process_ecm.xml

<?xml version="1.0"?>
<tool id="ecm-process" name="Process LCMS data for ECM pipeline" version="1.0" hidden="false">
<description></description>
<requirements>
    <container type="docker">process_ecm</container>
</requirements>

<command>
ID_FILE_TYPE="$idfile.ext" MS_FILE_TYPE="$mzmlfile.ext" ECM_PY_SCRIPT="$__tool_directory__/process_ecm.py" $__tool_directory__/process_ecm.sh $mzmlfile $idfile $ecm_db $protout "$sample_name"
</command>

<inputs>
<param name="sample_name" type="text" label="Sample name"/>
<param name="mzmlfile" type="data" format="mzml" label="mzML File"/>
<param name="idfile" type="data" format="pepxml,mzid,idxml" label="Peptide ID File (pepXML, idXML, mzIdentML)"/>
<param name="ecm_db" type="library_data" format="tabular" label="ECM Annotation Reference"/>
</inputs>

<outputs>
<data format="tabular" name="protout" label="${tool.name} on ${on_string}: Annotated and quantified proteins"/>
</outputs>

<help>
===========
Description
===========

Tool will process mzML and idXML/pepXML file to obtain PSM counts and EIC intensities
for each peptide then annotate proteins using ECM database

usage: ./process_ecm.sh [mzML file] [idXML/pepXML file] [ECM DB file] [output peptide table] [output protein table]

</help>
</tool>