diff SeedListGenerator.xml @ 7:f3c72f54b9eb draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3

--- a/SeedListGenerator.xml	Fri Nov 06 20:00:45 2020 +0000
+++ b/SeedListGenerator.xml	Thu Dec 01 19:04:23 2022 +0000
@@ -1,13 +1,11 @@
 <?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: [Quantitation]-->
-<tool id="SeedListGenerator" name="SeedListGenerator" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<tool id="SeedListGenerator" name="SeedListGenerator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Generates seed lists for feature detection.</description>
   <macros>
     <token name="@EXECUTABLE@">SeedListGenerator</token>
     <import>macros.xml</import>
-    <import>macros_autotest.xml</import>
-    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
@@ -18,7 +16,7 @@
 ## Preprocessing
 mkdir in &&
 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
-mkdir out &&
+mkdir out_prefix &&
 
 ## Main program call
 
@@ -28,11 +26,10 @@
 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
 -in
 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
--out
-'out/output.${gxy2omsext("featurexml")}'
+-out_prefix
+out_prefix/
 
 ## Postprocessing
-&& mv 'out/output.${gxy2omsext("featurexml")}' '$out'
 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
   && mv '@EXECUTABLE@.ctd' '$ctd_out'
 #end if]]></command>
@@ -41,12 +38,12 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param name="in" argument="-in" type="data" format="featurexml,idxml,mzml" optional="false" label="Input file (see below for details)" help=" select featurexml,idxml,mzml data sets(s)"/>
-    <param name="use_peptide_mass" argument="-use_peptide_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[idXML input only] Use the monoisotopic mass of the best peptide hit for the m/z position (default: use precursor m/z)" help=""/>
+    <param argument="-in" type="data" format="featurexml,idxml,mzml" optional="false" label="Input file (see below for details)" help=" select featurexml,idxml,mzml data sets(s)"/>
+    <param argument="-use_peptide_mass" type="boolean" truevalue="true" falsevalue="false" checked="false" label="[idXML input only] Use the monoisotopic mass of the best peptide hit for the m/z position (default: use precursor m/z)" help=""/>
     <expand macro="adv_opts_macro">
-      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
-      <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
-        <expand macro="list_string_san"/>
+      <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="">
+        <expand macro="list_string_san" name="test"/>
       </param>
     </expand>
     <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
@@ -54,18 +51,67 @@
     </param>
   </inputs>
   <outputs>
-    <data name="out" label="${tool.name} on ${on_string}: out" format="featurexml"/>
+    <collection type="list" name="out_prefix" label="${tool.name} on ${on_string}: out_prefix">
+      <discover_datasets directory="out_prefix" recurse="true" format="featurexml" pattern="_?(?P&lt;designation&gt;.*)\.[^.]*"/>
+    </collection>
     <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_SeedListGenerator"/>
-    <expand macro="manutest_SeedListGenerator"/>
-  </tests>
+  <tests><!-- TOPP_SeedListGenerator_1 -->
+    <!-- TOPP_SeedListGenerator_2 -->
+    <!-- TOPP_SeedListGenerator_3 -->
+  <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="PepXMLFile_test.mzML"/>
+      <output_collection name="out_prefix" count="1">
+        <element name="0" file="SeedListGenerator_1_output_tmp_0.featureXML" ftype="featurexml"/>
+      </output_collection>
+      <param name="use_peptide_mass" value="false"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test><test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="IDMapper_1_output.featureXML"/>
+      <output_collection name="out_prefix" count="1">
+        <element name="0" file="SeedListGenerator_2_output_tmp_0.featureXML" ftype="featurexml"/>
+      </output_collection>
+      <param name="use_peptide_mass" value="false"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test><test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="ConsensusXMLFile_1.consensusXML"/>
+      <output_collection name="out_prefix" count="2">
+        <element name="0" file="SeedListGenerator_3_output_tmp_0.featureXML" ftype="featurexml"/>
+        <element name="1" file="SeedListGenerator_3_output_tmp_1.featureXML" ftype="featurexml"/>
+      </output_collection>
+      <param name="use_peptide_mass" value="false"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+    </test>
+</tests>
   <help><![CDATA[Generates seed lists for feature detection.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_SeedListGenerator.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_SeedListGenerator.html]]></help>
   <expand macro="references"/>
 </tool>