annotate XFDR.xml @ 3:0fb75f784e2d draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5-dirty

<?xml version='1.0' encoding='UTF-8'?>
<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
<!--Proposed Tool Section: [Utilities]-->
<tool id="XFDR" name="XFDR" version="2.3.0">
  <description>Calculates false discovery rate estimates on crosslink identifications</description>
  <macros>
    <token name="@EXECUTABLE@">XFDR</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command detect_errors="aggressive"><![CDATA[XFDR

#if $param_in:
  -in $param_in
#end if
#if $param_out_idXML:
  -out_idXML $param_out_idXML
#end if
#if $param_out_mzIdentML:
  -out_mzIdentML $param_out_mzIdentML
#end if
#if $param_minborder:
  -minborder $param_minborder
#end if
#if $param_maxborder:
  -maxborder $param_maxborder
#end if
#if $param_mindeltas:
  -mindeltas $param_mindeltas
#end if
#if $param_minionsmatched:
  -minionsmatched $param_minionsmatched
#end if
#if $param_uniquexl:
  -uniquexl
#end if
#if $param_no_qvalues:
  -no_qvalues
#end if
#if $param_minscore:
  -minscore $param_minscore
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
]]></command>
  <inputs>
    <param name="param_in" type="data" format="xml,idxml,mzid" optional="True" label="Crosslink Identifications in either xquest.xml, idXML, or mzIdentML format (as produced by OpenPepXL)" help="(-in) "/>
    <param name="param_minborder" type="integer" value="-1" label="Filter for minimum precursor mass error (ppm)" help="(-minborder) Can only be applied for xquest.xml input"/>
    <param name="param_maxborder" type="integer" value="-1" label="Filter for maximum precursor mass error (ppm)" help="(-maxborder) Can only be applied for xquest.xml input"/>
    <param name="param_mindeltas" type="float" min="0.0" max="1.0" optional="True" value="0.0" label="Filter for delta score, 0 is no filte" help="(-mindeltas) Minimum delta score required, hits are rejected if larger or equal. Can only be applied for xquest.xml input"/>
    <param name="param_minionsmatched" type="integer" min="0" optional="True" value="0" label="Filter for minimum matched ions per peptide" help="(-minionsmatched) Can only be applied for xquest.xml input"/>
    <param name="param_uniquexl" display="radio" type="boolean" truevalue="-uniquexl" falsevalue="" checked="false" optional="True" label="Calculate statistics based on unique IDs" help="(-uniquexl) Can only be applied for xquest.xml input"/>
    <param name="param_no_qvalues" display="radio" type="boolean" truevalue="-no_qvalues" falsevalue="" checked="false" optional="True" label="Do not transform simple FDR to q-values" help="(-no_qvalues) "/>
    <param name="param_minscore" type="integer" value="0" label="Minimum score to be considered for FDR calculation" help="(-minscore) "/>
    <expand macro="advanced_options">
      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out_idXML" format="idxml"/>
    <data name="param_out_mzIdentML" format="mzid"/>
  </outputs>
  <help>Calculates false discovery rate estimates on crosslink identifications


For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_XFDR.html</help>
</tool>