Mercurial > repos > bgruening > diffbind
changeset 15:aefe2a771a95 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 10052765d6b712cf7d38356af4251fcc38a339b6-dirty
| author | bgruening |
|---|---|
| date | Fri, 26 Feb 2016 13:35:28 -0500 |
| parents | 4de6355eca00 |
| children | 128584543be7 |
| files | diffbind.tar.bz2 diffbind.xml tool_dependencies.xml |
| diffstat | 3 files changed, 47 insertions(+), 29 deletions(-) [+] |
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--- a/diffbind.xml Sat Mar 15 05:21:59 2014 -0400 +++ b/diffbind.xml Fri Feb 26 13:35:28 2016 -0500 @@ -6,37 +6,38 @@ <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> - <requirement type="set_environment">DIFFBIND_SCRIPT_PATH</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 \$DIFFBIND_SCRIPT_PATH/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> @@ -50,7 +51,7 @@ <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"> @@ -82,21 +83,41 @@ </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>
--- a/tool_dependencies.xml Sat Mar 15 05:21:59 2014 -0400 +++ b/tool_dependencies.xml Fri Feb 26 13:35:28 2016 -0500 @@ -1,19 +1,16 @@ <?xml version="1.0"?> <tool_dependency> <package name="R" version="3.0.3"> - <repository changeset_revision="232ebc8b1c0d" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="9a289bea9051" name="package_r_3_0_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="deseq2" version="1.2.10"> - <repository changeset_revision="2d3eb2823bf7" name="package_deseq2_1_2_10" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="e8df6ebba5ff" name="package_deseq2_1_2_10" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> - <set_environment version="1.0"> - <environment_variable action="set_to" name="DIFFBIND_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable> - </set_environment> <package name="diffbind" version="1.8.3"> <install version="1.0"> <actions> <action type="setup_r_environment"> - <repository changeset_revision="232ebc8b1c0d" name="package_r_3_0_3" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu"> + <repository changeset_revision="9a289bea9051" name="package_r_3_0_3" owner="iuc" toolshed="https://testtoolshed.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>