diff IDMerger.xml @ 16:bdcdd2a5ea43 draft default tip

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

--- a/IDMerger.xml	Thu Dec 01 19:18:45 2022 +0000
+++ b/IDMerger.xml	Fri Jun 14 21:40:49 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: [File Handling]-->
+<!--Proposed Tool Section: [File Filtering / Extraction / Merging]-->
 <tool id="IDMerger" name="IDMerger" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Merges several protein/peptide identification files into one file.</description>
+  <description>Merges several protein/peptide identification files into one file</description>
   <macros>
     <token name="@EXECUTABLE@">IDMerger</token>
     <import>macros.xml</import>
@@ -17,14 +16,14 @@
 mkdir in_cond.in &&
 #if $in_cond.in_select == "no"
 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} && 
-${' '.join(["ln -s '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
+${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
 #else
-ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
+cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
 #end if
 mkdir out &&
 #if $add_to:
   mkdir add_to &&
-  ln -s '$add_to' 'add_to/${re.sub("[^\w\-_]", "_", $add_to.element_identifier)}.$gxy2omsext($add_to.ext)' &&
+  cp '$add_to' 'add_to/${re.sub("[^\w\-_]", "_", $add_to.element_identifier)}.$gxy2omsext($add_to.ext)' &&
 #end if
 
 ## Main program call
@@ -62,15 +61,16 @@
         <option value="yes">Yes: process each dataset in an independent job</option>
       </param>
       <when value="no">
-        <param argument="-in" type="data" format="idxml,sqlite" multiple="true" optional="false" label="Input files separated by blanks (all must have the same type)" help=" select idxml,sqlite data sets(s)"/>
+        <param argument="-in" type="data" format="idxml,sqlite" multiple="true" label="Input files separated by blanks (all must have the same type)" help=" select idxml,sqlite data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-in" type="data" format="idxml,sqlite" multiple="false" optional="false" label="Input files separated by blanks (all must have the same type)" help=" select idxml,sqlite data sets(s)"/>
+        <param argument="-in" type="data" format="idxml,sqlite" label="Input files separated by blanks (all must have the same type)" help=" select idxml,sqlite data sets(s)"/>
       </when>
     </conditional>
-    <param argument="-out_type" display="radio" type="select" optional="false" label="Output file type (default: determined from file extension)" help="">
+    <param argument="-out_type" type="select" label="Output file type (default: determined from file extension)" help="">
       <option value="idXML">idxml</option>
       <option value="oms">sqlite (oms)</option>
+      <validator type="expression" message="A value needs to be selected">value != "select a value"</validator>
       <expand macro="list_string_san" name="out_type"/>
     </param>
     <param argument="-add_to" type="data" format="idxml" optional="true" label="Optional input file" help="IDs from 'in' are added to this file, but only if the (modified) peptide sequences are not present yet (considering only best hits per spectrum) select idxml data sets(s)"/>
@@ -79,7 +79,7 @@
     <param argument="-merge_proteins_add_PSMs" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Merge all identified proteins by accession into one protein identification run but keep all the PSMs with updated links to potential new protein ID#s" help="Not compatible with 'add_to'"/>
     <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>
@@ -97,7 +97,8 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_IDMerger_1 -->
+  <tests>
+    <!-- TOPP_IDMerger_1 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -106,7 +107,7 @@
       <conditional name="in_cond">
         <param name="in" value="IDMerger_1_input1.idXML,IDMerger_1_input2.idXML"/>
       </conditional>
-      <output name="out" file="IDMerger_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDMerger_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="out_type" value="idXML"/>
       <param name="annotate_file_origin" value="true"/>
       <param name="pepxml_protxml" value="false"/>
@@ -117,6 +118,9 @@
           <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_IDMerger_2 -->
     <test expect_num_outputs="2">
@@ -127,7 +131,7 @@
       <conditional name="in_cond">
         <param name="in" value="IDMerger_2_input1.idXML,IDMerger_2_input2.idXML"/>
       </conditional>
-      <output name="out" file="IDMerger_2_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDMerger_2_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="out_type" value="idXML"/>
       <param name="annotate_file_origin" value="false"/>
       <param name="pepxml_protxml" value="true"/>
@@ -138,6 +142,9 @@
           <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_IDMerger_3 -->
     <test expect_num_outputs="2">
@@ -146,9 +153,9 @@
         <param name="test" value="true"/>
       </section>
       <conditional name="in_cond">
-        <param name="in" value="IDMerger_1_input1.idXML,IDMerger_1_input1_2.idXML"/>
+        <param name="in" value="IDMerger_1_input1_0.idXML,IDMerger_1_input1_1.idXML"/>
       </conditional>
-      <output name="out" file="IDMerger_3_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDMerger_3_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="out_type" value="idXML"/>
       <param name="annotate_file_origin" value="false"/>
       <param name="pepxml_protxml" value="false"/>
@@ -159,6 +166,9 @@
           <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_IDMerger_4 -->
     <test expect_num_outputs="2">
@@ -167,9 +177,9 @@
         <param name="test" value="true"/>
       </section>
       <conditional name="in_cond">
-        <param name="in" value="degenerated_empty.idXML,degenerated_empty_2.idXML"/>
+        <param name="in" value="degenerated_empty_0.idXML,degenerated_empty_1.idXML"/>
       </conditional>
-      <output name="out" file="IDMerger_4_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDMerger_4_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="out_type" value="idXML"/>
       <param name="annotate_file_origin" value="false"/>
       <param name="pepxml_protxml" value="false"/>
@@ -180,6 +190,9 @@
           <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_IDMerger_5 -->
     <test expect_num_outputs="2">
@@ -190,7 +203,7 @@
       <conditional name="in_cond">
         <param name="in" value="IDMerger_2_input1.idXML"/>
       </conditional>
-      <output name="out" file="IDMerger_5_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDMerger_5_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="out_type" value="idXML"/>
       <param name="add_to" value="IDMerger_5_input1.idXML"/>
       <param name="annotate_file_origin" value="false"/>
@@ -202,6 +215,9 @@
           <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_IDMerger_6 -->
     <test expect_num_outputs="2">
@@ -212,7 +228,7 @@
       <conditional name="in_cond">
         <param name="in" value="IDMerger_6_input1.oms,IDMerger_6_input2.oms"/>
       </conditional>
-      <output name="out" file="IDMerger_6_output1.oms" compare="sim_size" delta_frac="0.7" ftype="sqlite"/>
+      <output name="out" value="IDMerger_6_output1.oms" compare="sim_size" delta_frac="0.7" ftype="sqlite"/>
       <param name="out_type" value="oms"/>
       <param name="annotate_file_origin" value="true"/>
       <param name="pepxml_protxml" value="false"/>
@@ -223,6 +239,9 @@
           <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_IDRipper_3_prep -->
     <test expect_num_outputs="2">
@@ -233,7 +252,7 @@
       <conditional name="in_cond">
         <param name="in" value="IDRipper_3_input1.idXML,IDRipper_3_input2.idXML"/>
       </conditional>
-      <output name="out" file="IDRipper_3_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
+      <output name="out" value="IDRipper_3_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
       <param name="out_type" value="idXML"/>
       <param name="annotate_file_origin" value="true"/>
       <param name="pepxml_protxml" value="false"/>
@@ -244,11 +263,14 @@
           <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[Merges several protein/peptide identification files into one file.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_IDMerger.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_IDMerger.html]]></help>
   <expand macro="references"/>
 </tool>