diff SpecLibCreator.xml @ 0:564a6acb89e8 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/SpecLibCreator.xml	Wed Mar 01 12:36:58 2017 -0500
@@ -0,0 +1,59 @@
+<?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="SpecLibCreator" name="SpecLibCreator" version="2.1.0">
+  <description>Creates an MSP formatted spectral library.</description>
+  <macros>
+    <token name="@EXECUTABLE@">SpecLibCreator</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="references"/>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>SpecLibCreator
+
+#if $param_info:
+  -info $param_info
+#end if
+#if $param_itemseperator:
+  -itemseperator     "$param_itemseperator"
+#end if
+#if $param_itemenclosed:
+  -itemenclosed
+#end if
+#if $param_spec:
+  -spec $param_spec
+#end if
+#if $param_out:
+  -out $param_out
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_force:
+  -force
+#end if
+#end if
+</command>
+  <inputs>
+    <param name="param_info" type="data" format="tabular" optional="False" label="Holds id, peptide, retention time etc" help="(-info) "/>
+    <param name="param_itemseperator" type="text" size="30" value="," label=" Seperator between items. e.g. ," help="(-itemseperator) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <param name="param_itemenclosed" display="radio" type="boolean" truevalue="-itemenclosed" falsevalue="" checked="false" optional="True" label="'true' or 'false' if true every item is enclosed" help="(-itemenclosed) e.g. '$peptide$,$run$"/>
+    <param name="param_spec" type="data" format="mzxml" optional="False" label="spectra" help="(-spec) "/>
+    <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="msp"/>
+  </outputs>
+  <help>Creates an MSP formatted spectral library.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_SpecLibCreator.html</help>
+</tool>