diff OpenSwathRewriteToFeatureXML.xml @ 0:7bc05daed12c draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/OpenSwathRewriteToFeatureXML.xml	Wed Mar 01 10:19:34 2017 -0500
@@ -0,0 +1,48 @@
+<?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 CTD2Galaxy.-->
+<!--Proposed Tool Section: [Targeted Experiments]-->
+<tool id="OpenSwathRewriteToFeatureXML" name="OpenSwathRewriteToFeatureXML" version="2.1.0">
+  <description>Combines featureXML and mProphet tsv to FDR filtered featureXML.</description>
+  <macros>
+    <token name="@EXECUTABLE@">OpenSwathRewriteToFeatureXML</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="references"/>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>OpenSwathRewriteToFeatureXML
+
+#if $param_csv:
+  -csv $param_csv
+#end if
+#if $param_featureXML:
+  -featureXML $param_featureXML
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_FDR_cutoff:
+  -FDR_cutoff $param_FDR_cutoff
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_force:
+  -force
+#end if
+#end if
+</command>
+  <inputs>
+    <param name="param_csv" type="data" format="tabular" optional="True" label="mProphet tsv output file: &quot;all_peakgroups.xls&quot;" help="(-csv) "/>
+    <param name="param_featureXML" type="data" format="featurexml" optional="False" label="input featureXML file" help="(-featureXML) "/>
+    <param name="param_FDR_cutoff" type="float" value="-1.0" label="FDR cutoff (" help="(-FDR_cutoff) e.g. to remove all features with a an m_score above 0.05 use 0.05 here)"/>
+    <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" format="featurexml"/>
+  </outputs>
+  <help>Combines featureXML and mProphet tsv to FDR filtered featureXML.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/doxygen/parameters/output/TOPP_OpenSwathRewriteToFeatureXML.html</help>
+</tool>