diff SvmTheoreticalSpectrumGeneratorTrainer.xml @ 13:3c5de1c6c08a draft default tip

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

--- a/SvmTheoreticalSpectrumGeneratorTrainer.xml	Fri Nov 06 20:02:14 2020 +0000
+++ b/SvmTheoreticalSpectrumGeneratorTrainer.xml	Thu Dec 01 19:21:45 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: [Utilities]-->
-<tool id="SvmTheoreticalSpectrumGeneratorTrainer" name="SvmTheoreticalSpectrumGeneratorTrainer" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
+<tool id="SvmTheoreticalSpectrumGeneratorTrainer" name="SvmTheoreticalSpectrumGeneratorTrainer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Trainer for SVM models as input for SvmTheoreticalSpectrumGenerator</description>
   <macros>
     <token name="@EXECUTABLE@">SvmTheoreticalSpectrumGeneratorTrainer</token>
     <import>macros.xml</import>
-    <import>macros_autotest.xml</import>
-    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
@@ -45,10 +43,10 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param name="in_spectra" argument="-in_spectra" type="data" format="mzml" optional="false" label="Input Training Spectra in mzML" help=" select mzml data sets(s)"/>
-    <param name="in_identifications" argument="-in_identifications" type="data" format="idxml" optional="false" label="Input file with corresponding sequences in idXML" help=" select idxml data sets(s)"/>
-    <param name="precursor_charge" argument="-precursor_charge" type="integer" optional="true" min="1" max="3" value="2" label="Precursor charge state used for model training" help=""/>
-    <param name="write_training_files" argument="-write_training_files" type="boolean" truevalue="true" falsevalue="false" checked="false" label="No models are trained but input training files for libSVM command line tools are produced" help=""/>
+    <param argument="-in_spectra" type="data" format="mzml" optional="false" label="Input Training Spectra in mzML" help=" select mzml data sets(s)"/>
+    <param argument="-in_identifications" type="data" format="idxml" optional="false" label="Input file with corresponding sequences in idXML" help=" select idxml data sets(s)"/>
+    <param argument="-precursor_charge" type="integer" optional="true" min="1" max="3" value="2" label="Precursor charge state used for model training" help=""/>
+    <param argument="-write_training_files" type="boolean" truevalue="true" falsevalue="false" checked="false" label="No models are trained but input training files for libSVM command line tools are produced" help=""/>
     <section name="algorithm" title="" help="" expanded="false">
       <param name="number_intensity_levels" argument="-algorithm:number_intensity_levels" type="integer" optional="true" value="7" label="The number of intensity bins (for secondary type models)" help=""/>
       <param name="number_regions" argument="-algorithm:number_regions" type="integer" optional="true" value="3" label="The number of regions each spectrum is split to (for secondary type models)" help=""/>
@@ -118,9 +116,9 @@
       </section>
     </section>
     <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">
@@ -133,13 +131,11 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests>
-    <expand macro="autotest_SvmTheoreticalSpectrumGeneratorTrainer"/>
-    <expand macro="manutest_SvmTheoreticalSpectrumGeneratorTrainer"/>
-  </tests>
+  <tests><!-- -TODO model_output_file creates multiple files-->
+</tests>
   <help><![CDATA[Trainer for SVM models as input for SvmTheoreticalSpectrumGenerator
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_SvmTheoreticalSpectrumGeneratorTrainer.html]]></help>
+For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_SvmTheoreticalSpectrumGeneratorTrainer.html]]></help>
   <expand macro="references"/>
 </tool>