diff IDExtractor.xml @ 0:f42812df11d8 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/IDExtractor.xml	Wed Mar 01 12:58:44 2017 -0500
@@ -0,0 +1,52 @@
+<?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: [Utilities]-->
+<tool id="IDExtractor" name="IDExtractor" version="2.1.0">
+  <description>Extracts 'n' peptides randomly or best 'n' from idXML files.</description>
+  <macros>
+    <token name="@EXECUTABLE@">IDExtractor</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="references"/>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>IDExtractor
+
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $param_number_of_peptides:
+  -number_of_peptides $param_number_of_peptides
+#end if
+#if $param_number_of_rand_invokations:
+  -number_of_rand_invokations $param_number_of_rand_invokations
+#end if
+#if $param_best_hits:
+  -best_hits
+#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="idxml" optional="False" label="input file" help="(-in) "/>
+    <param name="param_number_of_peptides" type="integer" min="1" optional="True" value="10" label="Number of randomly chosen peptides" help="(-number_of_peptides) "/>
+    <param name="param_number_of_rand_invokations" type="integer" min="0" optional="True" value="0" label="Number of rand invocations before random draw" help="(-number_of_rand_invokations) "/>
+    <param name="param_best_hits" display="radio" type="boolean" truevalue="-best_hits" falsevalue="" checked="false" optional="True" label="If this flag is set the best n peptides are chosen" help="(-best_hits) "/>
+    <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="idxml"/>
+  </outputs>
+  <help>Extracts 'n' peptides randomly or best 'n' from idXML files.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_IDExtractor.html</help>
+</tool>