diff CVInspector.xml @ 0:7fd35becd995 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/CVInspector.xml	Wed Mar 01 10:07:15 2017 -0500
@@ -0,0 +1,94 @@
+<?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="CVInspector" name="CVInspector" version="2.1.0">
+  <description>A tool for visualization and validation of PSI mapping and CV files.</description>
+  <macros>
+    <token name="@EXECUTABLE@">CVInspector</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="references"/>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>CVInspector
+
+-cv_files
+  #for token in $param_cv_files:
+    $token
+  #end for
+
+#if $rep_param_cv_names:
+-cv_names
+  #for token in $rep_param_cv_names:
+    #if " " in str(token):
+      "$token.param_cv_names"
+    #else
+      $token.param_cv_names
+    #end if
+  #end for
+#end if
+#if $param_mapping_file:
+  -mapping_file $param_mapping_file
+#end if
+
+#if $rep_param_ignore_cv:
+-ignore_cv
+  #for token in $rep_param_ignore_cv:
+    #if " " in str(token):
+      "$token.param_ignore_cv"
+    #else
+      $token.param_ignore_cv
+    #end if
+  #end for
+#end if
+#if $param_html:
+  -html $param_html
+#end if
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_force:
+  -force
+#end if
+#end if
+</command>
+  <inputs>
+    <param name="param_cv_files" type="data" format="" multiple="true" optional="False" size="30" label="List of ontology files in OBO format" help="(-cv_files) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <repeat name="rep_param_cv_names" min="1" max="1" title="param_cv_names">
+      <param name="param_cv_names" type="text" size="30" label="List of identifiers (one for each ontology file)" help="(-cv_names) ">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+    </repeat>
+    <param name="param_mapping_file" type="data" format="xml" optional="True" label="Mapping file in CVMapping (XML) format" help="(-mapping_file) "/>
+    <repeat name="rep_param_ignore_cv" min="0" max="1" title="param_ignore_cv">
+      <param name="param_ignore_cv" type="text" size="30" value="UO PATO BTO" label="A list of CV identifiers which should be ignored" help="(-ignore_cv) ">
+        <sanitizer>
+          <valid initial="string.printable">
+            <remove value="'"/>
+            <remove value="&quot;"/>
+          </valid>
+        </sanitizer>
+      </param>
+    </repeat>
+    <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_html" format="html"/>
+  </outputs>
+  <help>A tool for visualization and validation of PSI mapping and CV files.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_CVInspector.html</help>
+</tool>