diff SemanticValidator.xml @ 0:3070d71e0e5c draft

Uploaded
author bgruening
date Thu, 16 Apr 2015 08:37:04 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SemanticValidator.xml	Thu Apr 16 08:37:04 2015 -0400
@@ -0,0 +1,55 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<tool id="SemanticValidator" name="SemanticValidator" version="2.0.0">
+  <description>SemanticValidator for semantically validating certain XML files.</description>
+  <macros>
+    <token name="@EXECUTABLE@">SemanticValidator</token>
+    <import>macros.xml</import>
+  </macros>
+  <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
+-threads \${GALAXY_SLOTS:-24} 
+#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="xml,traml,mzml" optional="False" label="Input file (any xml file)" help="(-in) "/>
+    <param name="param_mapping_file" type="data" format="xml" 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="obo" 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" 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>**What it does**
+
+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>
+  <expand macro="references"/>
+</tool>