diff IDRipper.xml @ 14:e64214bd2f6e draft default tip

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

--- a/IDRipper.xml	Thu Dec 01 19:15:32 2022 +0000
+++ b/IDRipper.xml	Fri Jun 14 21:45:30 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="IDRipper" name="IDRipper" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Split protein/peptide identification file into several files according to identification run and annotated file origin.</description>
+  <description>Split protein/peptide identification file into several files according to identification run and annotated file origin</description>
   <macros>
     <token name="@EXECUTABLE@">IDRipper</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
@@ -38,12 +37,12 @@
     <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, in which the protein/peptide identifications must be tagged with 'file_origin'" help=" select idxml data sets(s)"/>
+    <param argument="-in" type="data" format="idxml" label="Input file, in which the protein/peptide identifications must be tagged with 'file_origin'" help=" select idxml data sets(s)"/>
     <param argument="-numeric_filenames" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not infer output filenames from spectra_data or file_origin but use the input filename with numeric suffixes" help=""/>
     <param argument="-split_ident_runs" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Split different identification runs into separate files" 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>
@@ -59,11 +58,12 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- TOPP_IDRipper_1 -->
+  <tests>
+    <!-- TOPP_IDRipper_1 -->
     <!-- TOPP_IDRipper_2 -->
     <!-- TOPP_IDRipper_2a -->
     <!-- TOPP_IDRipper_3 -->
-  <test expect_num_outputs="2">
+    <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="test" value="true"/>
       </section>
@@ -80,7 +80,8 @@
           <is_valid_xml/>
         </assert_contents>
       </output>
-    </test><test expect_num_outputs="2">
+    </test>
+    <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="test" value="true"/>
       </section>
@@ -98,7 +99,8 @@
           <is_valid_xml/>
         </assert_contents>
       </output>
-    </test><test expect_num_outputs="2">
+    </test>
+    <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="test" value="true"/>
       </section>
@@ -115,7 +117,8 @@
           <is_valid_xml/>
         </assert_contents>
       </output>
-    </test><test expect_num_outputs="2">
+    </test>
+    <test expect_num_outputs="2">
       <section name="adv_opts">
         <param name="test" value="true"/>
       </section>
@@ -133,10 +136,10 @@
         </assert_contents>
       </output>
     </test>
-</tests>
+  </tests>
   <help><![CDATA[Split protein/peptide identification file into several files according to identification run and annotated file origin.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_IDRipper.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_IDRipper.html]]></help>
   <expand macro="references"/>
 </tool>