diff FileMerger.xml @ 16:0643576e7f51 draft default tip

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

--- a/FileMerger.xml	Thu Dec 01 19:10:42 2022 +0000
+++ b/FileMerger.xml	Fri Jun 14 21:29:46 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: [File Handling]-->
+<!--Proposed Tool Section: [File Filtering / Extraction / Merging]-->
 <tool id="FileMerger" name="FileMerger" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Merges several MS files into one file.</description>
+  <description>Merges several MS files into one file</description>
   <macros>
     <token name="@EXECUTABLE@">FileMerger</token>
     <import>macros.xml</import>
@@ -17,9 +16,9 @@
 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($in_cond.in.ext)' &&
 #end if
 mkdir out &&
 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
@@ -68,13 +67,13 @@
         <option value="yes">Yes: process each dataset in an independent job</option>
       </param>
       <when value="no">
-        <param argument="-in" type="data" format="consensusxml,dta,dta2d,fasta,featurexml,mgf,mzdata,mzml,mzxml,traml" multiple="true" optional="false" label="Input files separated by blank" help=" select consensusxml,dta,dta2d,fasta,featurexml,mgf,mzdata,mzml,mzxml,traml data sets(s)"/>
+        <param argument="-in" type="data" format="consensusxml,dta,dta2d,fasta,featurexml,mgf,mzdata,mzml,mzxml,traml" multiple="true" label="Input files separated by blank" help=" select consensusxml,dta,dta2d,fasta,featurexml,mgf,mzdata,mzml,mzxml,traml data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-in" type="data" format="consensusxml,dta,dta2d,fasta,featurexml,mgf,mzdata,mzml,mzxml,traml" multiple="false" optional="false" label="Input files separated by blank" help=" select consensusxml,dta,dta2d,fasta,featurexml,mgf,mzdata,mzml,mzxml,traml data sets(s)"/>
+        <param argument="-in" type="data" format="consensusxml,dta,dta2d,fasta,featurexml,mgf,mzdata,mzml,mzxml,traml" label="Input files separated by blank" help=" select consensusxml,dta,dta2d,fasta,featurexml,mgf,mzdata,mzml,mzxml,traml data sets(s)"/>
       </when>
     </conditional>
-    <param name="out_type" type="select" optional="false" label="File type of output out (Output file)">
+    <param name="out_type" type="select" label="File type of output out (Output file)">
       <option value="mzML">mzml</option>
       <option value="featureXML">featurexml</option>
       <option value="consensusXML">consensusxml</option>
@@ -82,13 +81,13 @@
       <option value="fasta">fasta</option>
     </param>
     <param argument="-annotate_file_origin" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Store the original filename in each feature using meta value &quot;file_origin&quot; (for featureXML and consensusXML only)" help=""/>
-    <param argument="-append_method" type="select" optional="true" label="(ConsensusXML-only) Append quantitative information about features row-wise or column-wise" help="- 'append_rows' is usually used when the inputs come from the same MS run (e.g. caused by manual splitting or multiple algorithms on the same file). - 'append_cols' when you want to combine consensusXMLs from e.g. different fractions to be summarized in ProteinQuantifier or jointly exported with MzTabExporter">
+    <param argument="-append_method" type="select" label="(ConsensusXML-only) Append quantitative information about features row-wise or column-wise" help="- 'append_rows' is usually used when the inputs come from the same MS run (e.g. caused by manual splitting or multiple algorithms on the same file). - 'append_cols' when you want to combine consensusXMLs from e.g. different fractions to be summarized in ProteinQuantifier or jointly exported with MzTabExporter">
       <option value="append_rows" selected="true">append_rows</option>
       <option value="append_cols">append_cols</option>
       <expand macro="list_string_san" name="append_method"/>
     </param>
     <section name="rt_concat" title="Options for concatenating files in the retention time (RT) dimension" help="The RT ranges of inputs are adjusted so they don't overlap in the merged file (traML input not supported)" expanded="false">
-      <param name="gap" argument="-rt_concat:gap" type="float" optional="true" value="0.0" label="The amount of gap (in seconds) to insert between the RT ranges of different input files" help="RT concatenation is enabled if a value &gt; 0 is set"/>
+      <param name="gap" argument="-rt_concat:gap" type="float" value="0.0" label="The amount of gap (in seconds) to insert between the RT ranges of different input files" help="RT concatenation is enabled if a value &gt; 0 is set"/>
     </section>
     <section name="raw" title="Options for raw data input/output (primarily for DTA files)" help="" expanded="false">
       <param name="rt_auto" argument="-raw:rt_auto" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Assign retention times automatically (integers starting at 1)" help=""/>
@@ -96,11 +95,11 @@
         <expand macro="list_float_valsan" name="rt_custom"/>
       </param>
       <param name="rt_filename" argument="-raw:rt_filename" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Try to guess the retention time of a file based on the filename" help="This option is useful for merging DTA files, where filenames should contain the string 'rt' directly followed by a floating point number, e.g. 'my_spectrum_rt2795.15.dta'"/>
-      <param name="ms_level" argument="-raw:ms_level" type="integer" optional="true" value="0" label="If 1 or higher, this number is assigned to spectra as the MS level" help="This option is useful for DTA files which do not contain MS level information"/>
+      <param name="ms_level" argument="-raw:ms_level" type="integer" value="0" label="If 1 or higher, this number is assigned to spectra as the MS level" help="This option is useful for DTA files which do not contain MS level information"/>
     </section>
     <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>
@@ -126,7 +125,8 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_FileMerger_2 -->
+  <tests>
+    <!-- TOPP_FileMerger_2 -->
     <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="force" value="false"/>
@@ -136,7 +136,7 @@
         <param name="in" value="FileMerger_2_input1.dta,FileMerger_2_input2.dta" ftype="dta"/>
       </conditional>
       <param name="out_type" value="mzML"/>
-      <output name="out" file="FileMerger_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileMerger_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="annotate_file_origin" value="false"/>
       <param name="append_method" value="append_rows"/>
       <section name="rt_concat">
@@ -154,6 +154,9 @@
           <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_FileMerger_3 -->
     <test expect_num_outputs="2">
@@ -165,7 +168,7 @@
         <param name="in" value="FileMerger_3_input1.dta,FileMerger_3_input2.dta" ftype="dta"/>
       </conditional>
       <param name="out_type" value="mzML"/>
-      <output name="out" file="FileMerger_3_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileMerger_3_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="annotate_file_origin" value="false"/>
       <param name="append_method" value="append_rows"/>
       <section name="rt_concat">
@@ -173,7 +176,6 @@
       </section>
       <section name="raw">
         <param name="rt_auto" value="true"/>
-        <param name="rt_custom" value=""/>
         <param name="rt_filename" value="false"/>
         <param name="ms_level" value="0"/>
       </section>
@@ -183,6 +185,9 @@
           <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_FileMerger_4 -->
     <test expect_num_outputs="2">
@@ -194,7 +199,7 @@
         <param name="in" value="FileMerger_4_input1.dta2d,FileMerger_4_input2.dta2d" ftype="dta2d"/>
       </conditional>
       <param name="out_type" value="mzML"/>
-      <output name="out" file="FileMerger_4_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileMerger_4_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="annotate_file_origin" value="false"/>
       <param name="append_method" value="append_rows"/>
       <section name="rt_concat">
@@ -202,7 +207,6 @@
       </section>
       <section name="raw">
         <param name="rt_auto" value="false"/>
-        <param name="rt_custom" value=""/>
         <param name="rt_filename" value="false"/>
         <param name="ms_level" value="0"/>
       </section>
@@ -212,6 +216,9 @@
           <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_FileMerger_5 -->
     <test expect_num_outputs="2">
@@ -223,7 +230,7 @@
         <param name="in" value="FileMerger_5_input_rt1023.331.dta,FileMerger_5_input_rt2044.334.dta,FileMerger_5_input_rt889.32.dta" ftype="dta"/>
       </conditional>
       <param name="out_type" value="mzML"/>
-      <output name="out" file="FileMerger_5_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileMerger_5_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="annotate_file_origin" value="false"/>
       <param name="append_method" value="append_rows"/>
       <section name="rt_concat">
@@ -231,7 +238,6 @@
       </section>
       <section name="raw">
         <param name="rt_auto" value="false"/>
-        <param name="rt_custom" value=""/>
         <param name="rt_filename" value="true"/>
         <param name="ms_level" value="2"/>
       </section>
@@ -241,6 +247,9 @@
           <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_FileMerger_6 -->
     <test expect_num_outputs="2">
@@ -252,7 +261,7 @@
         <param name="in" value="FileMerger_6_input1.mzML,FileMerger_6_input2.mzML"/>
       </conditional>
       <param name="out_type" value="mzML"/>
-      <output name="out" file="FileMerger_6_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileMerger_6_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="annotate_file_origin" value="false"/>
       <param name="append_method" value="append_rows"/>
       <section name="rt_concat">
@@ -260,7 +269,6 @@
       </section>
       <section name="raw">
         <param name="rt_auto" value="false"/>
-        <param name="rt_custom" value=""/>
         <param name="rt_filename" value="false"/>
         <param name="ms_level" value="0"/>
       </section>
@@ -270,6 +278,9 @@
           <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_FileMerger_7 -->
     <test expect_num_outputs="2">
@@ -281,7 +292,7 @@
         <param name="in" value="FileMerger_7_input1.featureXML,FileMerger_7_input2.featureXML"/>
       </conditional>
       <param name="out_type" value="featureXML"/>
-      <output name="out" file="FileMerger_7_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
+      <output name="out" value="FileMerger_7_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
       <param name="annotate_file_origin" value="false"/>
       <param name="append_method" value="append_rows"/>
       <section name="rt_concat">
@@ -289,7 +300,6 @@
       </section>
       <section name="raw">
         <param name="rt_auto" value="false"/>
-        <param name="rt_custom" value=""/>
         <param name="rt_filename" value="false"/>
         <param name="ms_level" value="0"/>
       </section>
@@ -299,6 +309,9 @@
           <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_FileMerger_8 -->
     <test expect_num_outputs="2">
@@ -310,7 +323,7 @@
         <param name="in" value="FileMerger_8_input1.consensusXML,FileMerger_8_input2.consensusXML"/>
       </conditional>
       <param name="out_type" value="consensusXML"/>
-      <output name="out" file="FileMerger_8_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FileMerger_8_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="annotate_file_origin" value="false"/>
       <param name="append_method" value="append_rows"/>
       <section name="rt_concat">
@@ -318,7 +331,6 @@
       </section>
       <section name="raw">
         <param name="rt_auto" value="false"/>
-        <param name="rt_custom" value=""/>
         <param name="rt_filename" value="false"/>
         <param name="ms_level" value="0"/>
       </section>
@@ -328,6 +340,9 @@
           <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_FileMerger_9 -->
     <test expect_num_outputs="2">
@@ -339,7 +354,7 @@
         <param name="in" value="FileMerger_9_input1.traML,FileMerger_9_input2.traML"/>
       </conditional>
       <param name="out_type" value="traML"/>
-      <output name="out" file="FileMerger_9_output.traML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
+      <output name="out" value="FileMerger_9_output.traML" compare="sim_size" delta_frac="0.7" ftype="traml"/>
       <param name="annotate_file_origin" value="false"/>
       <param name="append_method" value="append_rows"/>
       <section name="rt_concat">
@@ -347,7 +362,6 @@
       </section>
       <section name="raw">
         <param name="rt_auto" value="false"/>
-        <param name="rt_custom" value=""/>
         <param name="rt_filename" value="false"/>
         <param name="ms_level" value="0"/>
       </section>
@@ -357,6 +371,9 @@
           <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_FileMerger_10 -->
     <test expect_num_outputs="3">
@@ -365,10 +382,10 @@
         <param name="test" value="true"/>
       </section>
       <conditional name="in_cond">
-        <param name="in" value="FileMerger_6_input2.mzML,FileMerger_6_input2_2.mzML"/>
+        <param name="in" value="FileMerger_6_input2_0.mzML,FileMerger_6_input2_1.mzML"/>
       </conditional>
       <param name="out_type" value="mzML"/>
-      <output name="out" file="FileMerger_10_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
+      <output name="out" value="FileMerger_10_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
       <param name="annotate_file_origin" value="false"/>
       <param name="append_method" value="append_rows"/>
       <section name="rt_concat">
@@ -377,7 +394,6 @@
       <output_collection name="rt_concat_trafo_out" count="2"/>
       <section name="raw">
         <param name="rt_auto" value="false"/>
-        <param name="rt_custom" value=""/>
         <param name="rt_filename" value="false"/>
         <param name="ms_level" value="0"/>
       </section>
@@ -387,6 +403,9 @@
           <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_FileMerger_11 -->
     <test expect_num_outputs="2">
@@ -398,7 +417,7 @@
         <param name="in" value="FileMerger_8_input1.consensusXML,FileMerger_8_input2.consensusXML"/>
       </conditional>
       <param name="out_type" value="consensusXML"/>
-      <output name="out" file="FileMerger_11_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
+      <output name="out" value="FileMerger_11_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
       <param name="annotate_file_origin" value="false"/>
       <param name="append_method" value="append_cols"/>
       <section name="rt_concat">
@@ -406,7 +425,6 @@
       </section>
       <section name="raw">
         <param name="rt_auto" value="false"/>
-        <param name="rt_custom" value=""/>
         <param name="rt_filename" value="false"/>
         <param name="ms_level" value="0"/>
       </section>
@@ -416,11 +434,14 @@
           <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 MS files into one file.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_FileMerger.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_FileMerger.html]]></help>
   <expand macro="references"/>
 </tool>