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modified:
diffbind.R diffbind.xml tool_dependencies.xml |
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| diff -r 7faaf4a5e4e1 -r 9e9f85c20d99 diffbind.R --- a/diffbind.R Thu Jan 16 04:15:09 2014 -0500 +++ b/diffbind.R Tue Sep 08 05:38:45 2015 -0400 |
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| @@ -27,9 +27,7 @@ q(status=1); } - library('DiffBind') -# used to save to BED, GFF or WIG format if ( !is.null(opt$plots) ) { pdf(opt$plots) |
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| diff -r 7faaf4a5e4e1 -r 9e9f85c20d99 diffbind.xml --- a/diffbind.xml Thu Jan 16 04:15:09 2014 -0500 +++ b/diffbind.xml Tue Sep 08 05:38:45 2015 -0400 |
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| @@ -1,41 +1,41 @@ -<tool id="diffbind" name="DiffBind" version="2.0.1"> +<tool id="diffbind" name="DiffBind" version="2.0.2"> <description> differential binding analysis of ChIP-Seq peak data</description> <requirements> - <requirement type="binary">Rscript</requirement> - <requirement type="R-module">DESeq2</requirement> - <requirement type="package" version="3.0.1">R_3_0_1</requirement> - <requirement type="package" version="1.0.17">deseq2</requirement> + <requirement type="package" version="3.0.3">R</requirement> + <requirement type="package" version="1.2.10">deseq2</requirement> <requirement type="package" version="1.8.3">diffbind</requirement> </requirements> <command> +<![CDATA[ ## seems that diffbind also needs file extensions to work properly #set $counter = 1 #for $sample in $samples: - ln -s $sample.bamreads #echo str($counter) + "_bamreads.bam"# && - ln -s ${sample.bamreads.metadata.bam_index} #echo str($counter) + "_bamreads.bai"# && - ln -s $sample.bamcontrol #echo str($counter) + "_bamcontrol.bam"# && - ln -s ${sample.bamcontrol.metadata.bam_index} #echo str($counter) + "_bamcontrol.bai"# && + ln -s $sample.bamreads #echo str($counter) + "_bamreads.bam"# && + ln -s ${sample.bamreads.metadata.bam_index} #echo str($counter) + "_bamreads.bai"# && + ln -s $sample.bamcontrol #echo str($counter) + "_bamcontrol.bam"# && + ln -s ${sample.bamcontrol.metadata.bam_index} #echo str($counter) + "_bamcontrol.bai"# && #set $counter = $counter + 1 #end for - Rscript /usr/local/galaxy/shed_tools/testtoolshed.g2.bx.psu.edu/repos/bgruening/diffbind/7929c8b3f6f9/diffbind/diffbind.R + Rscript $__tool_directory__/diffbind.R -i $infile -o $outfile -p $plots -f $format +]]> </command> <stdio> - <regex match="Execution halted" - source="both" - level="fatal" + <regex match="Execution halted" + source="both" + level="fatal" description="Execution halted." /> - <regex match="Input-Error 01" - source="both" - level="fatal" + <regex match="Input-Error 01" + source="both" + level="fatal" description="Error in your input parameters: Make sure you only apply factors to selected samples." /> - <regex match="Error in" - source="both" - level="fatal" + <regex match="Error in" + source="both" + level="fatal" description="An undefined error occured, please check your intput carefully and contact your administrator." /> </stdio> <inputs> @@ -49,7 +49,7 @@ <param format="bam" name="bamcontrol" type="data" label="Control BAM file" help="Specify the Control BAM file, used for Peak calling."/> <param format="bed" name="peaks" type="data" label="Peak file" help="Result of your Peak calling experiment."/> </repeat> - <param name="pdf" type="boolean" truevalue="" falsevalue="" checked="true" + <param name="pdf" type="boolean" truevalue="" falsevalue="" checked="true" label="Visualising the analysis results" help="output an additional PDF files" /> <param name="format" type="select" label="Output Format"> @@ -81,21 +81,41 @@ </outputs> <help> - -.. class:: infomark - -**What it does** +<![CDATA[ ------- +**What it does** + +Diffbind provides functions for processing ChIP-Seq data enriched for genomic loci where specific protein/DNA binding occurs, including peak sets identified by ChIP-Seq peak callers and aligned sequence read datasets. + +**Input** + +- You have to specify your samples. Here is one example: + +ID Tissue Factor Condition Treatment Replicate Caller Intervals +BT4741 BT474 ER Resistant Full-Media 1 raw 1084 + +- BAM file which contains the mapped sequencing reads can be associated with each +peakset -**References** +- Control BAM file represents a control dataset + +- Peak file: Result of your Peak calling experiment + + +**Output** -DiffBind_ Authors: Rory Stark, Gordon Brown +As output format you can choose BED, GFF, WIG. + + +**References** + +DiffBind_ Authors: Rory Stark, Gordon Brown (2011) .. _DiffBind: http://www.bioconductor.org/packages/release/bioc/html/DiffBind.html Wrapper authors: Bjoern Gruening, Pavankumar Videm +]]> </help> </tool> |
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| diff -r 7faaf4a5e4e1 -r 9e9f85c20d99 tool_dependencies.xml --- a/tool_dependencies.xml Thu Jan 16 04:15:09 2014 -0500 +++ b/tool_dependencies.xml Tue Sep 08 05:38:45 2015 -0400 |
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| @@ -1,18 +1,17 @@ <?xml version="1.0"?> <tool_dependency> - <package name="R_3_0_1" version="3.0.1"> - <repository changeset_revision="c5ff6dd33c79" name="package_r_3_0_1" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> + <package name="R" version="3.0.3"> + <repository changeset_revision="a8438aa1207c" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <package name="deseq2" version="1.0.17"> - <repository changeset_revision="0e80b1827773" name="package_deseq2_1_0_17" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> + <package name="deseq2" version="1.2.10"> + <repository changeset_revision="2d4a7ae561d6" name="package_deseq2_1_2_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <package name="diffbind" version="1.8.3"> <install version="1.0"> <actions> <action type="setup_r_environment"> - <repository changeset_revision="c5ff6dd33c79" name="package_r_3_0_1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu"> - <package name="R_3_0_1" version="3.0.1" /> + <repository changeset_revision="a8438aa1207c" name="package_r_3_0_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="R" version="3.0.3" /> </repository> <package>https://github.com/bgruening/download_store/raw/master/DiffBind-1_8_3/BiocGenerics_0.8.0.tar.gz</package> <package>https://github.com/bgruening/download_store/raw/master/DiffBind-1_8_3/IRanges_1.20.6.tar.gz</package> |