view RNPxlXICFilter.xml @ 0:3d84209d3178 draft

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<?xml version='1.0' encoding='UTF-8'?>
<tool id="RNPxlXICFilter" name="RNPxlXICFilter" version="1.12.0">
  <description>Remove MS2 spectra from treatment based on the fold change between control and treatment.</description>
  <macros>
    <token name="@EXECUTABLE@">RNPxlXICFilter</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>RNPxlXICFilter

-control ${param_control}
-treatment ${param_treatment}
-fold_change ${param_fold_change}
-rt_tol ${param_rt_tol}
-mz_tol ${param_mz_tol}
-out ${param_out}
-threads \${GALAXY_SLOTS:-24} 
</command>
  <inputs>
    <param name="param_control" type="data" format="mzML" optional="False" label="input mzML file" help="(-control)"/>
    <param name="param_treatment" type="data" format="mzML" optional="False" label="input mzML file" help="(-treatment)"/>
    <param name="param_fold_change" type="float" value="2.0" label="fold change between XICs" help="(-fold_change)"/>
    <param name="param_rt_tol" type="float" value="20.0" label="RT tolerance in [s] for finding max peak (whole RT range around RT middle)" help="(-rt_tol)"/>
    <param name="param_mz_tol" type="float" value="10.0" label="m/z tolerance in [ppm] for finding a peak" help="(-mz_tol)"/>
  </inputs>
  <outputs>
    <data name="param_out" label="output of the treatment file after XIC filtering." format="mzML"/>
  </outputs>
  <help>**What it does**

Remove MS2 spectra from treatment based on the fold change between control and treatment.


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

@REFERENCES@
</help>
</tool>