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view XFDR.xml @ 2:7c6217c5b13f draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
author | galaxyp |
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date | Wed, 15 May 2019 08:27:06 -0400 |
parents | b19847e8f0a1 |
children | 81402a5e4173 |
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<?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>