2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/eec910f20a4e/ changeset: r5575:eec910f20a4e user: fubar date: 2011-05-17 18:52:24 summary: separated ngs picard tools and removed fastqc wrapper lgpl annotation affected #: 2 files (192 bytes) --- a/tool_conf.xml.sample Tue May 17 12:14:32 2011 -0400 +++ b/tool_conf.xml.sample Tue May 17 12:52:24 2011 -0400 @@ -242,19 +242,6 @@ <section name="NGS: QC and manipulation" id="NGS_QC"><label text="FastQC: fastq/sam/bam" id="fastqcsambam" /><tool file="rgenetics/rgFastQC.xml" /> - <label text="QC/Metrics for sam/bam" id="qcsambam"/> - <tool file="picard/picard_BamIndexStats.xml" /> - <tool file="picard/rgPicardASMetrics.xml" /> - <tool file="picard/rgPicardGCBiasMetrics.xml" /> - <tool file="picard/rgPicardLibComplexity.xml" /> - <tool file="picard/rgPicardInsertSize.xml" /> - <tool file="picard/rgPicardHsMetrics.xml" /> - <label text="bam/sam Cleaning" id="picard-tools" /> - <tool file="picard/picard_AddOrReplaceReadGroups.xml" /> - <tool file="picard/picard_ReorderSam.xml" /> - <tool file="picard/picard_ReplaceSamHeader.xml" /> - <tool file="picard/rgPicardFixMate.xml" /> - <tool file="picard/rgPicardMarkDups.xml" /><label text="Illumina fastq" id="illumina" /><tool file="fastq/fastq_groomer.xml" /><tool file="fastq/fastq_paired_end_splitter.xml" /> @@ -293,6 +280,21 @@ <tool file="fastx_toolkit/fastx_reverse_complement.xml" /><tool file="fastx_toolkit/fastx_trimmer.xml" /></section> + <section name="NGS: Picard (beta)" id="picard_beta"> + <label text="QC/Metrics for sam/bam" id="qcsambam"/> + <tool file="picard/picard_BamIndexStats.xml" /> + <tool file="picard/rgPicardASMetrics.xml" /> + <tool file="picard/rgPicardGCBiasMetrics.xml" /> + <tool file="picard/rgPicardLibComplexity.xml" /> + <tool file="picard/rgPicardInsertSize.xml" /> + <tool file="picard/rgPicardHsMetrics.xml" /> + <label text="bam/sam Cleaning" id="picard-clean" /> + <tool file="picard/picard_AddOrReplaceReadGroups.xml" /> + <tool file="picard/picard_ReorderSam.xml" /> + <tool file="picard/picard_ReplaceSamHeader.xml" /> + <tool file="picard/rgPicardFixMate.xml" /> + <tool file="picard/rgPicardMarkDups.xml" /> + </section><!-- Keep this section commented until it includes tools that will be hosted on test/main. The velvet wrappers have been --- a/tools/rgenetics/rgFastQC.xml Tue May 17 12:14:32 2011 -0400 +++ b/tools/rgenetics/rgFastQC.xml Tue May 17 12:52:24 2011 -0400 @@ -55,15 +55,10 @@ This Galaxy tool wrapper is part of the rgenetics toolkit. Contaminants file parameter borrowed from the independently -developed fastqcwrapper contributed to the galaxy community tool shed +developed fastqcwrapper_ contributed to the galaxy community tool shed by j johnson -copyright Ross Lazarus at g mail dot com 2011 -Licensed under the LGPL_ - .. _fastqcwrapper: http%3A//community.g2.bx.psu.edu/tool/browse_tools%3F%26webapp%3Dcommunity%26operation%3Dview_tool%26id%3D256f9f17b153ce60 -.. _LGPL: http://www.gnu.org/copyleft/lesser.html - </help></tool> http://bitbucket.org/galaxy/galaxy-central/changeset/fa0480c6a01d/ changeset: r5576:fa0480c6a01d user: fubar date: 2011-05-17 19:04:35 summary: cleaned up picard tool names - own section so (picard) was redundant affected #: 12 files (349 bytes) --- a/tools/picard/picard_AddOrReplaceReadGroups.xml Tue May 17 12:52:24 2011 -0400 +++ b/tools/picard/picard_AddOrReplaceReadGroups.xml Tue May 17 13:04:35 2011 -0400 @@ -1,6 +1,5 @@ -<tool name="Add or Replace Groups:" id="picard_ARRG" version="0.2.0"> +<tool name="Add or Replace Groups" id="picard_ARRG" version="0.2.0"><requirements><requirement type="package">picard</requirement></requirements> - <description>(Picard)</description><command interpreter="python"> picard_wrapper.py --input="$inputFile" --- a/tools/picard/picard_BamIndexStats.xml Tue May 17 12:52:24 2011 -0400 +++ b/tools/picard/picard_BamIndexStats.xml Tue May 17 13:04:35 2011 -0400 @@ -1,6 +1,5 @@ -<tool name="BAM Index Statistics:" id="picard_BamIndexStats" version="0.2.0"> +<tool name="BAM Index Statistics" id="picard_BamIndexStats" version="0.2.0"><requirements><requirement type="package">picard</requirement></requirements> - <description>(Picard)</description><command interpreter="python"> picard_wrapper.py --input "$input_file" --- a/tools/picard/picard_MarkDuplicates.xml Tue May 17 12:52:24 2011 -0400 +++ b/tools/picard/picard_MarkDuplicates.xml Tue May 17 13:04:35 2011 -0400 @@ -1,5 +1,4 @@ -<tool name="Mark Duplicates:" id="picard_MarkDuplicates" version="0.01"> - <description>(Picard)</description> +<tool name="Mark Duplicates" id="picard_MarkDuplicates" version="0.01"><command interpreter="python"> picard_wrapper.py --input="$input_file" --- a/tools/picard/picard_ReorderSam.xml Tue May 17 12:52:24 2011 -0400 +++ b/tools/picard/picard_ReorderSam.xml Tue May 17 13:04:35 2011 -0400 @@ -1,6 +1,5 @@ -<tool name="Reorder SAM:" id="picard_ReorderSam" version="0.3.0"> +<tool name="Reorder SAM" id="picard_ReorderSam" version="0.3.0"><requirements><requirement type="package">picard</requirement></requirements> - <description>(Picard)</description><command interpreter="python"> picard_wrapper.py --input=$inputFile --- a/tools/picard/picard_ReplaceSamHeader.xml Tue May 17 12:52:24 2011 -0400 +++ b/tools/picard/picard_ReplaceSamHeader.xml Tue May 17 13:04:35 2011 -0400 @@ -1,6 +1,5 @@ -<tool name="Replace Sam Header:" id="picard_ReplaceSamHeader" version="0.2.0"> +<tool name="Replace Sam Header" id="picard_ReplaceSamHeader" version="0.2.0"><requirements><requirement type="package">picard</requirement></requirements> - <description>(Picard)</description><command interpreter="python"> picard_wrapper.py --input "$inputFile" --- a/tools/picard/rgPicardASMetrics.xml Tue May 17 12:52:24 2011 -0400 +++ b/tools/picard/rgPicardASMetrics.xml Tue May 17 13:04:35 2011 -0400 @@ -1,5 +1,4 @@ -<tool name="Sam/bam Alignment Summary Metrics:" id="PicardASMetrics" version="0.03"> - <description>(Picard)</description> +<tool name="Sam/bam Alignment Summary Metrics" id="PicardASMetrics" version="0.03"><command interpreter="python"> picard_wrapper.py -i "$input_file" -d "$html_file.files_path" -t "$html_file" --assumesorted "$sorted" -b "$bisulphite" --adaptors "$adaptors" --maxinsert "$maxinsert" -n "$out_prefix" --- a/tools/picard/rgPicardFixMate.xml Tue May 17 12:52:24 2011 -0400 +++ b/tools/picard/rgPicardFixMate.xml Tue May 17 13:04:35 2011 -0400 @@ -1,4 +1,4 @@ -<tool name="Paired Read Mate Fixer:" id="rgPicFixMate" version="0.2.0"> +<tool name="Paired Read Mate Fixer" id="rgPicFixMate" version="0.2.0"><description>for paired data</description><command interpreter="python"> picard_wrapper.py -i "$input_file" -o "$out_file" --tmpdir "${__new_file_path__}" -n "$out_prefix" --- a/tools/picard/rgPicardGCBiasMetrics.xml Tue May 17 12:52:24 2011 -0400 +++ b/tools/picard/rgPicardGCBiasMetrics.xml Tue May 17 13:04:35 2011 -0400 @@ -1,5 +1,4 @@ -<tool name="Sam/bam GC Bias Metrics:" id="PicardGCBiasMetrics" version="0.01"> - <description>(Picard)</description> +<tool name="Sam/bam GC Bias Metrics" id="PicardGCBiasMetrics" version="0.01"><command interpreter="python"> picard_wrapper.py -i "$input_file" -d "$html_file.files_path" -t "$html_file" --windowsize "$windowsize" --mingenomefrac "$mingenomefrac" -n "$out_prefix" --tmpdir "${__new_file_path__}" --- a/tools/picard/rgPicardHsMetrics.xml Tue May 17 12:52:24 2011 -0400 +++ b/tools/picard/rgPicardHsMetrics.xml Tue May 17 13:04:35 2011 -0400 @@ -1,4 +1,4 @@ -<tool name="Sam/bam Hybrid Selection Metrics:" id="PicardHsMetrics" version="0.01"> +<tool name="Sam/bam Hybrid Selection Metrics" id="PicardHsMetrics" version="0.01"><description>For (eg exome) targeted data</description><command interpreter="python"> --- a/tools/picard/rgPicardInsertSize.xml Tue May 17 12:52:24 2011 -0400 +++ b/tools/picard/rgPicardInsertSize.xml Tue May 17 13:04:35 2011 -0400 @@ -1,4 +1,4 @@ -<tool name="Insertion size metrics:" id="PicardInsertSize" version="0.3.0"> +<tool name="Insertion size metrics" id="PicardInsertSize" version="0.3.0"><description>for PAIRED data</description><requirements><requirement type="package">picard</requirement></requirements><command interpreter="python"> --- a/tools/picard/rgPicardLibComplexity.xml Tue May 17 12:52:24 2011 -0400 +++ b/tools/picard/rgPicardLibComplexity.xml Tue May 17 13:04:35 2011 -0400 @@ -1,5 +1,4 @@ -<tool name="Estimate Library Complexity:" id="rgEstLibComp" version="0.01"> - <description>(Picard)</description> +<tool name="Estimate Library Complexity" id="rgEstLibComp" version="0.01"><command interpreter="python"> picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" --minid "$minIDbases" --maxdiff "$maxDiff" --minmeanq "$minMeanQ" --readregex "$readRegex" --optdupdist "$optDupeDist" --- a/tools/picard/rgPicardMarkDups.xml Tue May 17 12:52:24 2011 -0400 +++ b/tools/picard/rgPicardMarkDups.xml Tue May 17 13:04:35 2011 -0400 @@ -1,5 +1,4 @@ -<tool name="Mark Duplicates:" id="rgPicardMarkDups" version="0.01"> - <description>(Picard)</description> +<tool name="Mark Duplicate reads" id="rgPicardMarkDups" version="0.01"><command interpreter="python"> picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" -o "$out_file" --remdups "$remDups" --assumesorted "$assumeSorted" --readregex "$readRegex" --optdupdist "$optDupeDist" Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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