ) else: - if not first_line: - fout.write( '\n' ) - fout.write( '%s\t%s' % ( current, '\t'.join( current_data ) ) ) - first_line = False + fout.write( '%s%s%s' % ( current, delimiter, delimiter.join( current_data ) ) ) + last_loc = loc old_current = current last_lines = ''.join( current_lines ).strip() - last_loc = loc + first_line = False + # fill trailing empty columns for final line + if last_loc < len( inputs ) - 1: + if not fill_empty: + filler = [ '' for col in range( ( len( inputs ) - last_loc - 1 ) * len( cols ) ) ] + else: + filler = [ fill_empty[ cols[ col % len( cols ) ] ] for col in range( ( len( inputs ) - last_loc - 1 ) * len( cols ) ) ] + fout.write( '%s%s' % ( delimiter, delimiter.join( filler ) ) ) fout.write( '\n' ) + fout.close() for f in tmp_input_files: os.unlink( f.name ) - fout.close() if __name__ == "__main__" : __main__() diff -r 5f59c890ee8d -r ab83e2ef8a99 tools/new_operations/column_join.xml --- a/tools/new_operations/column_join.xml Tue May 04 22:27:05 2010 -0400 +++ b/tools/new_operations/column_join.xml Wed May 05 11:34:29 2010 -0400 @@ -2,53 +2,111 @@ <description></description> <command interpreter="python"> column_join.py - $output - $input1 - $input2 - $hinge - $columns + --output=$output + --input1=$input1 + --input2=$input2 + --hinge=$hinge + --columns=$columns + #if $fill_empty_columns.fill_empty_columns_switch == "fill_empty": + --fill_options_file=$fill_options_file + #end if #for $f in $file_chooser: ${f.input} #end for </command> <inputs> <param name="input1" type="data" format="tabular" label="Choose the first file for the join" /> + <param name="hinge" type="data_column" data_ref="input1" multiple="false" numerical="false" label="Use this column and columns to left the 'hinge' (matching data for each join)" help="All columns to left of selected column (plus selected column) will be used. Select 2 for pileup" /> <param name="columns" type="data_column" data_ref="input1" multiple="true" numerical="false" label="Include these column" help="Multi-select list - hold the appropriate key while clicking to select multiple columns" /> - <param name="hinge" type="data_column" data_ref="input1" multiple="false" numerical="false" label="Use this column and columns to left the 'hinge' (matching data for each join)" help="All columns to left of selected column (plus selected column) will be used. Select 2 for pileup" /> + <conditional name="fill_empty_columns"> + <param name="fill_empty_columns_switch" type="select" label="Fill empty columns"> + <option value="no_fill" selected="True">No</option> + <option value="fill_empty">Yes</option> + </param> + <when value="no_fill" /> + <when value="fill_empty"> + <conditional name="do_fill_empty_columns"> + <param name="column_fill_type" type="select" label="Fill Columns by"> + <option value="single_fill_value" selected="True">Single fill value</option> + <option value="fill_value_by_column">Values by column</option> + </param> + <when value="single_fill_value"> + <param type="text" name="fill_value" label="Fill value" value="." /> + </when> + <when value="fill_value_by_column"> + <repeat name="column_fill" title="Fill Column"> + <param name="column_number" label="Column" type="data_column" data_ref="input1" /> + <param type="text" name="fill_value" value="." /> + </repeat> + </when> + </conditional> + </when> + </conditional> <param name="input2" type="data" format="tabular" label="Choose the second file for the join" /> <repeat name="file_chooser" title="Additional Input"> <param name="input" label="Additional input file" type="data" format="tabular" /> </repeat> </inputs> + <configfiles> + <configfile name="fill_options_file"><% +import simplejson +%> +#set $__fill_options = {} +#if $fill_empty_columns['fill_empty_columns_switch'] == 'fill_empty': + #if $fill_empty_columns['do_fill_empty_columns']['column_fill_type'] == 'single_fill_value': + #set $__start_fill = $fill_empty_columns['do_fill_empty_columns']['fill_value'].value + #else: + #set $__start_fill = "" + #end if + #set $__fill_options['file1_columns'] = [ __start_fill for i in range( int( $input1.metadata.columns ) ) ] + #if $fill_empty_columns['do_fill_empty_columns']['column_fill_type'] == 'fill_value_by_column': + #for column_fill in $fill_empty_columns['do_fill_empty_columns']['column_fill']: + #set $__fill_options['file1_columns'][ int( column_fill['column_number'].value ) - 1 ] = column_fill['fill_value'].value + #end for + #end if +#end if +${simplejson.dumps( __fill_options )} + </configfile> + </configfiles> <outputs> <data name="output" format="tabular" /> </outputs> <tests> <test> <param name="input1" value="column_join_in1.pileup" ftype="pileup" /> + <param name="hinge" value="2" /> <param name="columns" value="1,2,3,4,5,7" /> - <param name="hinge" value="1,2" /> + <param name="fill_empty_columns_switch" value="fill_empty" /> + <param name="column_fill_type" value="single_fill_value" /> + <param name="fill_value" value="?" /> <param name="input2" value="column_join_in2.pileup" ftype="pileup" /> <param name="input" value="column_join_in3.pileup" ftype="pileup" /> <output name="output" file="column_join_out1.pileup" ftype="tabular" /> </test> <test> <param name="input1" value="column_join_in4.pileup" ftype="pileup" /> + <param name="hinge" value="2" /> <param name="columns" value="1,2,3,4" /> - <param name="hinge" value="1,2" /> + <param name="fill_empty_columns_switch" value="no_fill" /> <param name="input2" value="column_join_in5.pileup" ftype="pileup" /> <param name="input" value="column_join_in6.pileup" ftype="pileup" /> <output name="output" file="column_join_out2.pileup" ftype="tabular" /> </test> + </tests> <help> **What it does**

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[hg] galaxy 3744: Fix bug that mucked up fetch for chrom lengths...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/5f59c890ee8d changeset: 3744:5f59c890ee8d user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Tue May 04 22:27:05 2010 -0400 description: Fix bug that mucked up fetch for chrom lengths in new track browsers. diffstat: lib/galaxy/web/controllers/tracks.py | 32 ++++++++++++++++++++------------ templates/tracks/browser.mako | 7 ++++++- 2 files changed, 26 insertions(+), 13 deletions(-) diffs (76 lines): diff -r b5c76e1a28ea -r 5f59c890ee8d lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py Tue May 04 21:57:26 2010 -0400 +++ b/lib/galaxy/web/controllers/tracks.py Tue May 04 22:27:05 2010 -0400 @@ -158,9 +158,9 @@ return trans.fill_template( 'tracks/browser.mako', config=config ) @web.json - def chroms(self, trans, vis_id=None ): + def chroms(self, trans, vis_id=None, dbkey=None ): """ - Returns a naturally sorted list of chroms/contigs for the given dbkey + Returns a naturally sorted list of chroms/contigs for either a given visualization or a given dbkey. """ def check_int(s): if s.isdigit(): @@ -171,25 +171,33 @@ def split_by_number(s): return [ check_int(c) for c in re.split('([0-9]+)', s) ] - # Get visualization and config. - visualization = self.get_visualization( trans, vis_id, check_ownership=False, check_accessible=True ) - visualization.config = self.get_visualization_config( trans, visualization ) - if visualization is None: - raise web.httpexceptions.HTTPNotFound() + # Must specify either vis_id or dbkey. + if not vis_id and not dbkey: + return trans.show_error_message("No visualization id or dbkey specified.") + + # Need to get user and dbkey in order to get chroms data. + if vis_id: + # Use user, dbkey from viz. + visualization = self.get_visualization( trans, vis_id, check_ownership=False, check_accessible=True ) + visualization.config = self.get_visualization_config( trans, visualization ) + vis_user = visualization.user + vis_dbkey = visualization.config['dbkey'] + else: + # No vis_id, so visualization is new. User is current user, dbkey must be given. + vis_user = trans.user + vis_dbkey = dbkey # Get chroms data. - chroms = self._chroms( trans, visualization ) + chroms = self._chroms( trans, vis_user, vis_dbkey ) to_sort = [{ 'chrom': chrom, 'len': length } for chrom, length in chroms.iteritems()] to_sort.sort(lambda a,b: cmp( split_by_number(a['chrom']), split_by_number(b['chrom']) )) return to_sort - def _chroms( self, trans, visualization ): + def _chroms( self, trans, user, dbkey ): """ - Called by the browser to get a list of valid chromosomes and lengths + Helper method that returns chrom lengths for a given user and dbkey. """ # If there is any dataset in the history of extension `len`, this will use it - user = visualization.user - dbkey = visualization.config['dbkey'] if 'dbkeys' in user.preferences: user_keys = from_json_string( user.preferences['dbkeys'] ) if dbkey in user_keys: diff -r b5c76e1a28ea -r 5f59c890ee8d templates/tracks/browser.mako --- a/templates/tracks/browser.mako Tue May 04 21:57:26 2010 -0400 +++ b/templates/tracks/browser.mako Tue May 04 22:27:05 2010 -0400 @@ -272,7 +272,12 @@ $.ajax({ url: "${h.url_for( action='chroms' )}", - data: { vis_id: view.vis_id }, + ## If vis is new, it doesn't have an id, so send the dbkey instead. + %if config.get('vis_id'): + data: { vis_id: view.vis_id }, + %else: + data: { dbkey: view.dbkey }, + %endif dataType: "json", success: function ( data ) { view.chrom_data = data;

1 0

[hg] galaxy 3742: trackster: fix BAM data error; display tweaks
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/49c11691bc2e changeset: 3742:49c11691bc2e user: Kanwei Li <kanwei(a)gmail.com> date: Tue May 04 15:43:34 2010 -0400 description: trackster: fix BAM data error; display tweaks diffstat: lib/galaxy/datatypes/converters/bed_to_summary_tree_converter.py | 2 +- lib/galaxy/visualization/tracks/data/bam.py | 11 +++++++++- lib/galaxy/visualization/tracks/data/summary_tree.py | 4 +- static/scripts/trackster.js | 5 ++- 4 files changed, 16 insertions(+), 6 deletions(-) diffs (84 lines): diff -r c7607fba91b9 -r 49c11691bc2e lib/galaxy/datatypes/converters/bed_to_summary_tree_converter.py --- a/lib/galaxy/datatypes/converters/bed_to_summary_tree_converter.py Tue May 04 14:21:21 2010 -0400 +++ b/lib/galaxy/datatypes/converters/bed_to_summary_tree_converter.py Tue May 04 15:43:34 2010 -0400 @@ -15,7 +15,7 @@ reader = BedReader( open( input_fname ) ) - st = SummaryTree(block_size=100, levels=4, draw_cutoff=100, detail_cutoff=20) + st = SummaryTree(block_size=25, levels=6, draw_cutoff=150, detail_cutoff=30) for chrom, chrom_start, chrom_end, name, score in reader: st.insert_range(chrom, chrom_start, chrom_end) diff -r c7607fba91b9 -r 49c11691bc2e lib/galaxy/visualization/tracks/data/bam.py --- a/lib/galaxy/visualization/tracks/data/bam.py Tue May 04 14:21:21 2010 -0400 +++ b/lib/galaxy/visualization/tracks/data/bam.py Tue May 04 15:43:34 2010 -0400 @@ -10,6 +10,8 @@ import logging log = logging.getLogger(__name__) +MAX_VALS = 50 # only display first MAX_VALS datapoints + class BamDataProvider( object ): """ Provides access to intervals from a sorted indexed BAM file. @@ -26,18 +28,25 @@ start, end = int(start), int(end) # Attempt to open the BAM file with index bamfile = csamtools.Samfile( filename=self.original_dataset.file_name, mode='rb', index_filename=self.index.file_name ) + message = None try: data = bamfile.fetch(start=start, end=end, reference=chrom) except ValueError, e: # Some BAM files do not prefix chromosome names with chr, try without if chrom.startswith( 'chr' ): - data = bamfile.fetch( start=start, end=end, reference=chrom[3:] ) + try: + data = bamfile.fetch( start=start, end=end, reference=chrom[3:] ) + except: + return None else: return None # Encode reads as list of dictionaries results = [] paired_pending = {} for read in data: + if len(results) > MAX_VALS: + message = "Only the first %s pairs are being displayed." % MAX_VALS + break qname = read.qname if read.is_proper_pair: if qname in paired_pending: # one in dict is always first diff -r c7607fba91b9 -r 49c11691bc2e lib/galaxy/visualization/tracks/data/summary_tree.py --- a/lib/galaxy/visualization/tracks/data/summary_tree.py Tue May 04 14:21:21 2010 -0400 +++ b/lib/galaxy/visualization/tracks/data/summary_tree.py Tue May 04 15:43:34 2010 -0400 @@ -32,12 +32,12 @@ level = int(max( level, 0 )) if level <= 0: return None - + stats = st.chrom_stats[chrom] results = st.query(chrom, int(start), int(end), level) if results == "detail": return None - elif results == "draw": + elif results == "draw" or level <= 1: return "no_detail" else: return results, stats[level]["max"], stats[level]["avg"], stats[level]["delta"] diff -r c7607fba91b9 -r 49c11691bc2e static/scripts/trackster.js --- a/static/scripts/trackster.js Tue May 04 14:21:21 2010 -0400 +++ b/static/scripts/trackster.js Tue May 04 15:43:34 2010 -0400 @@ -439,8 +439,9 @@ return; } - var data = this.data_cache.get(key); - if (data === null) { return; } + var result = this.data_cache.get(key); + if (result === null) { return; } + console.log(result); canvas.css( { position: "absolute",

1 0

[hg] galaxy 3743: Removing debugging msg.
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/b5c76e1a28ea changeset: 3743:b5c76e1a28ea user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Tue May 04 21:57:26 2010 -0400 description: Removing debugging msg. diffstat: tools/ngs_rna/cuffcompare_wrapper.py | 1 - 1 files changed, 0 insertions(+), 1 deletions(-) diffs (11 lines): diff -r 49c11691bc2e -r b5c76e1a28ea tools/ngs_rna/cuffcompare_wrapper.py --- a/tools/ngs_rna/cuffcompare_wrapper.py Tue May 04 15:43:34 2010 -0400 +++ b/tools/ngs_rna/cuffcompare_wrapper.py Tue May 04 21:57:26 2010 -0400 @@ -52,7 +52,6 @@ input2_file_name = tmp_output_dir + "/input2" os.symlink( options.input2, input2_file_name ) cmd += " %s" % input2_file_name - print cmd # Run command. try:

1 0

[hg] galaxy 3740: Secure=True by default for workflows.
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/68fc85a43bb8 changeset: 3740:68fc85a43bb8 user: Dannon Baker <dannon.baker(a)emory.edu> date: Tue May 04 14:19:44 2010 -0400 description: Secure=True by default for workflows. diffstat: lib/galaxy/workflow/modules.py | 6 +++--- 1 files changed, 3 insertions(+), 3 deletions(-) diffs (26 lines): diff -r 9057a05dc7d3 -r 68fc85a43bb8 lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py Tue May 04 13:45:57 2010 -0400 +++ b/lib/galaxy/workflow/modules.py Tue May 04 14:19:44 2010 -0400 @@ -96,7 +96,7 @@ module.state = dict( name="Input Dataset" ) return module @classmethod - def from_dict( Class, trans, d, secure=False ): + def from_dict( Class, trans, d, secure=True ): module = Class( trans ) state = from_json_string( d["tool_state"] ) module.state = dict( name=state.get( "name", "Input Dataset" ) ) @@ -172,11 +172,11 @@ module.state = module.tool.new_state( trans, all_pages=True ) return module @classmethod - def from_dict( Class, trans, d, secure=False ): + def from_dict( Class, trans, d, secure=True ): tool_id = d['tool_id'] module = Class( trans, tool_id ) module.state = DefaultToolState() - module.state.decode( d["tool_state"], module.tool, module.trans.app, secure=False ) + module.state.decode( d["tool_state"], module.tool, module.trans.app, secure=secure ) module.errors = d.get( "tool_errors", None ) return module

1 0

[hg] galaxy 3741: Fix the recentrly introduced grid filter / sea...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/c7607fba91b9 changeset: 3741:c7607fba91b9 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Tue May 04 14:21:21 2010 -0400 description: Fix the recentrly introduced grid filter / search bug. Revert the recently introduced grid filter_params hack for generating links since we now use a different approach to rendering links. Convert a few more 'message_type' params to be 'status' instead. Many fixes for the community space app. diffstat: lib/galaxy/tools/__init__.py | 4 +- lib/galaxy/web/framework/__init__.py | 2 +- lib/galaxy/web/framework/helpers/grids.py | 17 +- lib/galaxy/webapps/community/controllers/admin.py | 154 +++++++++++++------- lib/galaxy/webapps/community/controllers/common.py | 90 ++++++++--- lib/galaxy/webapps/community/controllers/tool.py | 157 +++++++++++--------- lib/galaxy/webapps/community/controllers/upload.py | 33 ++-- lib/galaxy/webapps/community/model/__init__.py | 4 +- templates/dataset/display_application/display.mako | 4 +- templates/display_common.mako | 4 +- templates/grid_base.mako | 16 +- templates/grid_base_async.mako | 2 +- templates/message.mako | 12 +- templates/page/select_items_grid_async.mako | 2 +- templates/webapps/community/admin/center.mako | 39 ++++- templates/webapps/community/tool/edit_tool.mako | 19 +- templates/webapps/community/tool/view_tool.mako | 25 ++- 17 files changed, 354 insertions(+), 230 deletions(-) diffs (1213 lines): diff -r 68fc85a43bb8 -r c7607fba91b9 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Tue May 04 14:19:44 2010 -0400 +++ b/lib/galaxy/tools/__init__.py Tue May 04 14:21:21 2010 -0400 @@ -837,7 +837,7 @@ assert isinstance( out_data, odict ) return 'tool_executed.mako', dict( out_data=out_data ) except: - return 'message.mako', dict( message_type='error', message='odict not returned from tool execution', refresh_frames=[] ) + return 'message.mako', dict( status='error', message='odict not returned from tool execution', refresh_frames=[] ) # Otherwise move on to the next page else: state.page += 1 @@ -890,7 +890,7 @@ self.sa_session.add( data ) self.sa_session.flush() # It's unlikely the user will ever see this. - return 'message.mako', dict( message_type='error', message='Your upload was interrupted. If this was uninentional, please retry it.', refresh_frames=[], cont=None ) + return 'message.mako', dict( status='error', message='Your upload was interrupted. If this was uninentional, please retry it.', refresh_frames=[], cont=None ) def update_state( self, trans, inputs, state, incoming, prefix="", context=None, update_only=False, old_errors={}, item_callback=None ): diff -r 68fc85a43bb8 -r c7607fba91b9 lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py Tue May 04 14:19:44 2010 -0400 +++ b/lib/galaxy/web/framework/__init__.py Tue May 04 14:21:21 2010 -0400 @@ -591,7 +591,7 @@ `refresh_frames`: names of frames in the interface that should be refreshed when the message is displayed """ - return self.fill_template( "message.mako", message_type=type, message=message, refresh_frames=refresh_frames, cont=cont, use_panels=use_panels, active_view=active_view ) + return self.fill_template( "message.mako", status=type, message=message, refresh_frames=refresh_frames, cont=cont, use_panels=use_panels, active_view=active_view ) def show_error_message( self, message, refresh_frames=[], use_panels=False, active_view="" ): """ Convenience method for displaying an error message. See `show_message`. diff -r 68fc85a43bb8 -r c7607fba91b9 lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py Tue May 04 14:19:44 2010 -0400 +++ b/lib/galaxy/web/framework/helpers/grids.py Tue May 04 14:21:21 2010 -0400 @@ -134,13 +134,16 @@ column_filter = unicode(column_filter) extra_url_args[ "f-" + column.key ] = column_filter.encode("utf-8") # Process sort arguments. - sort_key = sort_order = None + sort_key = None + sort_order = None if 'sort' in kwargs: sort_key = kwargs['sort'] elif base_sort_key: sort_key = base_sort_key encoded_sort_key = sort_key if sort_key: + # TODO: what if the model object of the grid column being sorted is not + # the same object as self.model_class? if sort_key.startswith( "-" ): sort_key = sort_key[1:] sort_order = 'desc' @@ -230,10 +233,10 @@ current_item=current_item, ids = kwargs.get( 'id', [] ), url = url, - message_type = status, + status = status, message = message, use_panels=use_panels, - webapp=self.webapp, + webapp=webapp, # Pass back kwargs so that grid template can set and use args without # grid explicitly having to pass them. kwargs=kwargs ) @@ -290,9 +293,7 @@ if self.format: value = self.format( value ) return value - def get_link( self, trans, grid, item, filter_params ): - # FIXME: filter_params is only here so we can do grid filtering from - # column links. remove once a better way is created. + def get_link( self, trans, grid, item ): if self.link and self.link( item ): return self.link( item ) return None @@ -449,7 +450,7 @@ class PublicURLColumn( TextColumn ): """ Column displays item's public URL based on username and slug. """ - def get_link( self, trans, grid, item, filter_params ): + def get_link( self, trans, grid, item ): if item.user.username and item.slug: return dict( action='display_by_username_and_slug', username=item.user.username, slug=item.slug ) elif not item.user.username: @@ -485,7 +486,7 @@ if item.published: sharing_statuses.append( "Published" ) return ", ".join( sharing_statuses ) - def get_link( self, trans, grid, item, filter_params ): + def get_link( self, trans, grid, item ): if not item.deleted and ( item.users_shared_with or item.importable or item.published ): return dict( operation="share or publish", id=item.id ) return None diff -r 68fc85a43bb8 -r c7607fba91b9 lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py Tue May 04 14:19:44 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/admin.py Tue May 04 14:21:21 2010 -0400 @@ -47,7 +47,7 @@ return "" class ToolsColumn( grids.TextColumn ): def get_value( self, trans, grid, user ): - return '<a href="browse_tools_by_user?operation=browse&id=%s">%s</a>' % ( trans.security.encode_id( user.id ), str( len( user.tools ) ) ) + return '<a href="browse_tools_by_user?operation=browse&id=%s&webapp=community">%s</a>' % ( trans.security.encode_id( user.id ), str( len( user.tools ) ) ) # Grid definition webapp = "community" @@ -77,7 +77,10 @@ attach_popup=False, filterable="advanced" ), # Columns that are valid for filtering but are not visible. - grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) + grids.DeletedColumn( "Deleted", + key="deleted", + visible=False, + filterable="advanced" ) ] columns.append( grids.MulticolFilterColumn( "Search", cols_to_filter=[ columns[0], columns[1] ], @@ -168,7 +171,10 @@ UsersColumn( "Users", attach_popup=False ), StatusColumn( "Status", attach_popup=False ), # Columns that are valid for filtering but are not visible. - grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) + grids.DeletedColumn( "Deleted", + key="deleted", + visible=False, + filterable="advanced" ) ] columns.append( grids.MulticolFilterColumn( "Search", cols_to_filter=[ columns[0], columns[1], columns[2] ], @@ -238,16 +244,20 @@ default_sort_key = "name" columns = [ NameColumn( "Name", - key="name", + #key="name", link=( lambda item: dict( operation="Manage users and roles", id=item.id, webapp="community" ) ), model_class=model.Group, - attach_popup=True, - filterable="advanced" ), + attach_popup=True + #filterable="advanced" + ), UsersColumn( "Users", attach_popup=False ), RolesColumn( "Roles", attach_popup=False ), StatusColumn( "Status", attach_popup=False ), # Columns that are valid for filtering but are not visible. - grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) + grids.DeletedColumn( "Deleted", + key="deleted", + visible=False, + filterable="advanced" ) ] columns.append( grids.MulticolFilterColumn( "Search", cols_to_filter=[ columns[0], columns[1], columns[2] ], @@ -309,14 +319,18 @@ attach_popup=False, filterable="advanced" ), DescriptionColumn( "Description", + key="description", model_class=model.Category, attach_popup=False, filterable="advanced" ), # Columns that are valid for filtering but are not visible. - grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) + grids.DeletedColumn( "Deleted", + key="deleted", + visible=False, + filterable="advanced" ) ] columns.append( grids.MulticolFilterColumn( "Search", - cols_to_filter=[ columns[0], columns[1], columns[2] ], + cols_to_filter=[ columns[0], columns[1] ], key="free-text-search", visible=False, filterable="standard" ) ) @@ -370,24 +384,34 @@ default_sort_key = "name" columns = [ NameColumn( "Name", - key="name", + # TODO: we cannot currently sort by columns since the grid may be filtered by tool ids + # and it is not clear if / how that will work. We need to be able to send to the grid helper + # the list of ids on which to filter when sorting on the column. + #key="name", + model_class=model.Category, link=( lambda item: dict( operation="Browse Category", id=item.id, webapp="community" ) ), - model_class=model.Category, - attach_popup=True, - filterable="advanced" ), + attach_popup=False + #filterable="advanced" + ), DescriptionColumn( "Description", + #key="description", model_class=model.Category, - attach_popup=False, - filterable="advanced" ), + attach_popup=False + #filterable="advanced" + ), ToolsColumn( "Tools", - model_class=model.Category, + model_class=model.Tool, attach_popup=False, filterable="advanced" ), # Columns that are valid for filtering but are not visible. - grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) + grids.DeletedColumn( "Deleted", + key="deleted", + visible=False, + filterable="advanced" ) ] columns.append( grids.MulticolFilterColumn( "Search", - cols_to_filter=[ columns[0], columns[1], columns[2] ], + #cols_to_filter=[ columns[0], columns[1] ], + cols_to_filter=[], key="free-text-search", visible=False, filterable="standard" ) ) @@ -399,10 +423,17 @@ num_rows_per_page = 50 preserve_state = False use_paging = True - def get_current_item( self, trans ): - return None def build_initial_query( self, session ): return session.query( self.model_class ) + def apply_default_filter( self, trans, query, **kwd ): + ids = kwd.get( 'ids', False ) + if ids: + if str( ids ).lower() == 'none': + # No tools for display + return query.filter( model.Tool.id == None ) + ids = util.listify( ids ) + query = query.filter( or_( *map( lambda id: self.model_class.id == id, ids ) ) ) + return query class ToolListGrid( grids.Grid ): class NameColumn( grids.TextColumn ): @@ -419,7 +450,7 @@ if tool.categories: rval = '' for tca in tool.categories: - rval += '<a href="browse_category?id=%s">%s</a><br/>\n' % ( trans.security.encode_id( tca.category.id ), tca.category.name ) + rval += '<a href="browse_category?id=%s&webapp=community">%s</a><br/>\n' % ( trans.security.encode_id( tca.category.id ), tca.category.name ) return rval return 'not set' class StateColumn( grids.GridColumn ): @@ -450,7 +481,7 @@ return accepted_filters class UserColumn( grids.TextColumn ): def get_value( self, trans, grid, tool ): - return '<a href="browse_tools_by_user?operation=browse&id=%s">%s</a>' % ( trans.security.encode_id( tool.user.id ), tool.user.username ) + return '<a href="browse_tools_by_user?operation=browse&id=%s&webapp=community">%s</a>' % ( trans.security.encode_id( tool.user.id ), tool.user.username ) # Grid definition title = "Tools" model_class = model.Tool @@ -458,19 +489,25 @@ default_sort_key = "name" columns = [ NameColumn( "Name", - key="name", + # TODO: we cannot currently sort by columns since the grid may be filtered by tool ids + # and it is not clear if / how that will work. We need to be able to send to the grid helper + # the list of ids on which to filter when sorting on the column. + #key="name", + link=( lambda item: dict( operation="View Tool", id=item.id, cntrller="admin", webapp="community" ) ), model_class=model.Tool, - link=( lambda item: dict( operation="View Tool", id=item.id, cntrller='admin', webapp="community" ) ), - attach_popup=True, - filterable="advanced" ), + attach_popup=True + #filterable="advanced" + ), VersionColumn( "Version", model_class=model.Tool, attach_popup=False, filterable="advanced" ), DescriptionColumn( "Description", - model_class=model.Tool, - attach_popup=False, - filterable="advanced" ), + #key="description", + model_class=model.Tool, + attach_popup=False + #filterable="advanced" + ), CategoryColumn( "Category", model_class=model.Category, attach_popup=False, @@ -479,15 +516,19 @@ model_class=model.Event, attach_popup=False ), UserColumn( "Uploaded By", - key="username", model_class=model.User, attach_popup=False, filterable="advanced" ), # Columns that are valid for filtering but are not visible. - grids.DeletedColumn( "Deleted", model_class=model.Tool, key="deleted", visible=False, filterable="advanced" ) + grids.DeletedColumn( "Deleted", + model_class=model.Tool, + key="deleted", + visible=False, + filterable="advanced" ) ] columns.append( grids.MulticolFilterColumn( "Search", - cols_to_filter=[ columns[0], columns[1] ], + #cols_to_filter=[ columns[0], columns[2], columns[5] ], + cols_to_filter=[], key="free-text-search", visible=False, filterable="standard" ) ) @@ -499,7 +540,7 @@ ] standard_filters = [ grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), - grids.GridColumnFilter( "All", args=dict( deleted='All' ) ) + grids.GridColumnFilter( "All", args=dict( deleted='All' ) ), ] default_filter = dict( name="All", deleted="False" ) num_rows_per_page = 50 @@ -508,15 +549,14 @@ def build_initial_query( self, session ): return session.query( self.model_class ) def apply_default_filter( self, trans, query, **kwd ): - tool_id = kwd.get( 'tool_id', False ) - if tool_id: - if str( tool_id ).lower() in [ '', 'none' ]: - # Return an empty query since the current user cannot view any - # tools (possibly due to state not being approved, etc). + ids = kwd.get( 'ids', False ) + if ids: + if str( ids ).lower() == 'none': + # No tools for display return query.filter( model.Tool.id == None ) - tool_id = util.listify( tool_id ) - query = query.filter( or_( *map( lambda id: self.model_class.id == id, tool_id ) ) ) - return query.filter( self.model_class.deleted==False ) + ids = util.listify( ids ) + query = query.filter( or_( *map( lambda id: self.model_class.id == id, ids ) ) ) + return query class AdminController( BaseController, Admin ): @@ -616,12 +656,12 @@ status='error' ) ) event = get_event( trans, id ) state = event.state - tool_id = get_tools_by_state( trans, state ) - if not tool_id: - tool_id = 'None' + ids = get_tools_by_state( trans, state ) + if not ids: + ids = 'none' return trans.response.send_redirect( web.url_for( controller='admin', action='browse_tools', - tool_id=tool_id ) ) + ids=ids ) ) @web.expose @web.require_admin def browse_category( self, trans, **kwd ): @@ -681,7 +721,10 @@ # If we're approving a tool, all previous versions must be set to archived for version in get_versions( trans, tool ): if version != tool and version.is_approved(): - self.set_tool_state( trans, trans.app.model.Tool.states.ARCHIVED, id=trans.app.security.encode_id( version.id ), redirect='False' ) + self.set_tool_state( trans, + trans.app.model.Tool.states.ARCHIVED, + id=trans.security.encode_id( version.id ), + redirect='False' ) event = trans.model.Event( state ) # Flush so we an get an id trans.sa_session.add( event ) @@ -842,33 +885,34 @@ ## ---- Utility methods ------------------------------------------------------- def get_tools_by_state( trans, state ): - tool_id = [] + # TODO: write this as a query using eagerload - will be much faster. + ids = [] if state == trans.model.Tool.states.NEW: for tool in get_tools( trans ): if tool.is_new(): - tool_id.append( tool.id ) + ids.append( tool.id ) elif state == trans.model.Tool.states.ERROR: for tool in get_tools( trans ): if tool.is_error(): - tool_id.append( tool.id ) + ids.append( tool.id ) elif state == trans.model.Tool.states.DELETED: for tool in get_tools( trans ): if tool.is_deleted(): - tool_id.append( tool.id ) + ids.append( tool.id ) elif state == trans.model.Tool.states.WAITING: for tool in get_tools( trans ): if tool.is_waiting(): - tool_id.append( tool.id ) + ids.append( tool.id ) elif state == trans.model.Tool.states.APPROVED: for tool in get_tools( trans ): if tool.is_approved(): - tool_id.append( tool.id ) + ids.append( tool.id ) elif state == trans.model.Tool.states.REJECTED: for tool in get_tools( trans ): if tool.is_rejected(): - tool_id.append( tool.id ) + ids.append( tool.id ) elif state == trans.model.Tool.states.ARCHIVED: for tool in get_tools( trans ): if tool.is_archived(): - tool_id.append( tool.id ) - return tool_id + ids.append( tool.id ) + return ids diff -r 68fc85a43bb8 -r c7607fba91b9 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py Tue May 04 14:19:44 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/common.py Tue May 04 14:21:21 2010 -0400 @@ -91,6 +91,35 @@ message=message, status=status ) @web.expose + def delete_tool( self, trans, cntrller, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + id = params.get( 'id', None ) + if not id: + message='Select a tool to delete' + status='error' + else: + tool = get_tool( trans, id ) + # Create a new event + event = trans.model.Event( state=trans.model.Tool.states.DELETED ) + # Flush so we can get an event id + trans.sa_session.add( event ) + trans.sa_session.flush() + # Associate the tool with the event + tea = trans.model.ToolEventAssociation( tool=tool, event=event ) + # Delete the tool, keeping state for categories, events and versions + tool.deleted = True + trans.sa_session.add_all( ( tool, tea ) ) + trans.sa_session.flush() + # TODO: What if the tool has versions, should they all be deleted? + message = "Tool '%s' has been marked deleted" + status = 'done' + return trans.response.send_redirect( web.url_for( controller=cntrller, + action='browse_tools', + message=message, + status=status ) ) + @web.expose def upload_new_tool_version( self, trans, cntrller, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) @@ -122,15 +151,15 @@ # If request came from the tool controller, then we need to filter by the state of the # tool in addition to the category. if cntrller == 'tool': - tool_id = get_approved_tools( trans, category=category ) + ids = get_approved_tools( trans, category=category ) else: # If request came from the admin controller, we don't filter on tool state. - tool_id = [ tca.tool.id for tca in category.tools ] - if not tool_id: - tool_id = 'None' + ids = [ tca.tool.id for tca in category.tools ] + if not ids: + ids = 'none' return trans.response.send_redirect( web.url_for( controller=cntrller, action='browse_tools', - tool_id=tool_id ) ) + ids=ids ) ) @web.expose def browse_tools_by_user( self, trans, cntrller, **kwd ): params = util.Params( kwd ) @@ -146,15 +175,21 @@ # If request came from the tool controller, then we need to filter by the state of the # tool if the user is not viewing his own tools if cntrller == 'tool': - tool_id = get_approved_tools( trans, user=user ) + ids = get_tools_uploaded_by( trans, user ) else: - # If request came from the admin controller, we don't filter on tool state. - tool_id = [ tool.id for tool in user.tools ] - if not tool_id: - tool_id = 'None' + # If request came from the admin controller we don't filter on tool state. + ids = [ tool.id for tool in user.tools ] + if not ids: + ids = 'none' + if cntrller == 'tool' and user != trans.user: + # If the user is browsing someone else's tools, then we do not want to + # use the BrowseToolsByUser list grid since it includes a status column. + return trans.response.send_redirect( web.url_for( controller=cntrller, + action='browse_tools', + ids=ids ) ) return trans.response.send_redirect( web.url_for( controller=cntrller, action='browse_tools_by_user', - tool_id=tool_id ) ) + ids=ids ) ) ## ---- Utility methods ------------------------------------------------------- @@ -202,30 +237,33 @@ return trans.sa_session.query( trans.model.Tool ).get( trans.app.security.decode_id( id ) ) def get_tools( trans ): return trans.sa_session.query( trans.model.Tool ).order_by( trans.model.Tool.name ) -def get_approved_tools( trans, category=None, user=None ): - tool_id = [] +def get_approved_tools( trans, category=None ): + # TODO: write this as a query using eagerload - will be much faster. + ids = [] if category: # Return only the approved tools in the category for tca in category.tools: tool = tca.tool if tool.is_approved(): - tool_id.append( tool.id ) - elif user: - if trans.user == user: - # If the current user is browsing his own tools, then don't filter on state - tool_id = [ tool.id for tool in user.tools ] - else: - # The current user is viewing all tools uploaded by another user, so show only - # approved tools - for tool in user.active_tools: - if tool.is_approved(): - tool_id.append( tool.id ) + ids.append( tool.id ) else: # Return all approved tools for tool in get_tools( trans ): if tool.is_approved(): - tool_id.append( tool.id ) - return tool_id + ids.append( tool.id ) + return ids +def get_tools_uploaded_by( trans, user ): + # TODO: write this as a query using eagerload - will be much faster. + ids = [] + if trans.user == user: + # If the current user is browsing his own tools, then don't filter on state + ids = [ tool.id for tool in user.tools ] + else: + # The current user is viewing tools uploaded by another user, so show only approved tools + for tool in user.active_tools: + if tool.is_approved(): + ids.append( tool.id ) + return ids def get_event( trans, id ): return trans.sa_session.query( trans.model.Event ).get( trans.security.decode_id( id ) ) def get_user( trans, id ): diff -r 68fc85a43bb8 -r c7607fba91b9 lib/galaxy/webapps/community/controllers/tool.py --- a/lib/galaxy/webapps/community/controllers/tool.py Tue May 04 14:19:44 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/tool.py Tue May 04 14:21:21 2010 -0400 @@ -26,12 +26,12 @@ if tool.categories: rval = '' for tca in tool.categories: - rval += '<a href="browse_category?id=%s">%s</a><br/>\n' % ( trans.security.encode_id( tca.category.id ), tca.category.name ) + rval += '<a href="browse_category?id=%s&webapp=community">%s</a><br/>\n' % ( trans.security.encode_id( tca.category.id ), tca.category.name ) return rval return 'not set' class UserColumn( grids.TextColumn ): def get_value( self, trans, grid, tool ): - return '<a href="browse_tools_by_user?operation=browse&id=%s">%s</a>' % ( trans.security.encode_id( tool.user.id ), tool.user.username ) + return '<a href="browse_tools_by_user?operation=browse&id=%s&webapp=community">%s</a>' % ( trans.security.encode_id( tool.user.id ), tool.user.username ) # Grid definition title = "Tools" model_class = model.Tool @@ -39,33 +39,44 @@ default_sort_key = "name" columns = [ NameColumn( "Name", - key="name", + # TODO: we cannot currently sort by columns since the grid may be filtered by tool ids + # and it is not clear if / how that will work. We need to be able to send to the grid helper + # the list of ids on which to filter when sorting on the column. + #key="name", model_class=model.Tool, link=( lambda item: dict( operation="View Tool", id=item.id, cntrller='tool', webapp="community" ) ), - attach_popup=True, - filterable="advanced" ), + attach_popup=True + #filterable="advanced" + ), VersionColumn( "Version", model_class=model.Tool, attach_popup=False, filterable="advanced" ), DescriptionColumn( "Description", - model_class=model.Tool, - attach_popup=False, - filterable="advanced" ), + #key="description", + model_class=model.Tool, + attach_popup=False + #filterable="advanced" + ), CategoryColumn( "Categories", model_class=model.Category, attach_popup=False, filterable="advanced" ), UserColumn( "Uploaded By", - key="username", + #key="username", model_class=model.User, - attach_popup=False, - filterable="advanced" ), + attach_popup=False + #filterable="advanced" + ), # Columns that are valid for filtering but are not visible. - grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) + grids.DeletedColumn( "Deleted", + key="deleted", + visible=False, + filterable="advanced" ) ] columns.append( grids.MulticolFilterColumn( "Search", - cols_to_filter=[ columns[0], columns[1] ], + #cols_to_filter=[ columns[0], columns[2], columns[4] ], + cols_to_filter=[], key="free-text-search", visible=False, filterable="standard" ) ) @@ -86,21 +97,15 @@ def build_initial_query( self, session ): return session.query( self.model_class ) def apply_default_filter( self, trans, query, **kwd ): - def filter_query( query, tool_id ): - if str( tool_id ).lower() in [ '', 'none' ]: - # Return an empty query since the current user cannot view any - # tools (possibly due to state not being approved, etc). - return query.filter( model.Tool.id == None ) - tool_id = util.listify( tool_id ) - query = query.filter( or_( *map( lambda id: self.model_class.id == id, tool_id ) ) ) - return query.filter( self.model_class.deleted==False ) - tool_id = kwd.get( 'tool_id', False ) - if not tool_id: + ids = kwd.get( 'ids', False ) + if not ids: # Display only approved tools - tool_id = get_approved_tools( trans ) - if not tool_id: - tool_id = 'None' - return filter_query( query, tool_id ) + ids = get_approved_tools( trans ) + if not ids or str( ids ).lower() == 'none': + return query.filter( trans.model.Tool.id == None ) + ids = util.listify( ids ) + query = query.filter( or_( *map( lambda id: self.model_class.id == id, ids ) ) ) + return query class ToolsByUserListGrid( grids.Grid ): class NameColumn( grids.TextColumn ): @@ -117,7 +122,7 @@ if tool.categories: rval = '' for tca in tool.categories: - rval += '<a href="browse_category?id=%s">%s</a><br/>\n' % ( trans.security.encode_id( tca.category.id ), tca.category.name ) + rval += '<a href="browse_category?id=%s&webapp=community">%s</a><br/>\n' % ( trans.security.encode_id( tca.category.id ), tca.category.name ) return rval return 'not set' class StateColumn( grids.GridColumn ): @@ -148,7 +153,7 @@ return accepted_filters class UserColumn( grids.TextColumn ): def get_value( self, trans, grid, tool ): - return '<a href="browse_tools_by_user?operation=browse&id=%s">%s</a>' % ( trans.security.encode_id( tool.user.id ), tool.user.username ) + return '<a href="browse_tools_by_user?operation=browse&id=%s&webapp=community">%s</a>' % ( trans.security.encode_id( tool.user.id ), tool.user.username ) # Grid definition title = "Tools By User" model_class = model.Tool @@ -156,19 +161,24 @@ default_sort_key = "name" columns = [ NameColumn( "Name", - key="name", + # TODO: we cannot currently sort by columns since the grid may be filtered by tool ids + # and it is not clear if / how that will work. We need to be able to send to the grid helper + # the list of ids on which to filter when sorting on the column. + #key="name", model_class=model.Tool, link=( lambda item: dict( operation="View Tool", id=item.id, cntrller='tool', webapp="community" ) ), - attach_popup=True, - filterable="advanced" ), + attach_popup=True + #filterable="advanced" + ), VersionColumn( "Version", model_class=model.Tool, - attach_popup=False, - filterable="advanced" ), + attach_popup=False ), DescriptionColumn( "Description", - model_class=model.Tool, - attach_popup=False, - filterable="advanced" ), + #key="description", + model_class=model.Tool, + attach_popup=False + #filterable="advanced" + ), CategoryColumn( "Categories", model_class=model.Category, attach_popup=False, @@ -177,15 +187,20 @@ model_class=model.Event, attach_popup=False ), UserColumn( "Uploaded By", - key="username", + #key="username", model_class=model.User, - attach_popup=False, - filterable="advanced" ), + attach_popup=False + #filterable="advanced" + ), # Columns that are valid for filtering but are not visible. - grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) + grids.DeletedColumn( "Deleted", + key="deleted", + visible=False, + filterable="advanced" ) ] columns.append( grids.MulticolFilterColumn( "Search", - cols_to_filter=[ columns[0], columns[1] ], + #cols_to_filter=[ columns[0], columns[2], columns[5] ], + cols_to_filter=[], key="free-text-search", visible=False, filterable="standard" ) ) @@ -199,30 +214,24 @@ grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), grids.GridColumnFilter( "All", args=dict( deleted='All' ) ) ] - default_filter = dict( name="All", deleted="False", username="All" ) + default_filter = dict( name="All", deleted="False" ) num_rows_per_page = 50 preserve_state = False use_paging = True def build_initial_query( self, session ): return session.query( self.model_class ) def apply_default_filter( self, trans, query, **kwd ): - def filter_query( query, tool_id ): - if str( tool_id ).lower() in [ '', 'none' ]: - # Return an empty query since the current user cannot view any - # tools (possibly due to state not being approved, etc). - return query.filter( model.Tool.id == None ) - tool_id = util.listify( tool_id ) - query = query.filter( or_( *map( lambda id: self.model_class.id == id, tool_id ) ) ) - return query.filter( self.model_class.deleted==False ) - tool_id = kwd.get( 'tool_id', False ) - if not tool_id: + ids = kwd.get( 'ids', False ) + if not ids: # Display only approved tools - tool_id = get_approved_tools( trans ) - if not tool_id: - tool_id = 'None' - return filter_query( query, tool_id ) + ids = get_approved_tools( trans ) + if not ids or str( ids ).lower() == 'none': + return query.filter( trans.model.Tool.id == None ) + ids = util.listify( ids ) + query = query.filter( or_( *map( lambda id: self.model_class.id == id, ids ) ) ) + return query -class CategoryListGrid( grids.Grid ): +class ToolsByCategoryListGrid( grids.Grid ): class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, category ): return category.name @@ -242,28 +251,36 @@ # Grid definition webapp = "community" - title = "Tool Categories" + title = "Tools by Category" model_class = model.Category template='/webapps/community/category/grid.mako' default_sort_key = "name" columns = [ NameColumn( "Name", - key="name", + # TODO: we cannot currently sort by columns since the grid may be filtered by tool ids + # and it is not clear if / how that will work. We need to be able to send to the grid helper + # the list of ids on which to filter when sorting on the column. + #key="name", model_class=model.Category, link=( lambda item: dict( operation="Browse Category", id=item.id, webapp="community" ) ), - attach_popup=False, - filterable="advanced" ), + attach_popup=False + #filterable="advanced" + ), DescriptionColumn( "Description", - key="description", - model_class=model.Category, - attach_popup=False, - filterable="advanced" ), + #key="description", + model_class=model.Category, + attach_popup=False + #filterable="advanced" + ), ToolsColumn( "Tools", model_class=model.Tool, attach_popup=False, filterable="advanced" ), # Columns that are valid for filtering but are not visible. - grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) + grids.DeletedColumn( "Deleted", + key="deleted", + visible=False, + filterable="advanced" ) ] columns.append( grids.MulticolFilterColumn( "Search", cols_to_filter=[ columns[0], columns[1] ], @@ -280,14 +297,12 @@ use_paging = True def build_initial_query( self, session ): return session.query( self.model_class ) - def apply_default_filter( self, trans, query, **kwd ): - return query.filter( self.model_class.deleted==False ) class ToolController( BaseController ): tool_list_grid = ToolListGrid() tools_by_user_list_grid = ToolsByUserListGrid() - category_list_grid = CategoryListGrid() + tools_by_category_list_grid = ToolsByCategoryListGrid() @web.expose def index( self, trans, **kwd ): @@ -312,7 +327,7 @@ cntrller='tool', **kwd ) ) # Render the list view - return self.category_list_grid( trans, **kwd ) + return self.tools_by_category_list_grid( trans, **kwd ) @web.expose def browse_category( self, trans, **kwd ): return trans.response.send_redirect( web.url_for( controller='common', diff -r 68fc85a43bb8 -r c7607fba91b9 lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py Tue May 04 14:19:44 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/upload.py Tue May 04 14:21:21 2010 -0400 @@ -60,28 +60,26 @@ obj = datatype.create_model_object( meta ) trans.sa_session.add( obj ) if isinstance( obj, trans.app.model.Tool ): - existing = trans.sa_session.query( trans.app.model.Tool ).filter_by( tool_id = meta.id ).all() + existing = trans.sa_session.query( trans.app.model.Tool ).filter_by( tool_id = meta.id ).first() if existing and replace_id is None: raise UploadError( 'A tool with the same ID already exists. If you are trying to update this tool to a new version, please use the upload form on the "Edit Tool" page. Otherwise, please choose a new ID.' ) elif existing: - replace_version = trans.sa_session.query( trans.app.model.Tool ).get( int( trans.app.security.decode_id( replace_id ) ) ) + replace_version = trans.sa_session.query( trans.app.model.Tool ).get( trans.security.decode_id( replace_id ) ) if replace_version.newer_version: # If the user has picked an old version, switch to the newest version replace_version = get_versions( trans, replace_version )[0] - if trans.user != replace_version.user: - raise UploadError( 'You are not the owner of this tool and may not upload new versions of it.' ) if replace_version.tool_id != meta.id: - raise UploadError( 'The new tool id (%s) does not match the old tool id (%s). Please check the tool XML file' % ( meta.id, replace_version.tool_id ) ) + raise UploadError( 'The new tool id (%s) does not match the old tool id (%s). Check the tool XML file' % ( meta.id, replace_version.tool_id ) ) for old_version in get_versions( trans, replace_version ): if old_version.version == meta.version: - raise UploadError( 'The new version (%s) matches an old version. Please check your version in the tool XML file' % meta.version ) + raise UploadError( 'The new version (%s) matches an old version. Check your version in the tool XML file' % meta.version ) if old_version.is_new(): - raise UploadError( 'There is an existing version of this tool which is unsubmitted. Please either <a href="%s">submit or delete it</a> before uploading a new version.' % url_for( controller='common', - action='view_tool', - cntrller='tool', - id=trans.app.security.encode_id( old_version.id ) ) ) + raise UploadError( 'There is an existing version of this tool which has not yet been submitted for approval, so either <a href="%s">submit or delete it</a> before uploading a new version.' % url_for( controller='common', + action='view_tool', + cntrller='tool', + id=trans.security.encode_id( old_version.id ) ) ) if old_version.is_waiting(): - raise UploadError( 'There is an existing version of this tool which is waiting for administrative approval. Please contact an administrator for help.' ) + raise UploadError( 'There is an existing version of this tool which is waiting for administrative approval, so contact an administrator for help.' ) # Defer setting the id since the newer version id doesn't exist until the new Tool object is flushed if category_ids: for category_id in category_ids: @@ -91,12 +89,15 @@ trans.sa_session.add( tca ) # Initialize the tool event event = trans.app.model.Event( state=trans.app.model.Tool.states.NEW ) + # Flush to get an event id + trans.sa_session.add( event ) + trans.sa_session.flush() tea = trans.app.model.ToolEventAssociation( obj, event ) - trans.sa_session.add_all( ( event, tea ) ) - trans.sa_session.flush() + trans.sa_session.add( tea ) if replace_version and replace_id: replace_version.newer_version_id = obj.id - trans.sa_session.flush() + trans.sa_session.add( replace_version ) + trans.sa_session.flush() try: os.link( uploaded_file.name, obj.file_name ) except OSError: @@ -117,10 +118,10 @@ old_version = None for old_version in get_versions( trans, replace_version ): if old_version.is_new(): - message = 'There is an existing version of this tool which is unsubmitted. Please either submit or delete it before uploading a new version.' + message = 'There is an existing version of this tool which has not been submitted for approval, so either submit or delete it before uploading a new version.' break if old_version.is_waiting(): - message = 'There is an existing version of this tool which is waiting for administrative approval. Please contact an administrator for help.' + message = 'There is an existing version of this tool which is waiting for administrative approval, so contact an administrator for help.' break else: old_version = None diff -r 68fc85a43bb8 -r c7607fba91b9 lib/galaxy/webapps/community/model/__init__.py --- a/lib/galaxy/webapps/community/model/__init__.py Tue May 04 14:19:44 2010 -0400 +++ b/lib/galaxy/webapps/community/model/__init__.py Tue May 04 14:21:21 2010 -0400 @@ -94,7 +94,8 @@ APPROVED = 'approved', REJECTED = 'rejected', ARCHIVED = 'archived' ) - def __init__( self, guid=None, tool_id=None, name=None, description=None, user_description=None, category=None, version=None, user_id=None, external_filename=None ): + def __init__( self, guid=None, tool_id=None, name=None, description=None, user_description=None, + category=None, version=None, user_id=None, external_filename=None ): self.guid = guid self.tool_id = tool_id self.name = name or "Unnamed tool" @@ -103,6 +104,7 @@ self.version = version or "1.0.0" self.user_id = user_id self.external_filename = external_filename + self.deleted = False self.__extension = None def get_file_name( self ): if not self.external_filename: diff -r 68fc85a43bb8 -r c7607fba91b9 templates/dataset/display_application/display.mako --- a/templates/dataset/display_application/display.mako Tue May 04 14:19:44 2010 -0400 +++ b/templates/dataset/display_application/display.mako Tue May 04 14:21:21 2010 -0400 @@ -1,8 +1,8 @@ <%inherit file="/base.mako"/> <%namespace file="/message.mako" import="render_msg" /> <%def name="title()">Display Application: ${display_link.link.display_application.name} ${display_link.link.name}</%def> -%for message, message_type in msg: - ${render_msg( message, message_type )} +%for message, status in msg: + ${render_msg( message, status )} %endfor %if refresh: <%def name="metas()"><meta http-equiv="refresh" content="10" /></%def> diff -r 68fc85a43bb8 -r c7607fba91b9 templates/display_common.mako --- a/templates/display_common.mako Tue May 04 14:19:44 2010 -0400 +++ b/templates/display_common.mako Tue May 04 14:21:21 2010 -0400 @@ -129,10 +129,10 @@ </%def> ## Render message. -<%def name="render_message( message, message_type )"> +<%def name="render_message( message, status )"> %if message: <p> - <div class="${message_type}message transient-message">${util.restore_text( message )}</div> + <div class="${status}message transient-message">${util.restore_text( message )}</div> <div style="clear: both"></div> </p> %endif diff -r 68fc85a43bb8 -r c7607fba91b9 templates/grid_base.mako --- a/templates/grid_base.mako Tue May 04 14:19:44 2010 -0400 +++ b/templates/grid_base.mako Tue May 04 14:21:21 2010 -0400 @@ -508,12 +508,10 @@ webapp = href_parms[index].split('=')[1]; } } - // Do operation. do_operation(webapp, operation, id); return false; } - } // Navigate window to the URL defined by url_args. This method should be used to short-circuit grid AJAXing. @@ -678,7 +676,7 @@ <tr> <td width="75%">${self.render_grid_header( grid )}</td> <td></td> - <td width="25%" id="grid-message" valign="top">${render_message( message, message_type )}</td> + <td width="25%" id="grid-message" valign="top">${render_message( message, status )}</td> </tr> </table> @@ -774,10 +772,6 @@ ## Render grid table body contents. <%def name="render_grid_table_body_contents(grid, show_item_checkboxes=False)"> - ## Include the webapp value in the form - <td style="width: 1.5em;"> - <input type="hidden" name="webapp" value="${webapp}" /> - </td> <% num_rows_rendered = 0 %> %if query.count() == 0: ## No results. @@ -801,12 +795,8 @@ %for column in grid.columns: %if column.visible: <% - # Get filter params for generating filter links - filter_params = {} - for k, v in cur_filter_dict.items(): - filter_params['f-' + k] = v # Link - link = column.get_link( trans, grid, item, filter_params ) + link = column.get_link( trans, grid, item ) if link: href = url( **link ) else: @@ -831,6 +821,7 @@ cls = "menubutton" if column.attach_popup and href: cls = "menubutton split" + %> %if href: <td><div id="${id}" class="${cls}" style="float: left;"><a class="label" href="${href}">${v}</a></div></td> @@ -915,3 +906,4 @@ </tr> %endif </%def> + diff -r 68fc85a43bb8 -r c7607fba91b9 templates/grid_base_async.mako --- a/templates/grid_base_async.mako Tue May 04 14:19:44 2010 -0400 +++ b/templates/grid_base_async.mako Tue May 04 14:21:21 2010 -0400 @@ -13,4 +13,4 @@ ***** ${num_pages} ***** -${render_message( message, message_type )} \ No newline at end of file +${render_message( message, status )} \ No newline at end of file diff -r 68fc85a43bb8 -r c7607fba91b9 templates/message.mako --- a/templates/message.mako Tue May 04 14:19:44 2010 -0400 +++ b/templates/message.mako Tue May 04 14:21:21 2010 -0400 @@ -66,21 +66,21 @@ ## <%def name="center_panel()"> - ${render_large_message( message, message_type )} + ${render_large_message( message, status )} </%def> <%def name="body()"> - ${render_large_message( message, message_type )} + ${render_large_message( message, status )} </%def> ## Render large message. -<%def name="render_large_message( message, message_type )"> - <div class="${message_type}messagelarge" style="margin: 1em">${_(message)}</div> +<%def name="render_large_message( message, status )"> + <div class="${status}messagelarge" style="margin: 1em">${_(message)}</div> </%def> ## Render a message -<%def name="render_msg( msg, messagetype='done' )"> - <div class="${messagetype}message">${_(msg)}</div> +<%def name="render_msg( msg, status='done' )"> + <div class="${status}message">${_(msg)}</div> <br/> </%def> diff -r 68fc85a43bb8 -r c7607fba91b9 templates/page/select_items_grid_async.mako --- a/templates/page/select_items_grid_async.mako Tue May 04 14:19:44 2010 -0400 +++ b/templates/page/select_items_grid_async.mako Tue May 04 14:21:21 2010 -0400 @@ -6,4 +6,4 @@ ***** ${num_pages} ***** -${render_message( message, message_type )} \ No newline at end of file +${render_message( message, status )} \ No newline at end of file diff -r 68fc85a43bb8 -r c7607fba91b9 templates/webapps/community/admin/center.mako --- a/templates/webapps/community/admin/center.mako Tue May 04 14:19:44 2010 -0400 +++ b/templates/webapps/community/admin/center.mako Tue May 04 14:21:21 2010 -0400 @@ -6,7 +6,36 @@ <p>The menu on the left provides the following features</p> <ul> - <li><strong>Security</strong> - see the <strong>Data Security and Data Libraries</strong> section below for details + <li> + <strong>Tools</strong> + <p/> + <ul> + <li> + <strong>Tools awaiting approval</strong> + </li> + <p/> + <li> + <strong>Browse by category</strong> + </li> + <p/> + <li> + <strong>Browse all tools</strong> + </li> + <p/> + </ul> + </li> + <li> + <strong>Categories</strong> + <p/> + <ul> + <li> + <strong>Manage categories</strong> + </li> + <p/> + </ul> + </li> + <li> + <strong>Security</strong> <p/> <ul> <li> @@ -29,13 +58,5 @@ </ul> </li> <p/> - <li><strong>Tools</strong> - <p/> - <ul> - <li> - <strong>Manage tools</strong> - coming soon... - </li> - </ul> - </li> </ul> <br/> diff -r 68fc85a43bb8 -r c7607fba91b9 templates/webapps/community/tool/edit_tool.mako --- a/templates/webapps/community/tool/edit_tool.mako Tue May 04 14:19:44 2010 -0400 +++ b/templates/webapps/community/tool/edit_tool.mako Tue May 04 14:21:21 2010 -0400 @@ -51,16 +51,21 @@ ${render_msg( message, status )} %endif -%if cntrller == 'admin' or ( tool.is_new() and trans.user == tool.user ): +%if cntrller == 'admin' or trans.user == tool.user: <form id="edit_tool" name="edit_tool" action="${h.url_for( controller='common', action='edit_tool' )}" method="post"> <div class="toolForm"> <div class="toolFormTitle">${tool.name} - <a id="tool-${tool.id}-popup" class="popup-arrow" style="display: none;">▼</a> - <div popupmenu="tool-${tool.id}-popup"> - <a class="action-button" href="${h.url_for( controller='common', action='view_tool', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">View information</a> - <a class="action-button" href="${h.url_for( controller='common', action='upload_new_tool_version', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">Upload a new version</a> - <a class="action-button" href="${h.url_for( controller='tool', action='download_tool', id=trans.app.security.encode_id( tool.id ) )}">Download tool</a> - </div> + %if not tool.deleted: + <a id="tool-${tool.id}-popup" class="popup-arrow" style="display: none;">▼</a> + <div popupmenu="tool-${tool.id}-popup"> + <a class="action-button" href="${h.url_for( controller='common', action='view_tool', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">View information</a> + <a class="action-button" href="${h.url_for( controller='tool', action='download_tool', id=trans.app.security.encode_id( tool.id ) )}">Download tool</a> + <a class="action-button" href="${h.url_for( controller='common', action='delete_tool', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">Delete tool</a> + %if not tool.is_new() and not tool.is_waiting(): + <a class="action-button" href="${h.url_for( controller='common', action='upload_new_tool_version', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">Upload a new version</a> + %endif + </div> + %endif </div> <div class="toolFormBody"> <input type="hidden" name="id" value="${trans.app.security.encode_id( tool.id )}"/> diff -r 68fc85a43bb8 -r c7607fba91b9 templates/webapps/community/tool/view_tool.mako --- a/templates/webapps/community/tool/view_tool.mako Tue May 04 14:19:44 2010 -0400 +++ b/templates/webapps/community/tool/view_tool.mako Tue May 04 14:21:21 2010 -0400 @@ -85,16 +85,21 @@ <div class="toolForm"> <div class="toolFormTitle">${tool.name} - <a id="tool-${tool.id}-popup" class="popup-arrow" style="display: none;">▼</a> - <div popupmenu="tool-${tool.id}-popup"> - %if cntrller=='admin' or can_edit: - <a class="action-button" href="${h.url_for( controller='common', action='edit_tool', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">Edit information</a> - %endif - %if cntrller=='admin' or can_upload_new_version: - <a class="action-button" href="${h.url_for( controller='common', action='upload_new_tool_version', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">Upload a new version</a> - %endif - <a class="action-button" href="${h.url_for( controller='tool', action='download_tool', id=trans.app.security.encode_id( tool.id ) )}">Download tool</a> - </div> + %if not tool.deleted: + <a id="tool-${tool.id}-popup" class="popup-arrow" style="display: none;">▼</a> + <div popupmenu="tool-${tool.id}-popup"> + %if cntrller=='admin' or can_edit: + <a class="action-button" href="${h.url_for( controller='common', action='edit_tool', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">Edit information</a> + %endif + <a class="action-button" href="${h.url_for( controller='tool', action='download_tool', id=trans.app.security.encode_id( tool.id ) )}">Download tool</a> + %if cntrller=='admin' or trans.user==tool.user: + <a class="action-button" href="${h.url_for( controller='common', action='delete_tool', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">Delete tool</a> + %endif + %if cntrller=='admin' or can_upload_new_version: + <a class="action-button" href="${h.url_for( controller='common', action='upload_new_tool_version', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">Upload a new version</a> + %endif + </div> + %endif </div> <div class="toolFormBody"> <div class="form-row">

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