diff SeedListGenerator.xml @ 0:c82757bc39d7 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/SeedListGenerator.xml	Mon Feb 12 13:50:06 2018 -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 CTDConverter.-->
+<!--Proposed Tool Section: [Quantitation]-->
+<tool id="SeedListGenerator" name="SeedListGenerator" version="2.3.0">
+  <description>Generates seed lists for feature detection.</description>
+  <macros>
+    <token name="@EXECUTABLE@">SeedListGenerator</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="references"/>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>SeedListGenerator
+
+#if $param_in:
+  -in $param_in
+#end if
+
+#if $rep_param_out:
+-out
+  #for token in $rep_param_out:
+    #if " " in str(token):
+      "$token.param_out"
+    #else
+      $token.param_out
+    #end if
+  #end for
+#end if
+#if $param_use_peptide_mass:
+  -use_peptide_mass
+#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="mzml,idxml,featurexml,consensusxml" optional="False" label="Input file (see below for details)" help="(-in) "/>
+    <param name="param_use_peptide_mass" display="radio" type="boolean" truevalue="-use_peptide_mass" falsevalue="" checked="false" optional="True" label="[idXML input only] Use the monoisotopic mass of the best peptide hit for the m/z position (default: use precursor m/z)" help="(-use_peptide_mass) "/>
+    <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>Generates seed lists for feature detection.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_SeedListGenerator.html</help>
+</tool>