diff SemanticValidator.xml @ 0:f5dfeed76b4c 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/SemanticValidator.xml	Wed Mar 01 12:45:53 2017 -0500
@@ -0,0 +1,54 @@
+<?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="SemanticValidator" name="SemanticValidator" version="2.1.0">
+  <description>SemanticValidator for semantically validating certain XML files.</description>
+  <macros>
+    <token name="@EXECUTABLE@">SemanticValidator</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="references"/>
+  <expand macro="stdio"/>
+  <expand macro="requirements"/>
+  <command>SemanticValidator
+
+#if $param_in:
+  -in $param_in
+#end if
+#if $param_mapping_file:
+  -mapping_file $param_mapping_file
+#end if
+-cv
+  #for token in $param_cv:
+    $token
+  #end for
+#if $adv_opts.adv_opts_selector=='advanced':
+    #if $adv_opts.param_force:
+  -force
+#end if
+#end if
+&gt; $param_stdout
+</command>
+  <inputs>
+    <param name="param_in" type="data" format="mzid,traml,mzml" optional="False" label="Input file (any xml file)" help="(-in) "/>
+    <param name="param_mapping_file" type="data" format="" optional="False" label="Mapping file which is used to semantically validate the given XML file against this mapping file (see 'share/OpenMS/MAPPING' for templates)" help="(-mapping_file) "/>
+    <param name="param_cv" type="data" format="" multiple="true" optional="True" size="30" label="Controlled Vocabulary files containg the CV terms (if left empty, a set of default files are used)" help="(-cv) ">
+      <sanitizer>
+        <valid initial="string.printable">
+          <remove value="'"/>
+          <remove value="&quot;"/>
+        </valid>
+      </sanitizer>
+    </param>
+    <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_stdout" format="text" label="Output from stdout"/>
+  </outputs>
+  <help>SemanticValidator for semantically validating certain XML files.
+
+
+For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_SemanticValidator.html</help>
+</tool>