diff IDConflictResolver.xml @ 16:5c9e1b5d3b95 draft default tip

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

--- a/IDConflictResolver.xml	Thu Dec 01 19:09:05 2022 +0000
+++ b/IDConflictResolver.xml	Fri Jun 14 21:41:35 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: [ID Processing]-->
+<!--Proposed Tool Section: [Identification Processing]-->
 <tool id="IDConflictResolver" name="IDConflictResolver" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Resolves ambiguous annotations of features with peptide identifications</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)' &&
 mkdir out &&
 
 ## Main program call
@@ -39,15 +38,15 @@
     <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" optional="false" label="Input file (data annotated with identifications)" help=" select consensusxml,featurexml data sets(s)"/>
-    <param argument="-resolve_between_features" type="select" optional="true" label="A map may contain multiple features with both identical (possibly modified" help="i.e. not stripped) sequence and charge state. The feature with the 'highest intensity' is very likely the most reliable one. When switched on, the filter removes the sequence annotation from the lower intensity features, thereby resolving the multiplicity. Only the most reliable features for each (possibly modified i.e. not stripped) sequence maintain annotated with this peptide sequence">
+    <param argument="-in" type="data" format="consensusxml,featurexml" label="Input file (data annotated with identifications)" help=" select consensusxml,featurexml data sets(s)"/>
+    <param argument="-resolve_between_features" type="select" label="A map may contain multiple features with both identical (possibly modified" help="i.e. not stripped) sequence and charge state. The feature with the 'highest intensity' is very likely the most reliable one. When switched on, the filter removes the sequence annotation from the lower intensity features, thereby resolving the multiplicity. Only the most reliable features for each (possibly modified i.e. not stripped) sequence maintain annotated with this peptide sequence">
       <option value="off" selected="true">off</option>
       <option value="highest_intensity">highest_intensity</option>
       <expand macro="list_string_san" name="resolve_between_features"/>
     </param>
     <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>
@@ -61,14 +60,15 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_IDConflictResolver_1 -->
+  <tests>
+    <!-- TOPP_IDConflictResolver_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="IDConflictResolver_1_input.featureXML"/>
-      <output name="out" file="IDConflictResolver_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="IDConflictResolver_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="resolve_between_features" value="off"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -76,6 +76,9 @@
           <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>
     <!-- TOPP_IDConflictResolver_2 -->
     <test expect_num_outputs="2">
@@ -84,7 +87,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDConflictResolver_2_input.consensusXML"/>
-      <output name="out" file="IDConflictResolver_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="IDConflictResolver_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="resolve_between_features" value="off"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -92,6 +95,9 @@
           <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>
     <!-- TOPP_IDConflictResolver_3 -->
     <test expect_num_outputs="2">
@@ -100,7 +106,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDConflictResolver_3_input.consensusXML"/>
-      <output name="out" file="IDConflictResolver_3_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="IDConflictResolver_3_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="resolve_between_features" value="off"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -108,6 +114,9 @@
           <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>
     <!-- TOPP_IDConflictResolver_4 -->
     <test expect_num_outputs="2">
@@ -116,7 +125,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="IDConflictResolver_4_input.featureXML"/>
-      <output name="out" file="IDConflictResolver_4_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="IDConflictResolver_4_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="resolve_between_features" value="highest_intensity"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -124,11 +133,14 @@
           <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[Resolves ambiguous annotations of features with peptide identifications
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_IDConflictResolver.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_IDConflictResolver.html]]></help>
   <expand macro="references"/>
 </tool>