diff IDSplitter.xml @ 14:ae90bc9b7936 draft default tip

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

--- a/IDSplitter.xml	Thu Dec 01 19:02:51 2022 +0000
+++ b/IDSplitter.xml	Fri Jun 14 21:39:18 2024 +0000
@@ -1,6 +1,5 @@
-<?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: [File Filtering / Extraction / Merging]-->
 <tool id="IDSplitter" name="IDSplitter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Splits protein/peptide identifications off of annotated data files</description>
   <macros>
@@ -15,7 +14,7 @@
 
 ## 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($in.ext)' &&
 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir out &&
 #end if
@@ -58,10 +57,10 @@
     <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,mzml" optional="false" label="Input file (data annotated with identifications)" help=" select consensusxml,featurexml,mzml data sets(s)"/>
+    <param argument="-in" type="data" format="consensusxml,featurexml,mzml" label="Input file (data annotated with identifications)" help=" select consensusxml,featurexml,mzml 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>
@@ -85,26 +84,30 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- UTILS_IDSplitter_1 -->
+  <tests>
+    <!-- TOPP_IDSplitter_1 -->
     <test expect_num_outputs="3">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDMapper_1_output.featureXML"/>
-      <output name="out" file="IDSplitter_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
-      <output name="id_out" file="IDSplitter_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDSplitter_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="id_out" value="IDSplitter_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,id_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
         <assert_contents>
           <is_valid_xml/>
         </assert_contents>
       </output>
+      <assert_stdout>
+        <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
+      </assert_stdout>
     </test>
   </tests>
   <help><![CDATA[Splits protein/peptide identifications off of annotated data files
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_IDSplitter.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_IDSplitter.html]]></help>
   <expand macro="references"/>
 </tool>