Mercurial > repos > messersc > jamm
view jamm.xml @ 1:243f75d0ed6e draft default tip
Uploaded.
Includes new release 1.0.7 with fixed optional controls.
author | messersc |
---|---|
date | Thu, 19 Feb 2015 05:39:45 -0500 |
parents | d42f4d78c85e |
children |
line wrap: on
line source
<tool id="jamm" name="JAMM" version="1.0.7"> <description>Calls peaks on NGS data</description> <requirements> <requirement>R</requirement> <requirement>perl</requirement> </requirements> <command interpreter="python"> <![CDATA[ jammwrapper.py -i #for $x in $input ${x.replicate.file_name} #end for #for $x in $control -c ${x.controlreplicate.file_name} #end for -g ${genomeSizeFile} -o $output -of $outputfiltered -m $mode -r $resolution -p $processes -t $type -f $fraglen -b $binsize ]]> </command> <stdio> <!-- Wrapper ensures anything other than zero is an error --> <exit_code range="1:" /> <exit_code range=":-1" /> </stdio> <inputs> <repeat name="input" title="Sample Replicates"> <param name="replicate" type="data" format="bed"></param> </repeat> <repeat name="control" title="Negative Control Replicates (e.g. input) - optional"> <param name="controlreplicate" type="data" format="bed"></param> </repeat> <param name="genomeSizeFile" type="data" label="File indicating chromosome sizes" description="Chromosome size"></param> <param name="mode" type="select" label="Mode (normal or narrow)"> <option value="normal">normal</option> <option value="narrow">narrow</option> </param> <param name="resolution" type="select" label="Resolution (peak or region)"> <option value="peak">peak</option> <option value="region">region</option> <option value="window">window</option> </param> <param name="type" type="select" label="Type of data (Single or paired. Paired requires BEDPE datasets)"> <option value="single" selected="true">single</option> <option value="paired">paired</option> </param> <param name="fraglen" type="text" value="ns" label="Fragment length. Estimated by default (ns)" /> <param name="binsize" type="text" value="ns" label="Bin size. Estimated by default (ns)" /> <param name="processes" type="text" value="4" label="Number of threads used by R" help="Depending on your Galaxy configuration, 1 should be safe and up to 4 should be fine." /> </inputs> <outputs> <data name="output" format="tabular" label="Narrowpeak tabular" /> <data name="outputfiltered" format="tabular" label="Narrowpeak tabular filtered" /> </outputs> <tests> <test> <param name="replicate" value="test1.bed" ftype="bed"/> <param name="replicate" value="test2.bed" ftype="bed"/> <param name="genomeSizeFile" value="chrSizes21.csize"/> <output name="output" ftype="tabular"> <assert_contents> <has_text text="chr21" /> </assert_contents> </output> </test> <test> <param name="replicate" value="test1.bed" ftype="bed"/> <param name="replicate" value="test2.bed" ftype="bed"/> <param name="controlreplicate" value="control.bed" /> <param name="genomeSizeFile" value="chrSizes21.csize"/> <param name="resolution" value="region" /> <output name="output" ftype="tabular"> <assert_contents> <has_text text="chr21" /> </assert_contents> </output> </test> </tests> <citations> <!-- Example of annotating a citation using a DOI. --> <citation type="doi">10.1093/bioinformatics/btu568</citation> </citations> <help> **What it does** JAMM calls peaks on NGS data, i.e. for finding binding sites. .. class:: warningmark This tool requires files in *bed* format. .. class:: infomark If you are just starting out, you can find some sensible parameter choices here: http://code.google.com/p/jamm-peak-finder/wiki/Usage#Examples * ChIP-Seq TF: everything default * ChIP-Seq HM: Binsize=200 * ChIP-Seq Broad HM: Binsize=200 Resolution=region * ChIP-Seq Very Broad HM: Binsize=10000 Resolution=window * DNase-seq: Fragment length=1 </help> </tool>