view QCCalculator.xml @ 0:3d84209d3178 draft

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<?xml version='1.0' encoding='UTF-8'?>
<tool id="QCCalculator" name="QCCalculator" version="1.12.0">
  <description>Calculates basic quality parameters from MS experiments and subsequent analysis data as identification or feature detection.</description>
  <macros>
    <token name="@EXECUTABLE@">QCCalculator</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>QCCalculator

-in ${param_in}
-out ${param_out}
-id ${param_id}
-feature ${param_feature}
-consensus ${param_consensus}
${param_remove_duplicate_features}
-threads \${GALAXY_SLOTS:-24} 
</command>
  <inputs>
    <param name="param_in" type="data" format="mzML" optional="False" label="raw data input file (this is relevant if you want to look at MS1, MS2 and precursor peak information)" help="(-in)"/>
    <param name="param_id" type="data" format="idXML" optional="True" label="Input idXML file containing the identifications. Your identifications will be exported in an easy-to-read format" help="(-id)"/>
    <param name="param_feature" type="data" format="featureXML" optional="True" label="feature input file (this is relevant for most QC issues)" help="(-feature)"/>
    <param name="param_consensus" type="data" format="consensusXML" optional="True" label="consensus input file (this is only used for charge state deconvoluted output. Use the consensusXML output form the DeCharger)" help="(-consensus)"/>
    <param name="param_remove_duplicate_features" type="boolean" truevalue="-remove_duplicate_features true" falsevalue="-remove_duplicate_features false" checked="false" optional="True" label="This flag should be set, if you work with a set of merged features." help="(-remove_duplicate_features)"/>
  </inputs>
  <outputs>
    <data name="param_out" label="Your qcML file." format="data"/>
  </outputs>
  <help>**What it does**

Calculates basic quality parameters from MS experiments and subsequent analysis data as identification or feature detection.


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_QCCalculator.html

@REFERENCES@
</help>
</tool>