diff XMLValidator.xml @ 14:ad2ba3a95a02 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906

--- a/XMLValidator.xml	Thu Dec 01 19:11:46 2022 +0000
+++ b/XMLValidator.xml	Fri Jun 14 21:37:46 2024 +0000
@@ -1,8 +1,7 @@
-<?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: [Utilities]-->
+<!--Proposed Tool Section: [[for Developers]]-->
 <tool id="XMLValidator" name="XMLValidator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Validates XML files against an XSD schema.</description>
+  <description>Validates XML files against an XSD schema</description>
   <macros>
     <token name="@EXECUTABLE@">XMLValidator</token>
     <import>macros.xml</import>
@@ -15,10 +14,10 @@
 
 ## Preprocessing
 mkdir in &&
-ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 #if $schema:
   mkdir schema &&
-  ln -s '$schema' 'schema/${re.sub("[^\w\-_]", "_", $schema.element_identifier)}.$gxy2omsext($schema.ext)' &&
+  cp '$schema' 'schema/${re.sub("[^\w\-_]", "_", $schema.element_identifier)}.$gxy2omsext($schema.ext)' &&
 #end if
 
 ## Main program call
@@ -44,11 +43,11 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="consensusxml,featurexml,idxml,mzdata,mzid,mzml,mzxml,pepxml,traml,xml" optional="false" label="file to validate" help=" select consensusxml,featurexml,idxml,mzdata,mzid,mzml,mzxml,pepxml,traml,xml data sets(s)"/>
-    <param argument="-schema" type="data" format="xml" optional="true" label="schema to validate against" help="If no schema is given, the file is validated against the latest schema of the file type select xml data sets(s)"/>
+    <param argument="-in" type="data" format="consensusxml,featurexml,idxml,mzdata,mzid,mzml,mzxml,pepxml,traml,xml" label="file to validate" help=" select consensusxml,featurexml,idxml,mzdata,mzid,mzml,mzxml,pepxml,traml,xml data sets(s)"/>
+    <param argument="-schema" type="data" format="xsd" optional="true" label="schema to validate against" help="If no schema is given, the file is validated against the latest schema of the file type select xsd data sets(s)"/>
     <expand macro="adv_opts_macro">
       <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+      <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
         <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
@@ -64,17 +63,32 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><test expect_num_outputs="1"><!-- just chosen an arbitrary input and autgenerated output-->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" ftype="mzml" value="FileFilter_1_input.mzML"/>
-    <output name="stdout" ftype="txt" value="XMLValidator.stdout" lines_diff="4">
-       <assert_contents><has_text text="Success: the file is valid!"/></assert_contents>
-    </output>
-  </test>
-</tests>
+  <tests>
+    <test expect_num_outputs="1">
+      <!-- just chosen an arbitrary input and autgenerated output-->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in" ftype="mzml" value="FileFilter_1_input.mzML"/>
+      <output name="stdout" ftype="txt" value="XMLValidator.stdout" lines_diff="4">
+        <assert_contents>
+          <has_text text="Success: the file is valid!"/>
+        </assert_contents>
+      </output>
+    </test>
+    <test expect_num_outputs="1">
+      <!-- just chosen an arbitrary input and autgenerated output-->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in" ftype="mzml" value="FileFilter_1_input.mzML"/>
+      <param name="schema" ftype="xsd" location="https://raw.githubusercontent.com/HUPO-PSI/mzML/master/schema/schema_1.1/mzML1.1.0.xsd"/>
+      <output name="stdout" ftype="txt" value="XMLValidator.stdout" lines_diff="4">
+        <assert_contents>
+          <has_text text="Success: the file is valid!"/>
+        </assert_contents>
+      </output>
+    </test>
+  </tests>
   <help><![CDATA[Validates XML files against an XSD schema.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_XMLValidator.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_XMLValidator.html]]></help>
   <expand macro="references"/>
 </tool>