diff XFDR.xml @ 0:b19847e8f0a1 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/XFDR.xml	Mon Feb 12 13:27:44 2018 -0500
@@ -0,0 +1,72 @@
+<?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>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 http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_XFDR.html</help>
+</tool>