diff IDExtractor.xml @ 16:a6124b08daff draft default tip

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

--- a/IDExtractor.xml	Thu Dec 01 19:07:40 2022 +0000
+++ b/IDExtractor.xml	Fri Jun 14 21:28:53 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: [Utilities]-->
+<!--Proposed Tool Section: [Identification Processing]-->
 <tool id="IDExtractor" name="IDExtractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Extracts 'n' peptides randomly or best 'n' from idXML files.</description>
+  <description>Extracts 'n' peptides randomly or best 'n' from idXML files</description>
   <macros>
     <token name="@EXECUTABLE@">IDExtractor</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 &&
 
 ## Main program call
@@ -39,13 +38,13 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="idxml" optional="false" label="input file" help=" select idxml data sets(s)"/>
-    <param argument="-number_of_peptides" type="integer" optional="true" min="1" value="10" label="Number of randomly chosen peptides" help=""/>
-    <param argument="-number_of_rand_invokations" type="integer" optional="true" min="0" value="0" label="Number of rand invocations before random draw (basically a seed)" help=""/>
+    <param argument="-in" type="data" format="idxml" label="input file" help=" select idxml data sets(s)"/>
+    <param argument="-number_of_peptides" type="integer" min="1" value="10" label="Number of randomly chosen peptides" help=""/>
+    <param argument="-number_of_rand_invokations" type="integer" min="0" value="0" label="Number of rand invocations before random draw (basically a seed)" help=""/>
     <param argument="-best_hits" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this flag is set the best n peptides are chosen" help=""/>
     <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>
@@ -59,17 +58,19 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><test expect_num_outputs="1"><!--  -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML"/>
-    <param name="best_hits" value="true"/>
-    <param name="number_of_peptides" value="1"/>
-    <output name="out" value="IDExtractor.idXML" compare="sim_size"/>
-  </test>
-</tests>
+  <tests>
+    <test expect_num_outputs="1">
+      <!--  -->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML"/>
+      <param name="best_hits" value="true"/>
+      <param name="number_of_peptides" value="1"/>
+      <output name="out" value="IDExtractor.idXML" compare="sim_size"/>
+    </test>
+  </tests>
   <help><![CDATA[Extracts 'n' peptides randomly or best 'n' from idXML files.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_IDExtractor.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_IDExtractor.html]]></help>
   <expand macro="references"/>
 </tool>