diff MapNormalizer.xml @ 14:4b603a44b009 draft default tip

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

--- a/MapNormalizer.xml	Thu Dec 01 19:23:57 2022 +0000
+++ b/MapNormalizer.xml	Fri Jun 14 21:43:20 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: [Signal processing and preprocessing]-->
+<!--Proposed Tool Section: [Spectrum processing: peak smoothing / normalization]-->
 <tool id="MapNormalizer" name="MapNormalizer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Normalizes peak intensities in an MS run.</description>
+  <description>Normalizes peak intensities in an MS run</description>
   <macros>
     <token name="@EXECUTABLE@">MapNormalizer</token>
     <import>macros.xml</import>
@@ -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)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,10 +38,10 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/>
+    <param argument="-in" type="data" format="mzml" label="input file" help=" select 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>
@@ -56,25 +55,29 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_MapNormalizer_1 -->
+  <tests>
+    <!-- TOPP_MapNormalizer_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
         <param name="test" value="true"/>
       </section>
       <param name="in" value="MapNormalizer_input.mzML"/>
-      <output name="out" file="MapNormalizer.tmp" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="MapNormalizer_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_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[Normalizes peak intensities in an MS run.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MapNormalizer.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MapNormalizer.html]]></help>
   <expand macro="references"/>
 </tool>