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="Deprecated: Generic FASTQ data" id="fastq" /> + <tool file="next_gen_conversion/fastq_gen_conv.xml" /> + <tool file="fastx_toolkit/fastq_quality_converter.xml" /> + <tool file="fastx_toolkit/fastx_quality_statistics.xml" /> + <tool file="fastx_toolkit/fastq_quality_boxplot.xml" /> + <tool file="fastx_toolkit/fastx_nucleotides_distribution.xml" /> + <tool file="metag_tools/split_paired_reads.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"/>