jamm.xml

<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>