Mercurial > repos > galaxyp > openms_textexporter

diff TextExporter.xml @ 14:b5de4c3efbdd draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:44:36 +0000
parents 1b03536aa3c9
children
line wrap: on
line diff
--- a/TextExporter.xml	Thu Dec 01 19:08:22 2022 +0000
+++ b/TextExporter.xml	Fri Jun 14 21:44:36 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 Converter]-->
 <tool id="TextExporter" name="TextExporter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Exports various XML formats to a text file.</description>
+  <description>Exports various XML formats to a text file</description>
   <macros>
     <token name="@EXECUTABLE@">TextExporter</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($in.ext)' &&
 mkdir out &&
 #if "centroids_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
   mkdir consensus_centroids &&
@@ -72,17 +71,18 @@
     <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,idxml,mzml" optional="false" label="Input file" help=" select consensusxml,featurexml,idxml,mzml data sets(s)"/>
-    <param argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension, ambiguous file extensions are interpreted as tsv" help="">
+    <param argument="-in" type="data" format="consensusxml,featurexml,idxml,mzml" label="Input file" help=" select consensusxml,featurexml,idxml,mzml data sets(s)"/>
+    <param argument="-out_type" type="select" label="Output file type -- default: determined from file extension, ambiguous file extensions are interpreted as tsv" help="">
       <option value="csv">csv</option>
       <option value="tsv">tabular (tsv)</option>
       <option value="txt">txt</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="-replacement" type="text" optional="true" value="_" label="Used to replace occurrences of the separator in strings before writing, if 'quoting' is 'none'" help="">
+    <param argument="-replacement" type="text" value="_" label="Used to replace occurrences of the separator in strings before writing, if 'quoting' is 'none'" help="">
       <expand macro="list_string_san" name="replacement"/>
     </param>
-    <param argument="-quoting" type="select" optional="true" label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes" help="'escape' for quoting with backslash-escaping of embedded quotes">
+    <param argument="-quoting" type="select" label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes" help="'escape' for quoting with backslash-escaping of embedded quotes">
       <option value="none" selected="true">none</option>
       <option value="double">double</option>
       <option value="escape">escape</option>
@@ -91,19 +91,19 @@
     <param argument="-no_ids" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Suppresses output of identification data" help=""/>
     <section name="feature" title="Options for featureXML input files" help="" expanded="false">
       <param name="minimal" argument="-feature:minimal" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag to write only three attributes: RT, m/z, and intensity" help=""/>
-      <param name="add_metavalues" argument="-feature:add_metavalues" type="integer" optional="true" min="-1" max="100" value="-1" label="Add columns for meta values which occur with a certain frequency (0-100%)" help="Set to -1 to omit meta values (default)"/>
+      <param name="add_metavalues" argument="-feature:add_metavalues" type="integer" min="-1" max="100" value="-1" label="Add columns for meta values which occur with a certain frequency (0-100%)" help="Set to -1 to omit meta values (default)"/>
     </section>
     <section name="id" title="Options for idXML input files" help="" expanded="false">
       <param name="proteins_only" argument="-id:proteins_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag if you want only protein information from an idXML file" help=""/>
       <param name="peptides_only" argument="-id:peptides_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag if you want only peptide information from an idXML file" help=""/>
       <param name="protein_groups" argument="-id:protein_groups" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag if you want to also write indist" help="group information from an idXML file"/>
       <param name="first_dim_rt" argument="-id:first_dim_rt" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this flag is set the first_dim RT of the peptide hits will also be printed (if present)" help=""/>
-      <param name="add_metavalues" argument="-id:add_metavalues" type="integer" optional="true" min="-1" max="100" value="-1" label="Add columns for meta values of PeptideID (=spectrum) entries which occur with a certain frequency (0-100%)" help="Set to -1 to omit meta values (default)"/>
-      <param name="add_hit_metavalues" argument="-id:add_hit_metavalues" type="integer" optional="true" min="-1" max="100" value="-1" label="Add columns for meta values of PeptideHit (=PSM) entries which occur with a certain frequency (0-100%)" help="Set to -1 to omit meta values (default)"/>
-      <param name="add_protein_hit_metavalues" argument="-id:add_protein_hit_metavalues" type="integer" optional="true" min="-1" max="100" value="-1" label="Add columns for meta values on protein level which occur with a certain frequency (0-100%)" help="Set to -1 to omit meta values (default)"/>
+      <param name="add_metavalues" argument="-id:add_metavalues" type="integer" min="-1" max="100" value="-1" label="Add columns for meta values of PeptideID (=spectrum) entries which occur with a certain frequency (0-100%)" help="Set to -1 to omit meta values (default)"/>
+      <param name="add_hit_metavalues" argument="-id:add_hit_metavalues" type="integer" min="-1" max="100" value="-1" label="Add columns for meta values of PeptideHit (=PSM) entries which occur with a certain frequency (0-100%)" help="Set to -1 to omit meta values (default)"/>
+      <param name="add_protein_hit_metavalues" argument="-id:add_protein_hit_metavalues" type="integer" min="-1" max="100" value="-1" label="Add columns for meta values on protein level which occur with a certain frequency (0-100%)" help="Set to -1 to omit meta values (default)"/>
     </section>
     <section name="consensus" title="Options for consensusXML input files" help="" expanded="false">
-      <param name="sorting_method" argument="-consensus:sorting_method" type="select" optional="true" label="Sorting options can be combined" help="The precedence is: sort_by_size, sort_by_maps, sorting_method">
+      <param name="sorting_method" argument="-consensus:sorting_method" type="select" label="Sorting options can be combined" help="The precedence is: sort_by_size, sort_by_maps, sorting_method">
         <option value="none" selected="true">none</option>
         <option value="RT">RT</option>
         <option value="MZ">MZ</option>
@@ -115,10 +115,11 @@
       </param>
       <param name="sort_by_maps" argument="-consensus:sort_by_maps" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply a stable sort by the covered maps, lexicographically" help=""/>
       <param name="sort_by_size" argument="-consensus:sort_by_size" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply a stable sort by decreasing size" help="(i.e., the number of elements)"/>
+      <param name="add_metavalues" argument="-consensus:add_metavalues" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Add columns for ConsensusFeature meta values" help=""/>
     </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>
@@ -149,14 +150,15 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_TextExporter_1 -->
+  <tests>
+    <!-- TOPP_TextExporter_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="TextExporter_1_input.featureXML"/>
-      <output name="out" file="TextExporter_1_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
+      <output name="out" value="TextExporter_1_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
       <param name="out_type" value="txt"/>
       <param name="replacement" value="_"/>
       <param name="quoting" value="none"/>
@@ -178,6 +180,7 @@
         <param name="sorting_method" value="none"/>
         <param name="sort_by_maps" value="false"/>
         <param name="sort_by_size" value="false"/>
+        <param name="add_metavalues" value="false"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -185,6 +188,9 @@
           <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_TextExporter_2 -->
     <test expect_num_outputs="5">
@@ -193,7 +199,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="TextExporter_2_input.consensusXML"/>
-      <output name="out" file="TextExporter_2_consensus_tsv.tmp" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
+      <output name="out" value="TextExporter_2_consensus_tsv.tmp" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
       <param name="out_type" value="tsv"/>
       <param name="replacement" value="_"/>
       <param name="quoting" value="none"/>
@@ -215,16 +221,20 @@
         <param name="sorting_method" value="RT_then_MZ"/>
         <param name="sort_by_maps" value="true"/>
         <param name="sort_by_size" value="true"/>
+        <param name="add_metavalues" value="true"/>
       </section>
-      <output name="consensus_centroids" file="TextExporter_2_consensus_centroids.tmp" compare="sim_size" delta_frac="0.7" ftype="csv"/>
-      <output name="consensus_elements" file="TextExporter_2_consensus_elements.tmp" compare="sim_size" delta_frac="0.7" ftype="csv"/>
-      <output name="consensus_features" file="TextExporter_2_consensus_features.tmp" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="consensus_centroids" value="TextExporter_2_consensus_centroids.tmp" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="consensus_elements" value="TextExporter_2_consensus_elements.tmp" compare="sim_size" delta_frac="0.7" ftype="csv"/>
+      <output name="consensus_features" value="TextExporter_2_consensus_features.tmp" compare="sim_size" delta_frac="0.7" ftype="csv"/>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,centroids_FLAG,elements_FLAG,features_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>
     <!-- TOPP_TextExporter_3 -->
     <test expect_num_outputs="2">
@@ -233,7 +243,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="TextExporter_3_input.idXML"/>
-      <output name="out" file="TextExporter_3_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
+      <output name="out" value="TextExporter_3_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
       <param name="out_type" value="txt"/>
       <param name="replacement" value="_"/>
       <param name="quoting" value="none"/>
@@ -255,6 +265,7 @@
         <param name="sorting_method" value="none"/>
         <param name="sort_by_maps" value="false"/>
         <param name="sort_by_size" value="false"/>
+        <param name="add_metavalues" value="false"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -262,6 +273,9 @@
           <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_TextExporter_4 -->
     <test expect_num_outputs="2">
@@ -270,7 +284,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="TextExporter_3_input.idXML"/>
-      <output name="out" file="TextExporter_4_output_proteins.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
+      <output name="out" value="TextExporter_4_output_proteins.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
       <param name="out_type" value="txt"/>
       <param name="replacement" value="_"/>
       <param name="quoting" value="none"/>
@@ -292,6 +306,7 @@
         <param name="sorting_method" value="none"/>
         <param name="sort_by_maps" value="false"/>
         <param name="sort_by_size" value="false"/>
+        <param name="add_metavalues" value="false"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -299,6 +314,9 @@
           <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_TextExporter_5 -->
     <test expect_num_outputs="2">
@@ -307,7 +325,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="TextExporter_5_input.idXML"/>
-      <output name="out" file="TextExporter_5_output_peptides.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
+      <output name="out" value="TextExporter_5_output_peptides.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
       <param name="out_type" value="txt"/>
       <param name="replacement" value="_"/>
       <param name="quoting" value="none"/>
@@ -329,6 +347,7 @@
         <param name="sorting_method" value="none"/>
         <param name="sort_by_maps" value="false"/>
         <param name="sort_by_size" value="false"/>
+        <param name="add_metavalues" value="false"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -336,6 +355,9 @@
           <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_TextExporter_6 -->
     <test expect_num_outputs="2">
@@ -344,7 +366,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="TextExporter_6_input.featureXML"/>
-      <output name="out" file="TextExporter_6_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
+      <output name="out" value="TextExporter_6_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
       <param name="out_type" value="txt"/>
       <param name="replacement" value="_"/>
       <param name="quoting" value="none"/>
@@ -366,6 +388,7 @@
         <param name="sorting_method" value="none"/>
         <param name="sort_by_maps" value="false"/>
         <param name="sort_by_size" value="false"/>
+        <param name="add_metavalues" value="false"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -373,6 +396,9 @@
           <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_TextExporter_7 -->
     <test expect_num_outputs="2">
@@ -381,7 +407,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="TextExporter_7_input.consensusXML"/>
-      <output name="out" file="TextExporter_7_consensus_tsv.tmp" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
+      <output name="out" value="TextExporter_7_consensus_tsv.tmp" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
       <param name="out_type" value="tsv"/>
       <param name="replacement" value="_"/>
       <param name="quoting" value="none"/>
@@ -403,6 +429,7 @@
         <param name="sorting_method" value="RT_then_MZ"/>
         <param name="sort_by_maps" value="true"/>
         <param name="sort_by_size" value="true"/>
+        <param name="add_metavalues" value="false"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -410,6 +437,9 @@
           <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_TextExporter_8 -->
     <test expect_num_outputs="2">
@@ -418,7 +448,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="TextExporter_1_input.featureXML"/>
-      <output name="out" file="TextExporter_8_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
+      <output name="out" value="TextExporter_8_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
       <param name="out_type" value="txt"/>
       <param name="replacement" value="_"/>
       <param name="quoting" value="none"/>
@@ -440,6 +470,7 @@
         <param name="sorting_method" value="none"/>
         <param name="sort_by_maps" value="false"/>
         <param name="sort_by_size" value="false"/>
+        <param name="add_metavalues" value="false"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -447,6 +478,9 @@
           <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_TextExporter_9 -->
     <test expect_num_outputs="2">
@@ -455,7 +489,7 @@
         <param name="test" value="true"/>
       </section>
       <param name="in" value="TextExporter_9_input.idXML"/>
-      <output name="out" file="TextExporter_9_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
+      <output name="out" value="TextExporter_9_output.txt" compare="sim_size" delta_frac="0.7" ftype="txt"/>
       <param name="out_type" value="txt"/>
       <param name="replacement" value="_"/>
       <param name="quoting" value="none"/>
@@ -477,6 +511,7 @@
         <param name="sorting_method" value="none"/>
         <param name="sort_by_maps" value="false"/>
         <param name="sort_by_size" value="false"/>
+        <param name="add_metavalues" value="false"/>
       </section>
       <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
       <output name="ctd_out" ftype="xml">
@@ -484,11 +519,14 @@
           <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[Exports various XML formats to a text file.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_TextExporter.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_TextExporter.html]]></help>
   <expand macro="references"/>
 </tool>