details: http://www.bx.psu.edu/hg/galaxy/rev/8d3037d55621 changeset: 2711:8d3037d55621 user: Anton Nekrutenko <anton@bx.psu.edu> date: Fri Sep 18 10:27:03 2009 -0400 description: First pass of consolidating NGS tools 2 file(s) affected in this change: tool_conf.xml.sample tools/samtools/sam2interval.xml diffs (117 lines): diff -r cf02fb92ee6a -r 8d3037d55621 tool_conf.xml.sample --- a/tool_conf.xml.sample Fri Sep 18 10:15:09 2009 -0400 +++ b/tool_conf.xml.sample Fri Sep 18 10:27:03 2009 -0400 @@ -19,14 +19,6 @@ <tool file="data_source/epigraph_import_test.xml" /> <tool file="data_source/hbvar.xml" /> <tool file="validation/fix_errors.xml" /> - </section> - <section name="Get ENCODE Data" id="encode"> - <tool file="data_source/encode_import_chromatin_and_chromosomes.xml"/> - <tool file="data_source/encode_import_genes_and_transcripts.xml"/> - <tool file="data_source/encode_import_multi-species_sequence_analysis.xml"/> - <tool file="data_source/encode_import_transcription_regulation.xml"/> - <tool file="data_source/encode_import_all_latest_datasets.xml" /> - <tool file="data_source/encode_import_gencode.xml" /> </section> <section name="Send Data" id="send"> <tool file="data_destination/epigraph.xml" /> @@ -167,17 +159,63 @@ <tool file="taxonomy/lca.xml" /> <tool file="taxonomy/poisson2test.xml" /> </section> - <section name="Solexa tools" id="solexa_tools"> - <tool file="sr_mapping/fastq_statistics.xml" /> - <tool file="sr_mapping/lastz_wrapper.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: FASTQ QC and manipulation" id="cshl_library_information"> + <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="fastx_toolkit/fasta_clipping_histogram.xml" /> --> + <tool file="fastx_toolkit/fastq_to_fasta.xml" /> + <tool file="fastx_toolkit/fastq_quality_converter.xml" /> + <!-- <tool file="fastx_toolkit/fastx_clipper.xml" /> --> + <tool file="fastx_toolkit/fastx_trimmer.xml" /> + <tool file="fastx_toolkit/fastx_renamer.xml" /> + <tool file="fastx_toolkit/fastx_reverse_complement.xml" /> + <tool file="fastx_toolkit/fastx_artifacts_filter.xml" /> + <tool file="fastx_toolkit/fastq_quality_filter.xml" /> + <!--<tool file="fastx_toolkit/fastx_barcode_splitter.xml" />--> + <tool file="metag_tools/split_paired_reads.xml" /> + </section> + <section name="454: QC" id="short_read_analysis"> + <tool file="metag_tools/short_reads_figure_score.xml" /> + <tool file="metag_tools/short_reads_trim_seq.xml" /> + </section> + <section name="SOLiD: QC" id="solid_tools"> + <tool file="solid_tools/solid_qual_stats.xml" /> + <tool file="solid_tools/solid_qual_boxplot.xml" /> + <tool file="solid_tools/maq_cs_wrapper.xml" /> + </section> + <section name="NGS: Mapping" id="solexa_tools"> + <tool file="sr_mapping/lastz_wrapper.xml" /> + <tool file="metag_tools/megablast_wrapper.xml" /> + <tool file="metag_tools/megablast_xml_parser.xml" /> + <tool file="sr_mapping/bowtie_wrapper.xml" /> + <tool file="sr_mapping/bwa_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" /> + </section> +<!-- TODO: uncomment the following EMBOSS section whenever moving to test, but comment it in .sample to eliminate it from buildbot functional tests since these tools rarely change. - --> - <!-- +--> +<!-- <section name="EMBOSS" id="EMBOSSLite"> <tool file="emboss_5/emboss_antigenic.xml" /> <tool file="emboss_5/emboss_backtranseq.xml" /> @@ -287,6 +325,9 @@ <tool file="emboss_5/emboss_wordcount.xml" /> <tool file="emboss_5/emboss_wordmatch.xml" /> </section> +<<<<<<< local +--> +======= --> <section name="SOLiD Data Analysis" id="solid_tools"> <tool file="solid_tools/solid_qual_stats.xml" /> @@ -351,4 +392,5 @@ <tool file="samtools/pileup_parser.xml" /> <tool file="samtools/pileup_interval.xml" /> </section> +>>>>>>> other </toolbox> diff -r cf02fb92ee6a -r 8d3037d55621 tools/samtools/sam2interval.xml --- a/tools/samtools/sam2interval.xml Fri Sep 18 10:15:09 2009 -0400 +++ b/tools/samtools/sam2interval.xml Fri Sep 18 10:27:03 2009 -0400 @@ -31,7 +31,7 @@ **What it does** -Converts positional information from a SAM dataset into interval format with 0-based start and 1-based end. To calculate the end position the tool uses the CIGAR string. +Converts positional information from a SAM dataset into interval format with 0-based start and 1-based end. CIGAR string of SAM format is usd to compute the end coordinate. -----