diff QCShrinker.xml @ 14:047c8ea82162 draft default tip

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

--- a/QCShrinker.xml	Thu Dec 01 19:25:13 2022 +0000
+++ b/QCShrinker.xml	Fri Jun 14 21:29:23 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: []-->
 <tool id="QCShrinker" name="QCShrinker" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>This application is used to remove the verbose table attachments from a qcml file that are not needed anymore, e.g. for a final report.</description>
+  <description>This application is used to remove the verbose table attachments from a qcml file that are not needed anymore, e.g. for a final report</description>
   <macros>
     <token name="@EXECUTABLE@">QCShrinker</token>
     <import>macros.xml</import>
@@ -15,10 +14,10 @@
 
 ## 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)' &&
 #if $run:
   mkdir run &&
-  ln -s '$run' 'run/${re.sub("[^\w\-_]", "_", $run.element_identifier)}.$gxy2omsext($run.ext)' &&
+  cp '$run' 'run/${re.sub("[^\w\-_]", "_", $run.element_identifier)}.$gxy2omsext($run.ext)' &&
 #end if
 mkdir out &&
 
@@ -47,7 +46,7 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="qcml" optional="false" label="Input qcml file" help=" select qcml data sets(s)"/>
+    <param argument="-in" type="data" format="qcml" label="Input qcml file" help=" select qcml data sets(s)"/>
     <param argument="-qp_accessions" type="text" optional="true" value="" label="A list of cv accessions that should be removed" help="If empty, the usual suspects will be removed! (space separated list, in order to allow for spaces in list items surround them by single quotes)">
       <expand macro="list_string_val" name="qp_accessions"/>
       <expand macro="list_string_san" name="qp_accessions"/>
@@ -58,7 +57,7 @@
     <param argument="-run" type="data" format="mzml" optional="true" label="The file from which the name of the target run that contains the requested quality parameter is taken" help="This overrides the name parameter! select mzml data sets(s)"/>
     <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>
@@ -72,15 +71,17 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><test expect_num_outputs="1"><!-- just using an output of QCCalculator as input  -->
-    <param name="adv_opts|test" value="true"/>
-    <param name="in" ftype="qcml" value="QCCalculator1.qcML"/>
-    <output name="out" ftype="qcml" value="QCShrinker.qcML"/>
-  </test>
-</tests>
+  <tests>
+    <test expect_num_outputs="1">
+      <!-- just using an output of QCCalculator as input  -->
+      <param name="adv_opts|test" value="true"/>
+      <param name="in" ftype="qcml" value="QCCalculator1.qcML"/>
+      <output name="out" ftype="qcml" value="QCShrinker.qcML"/>
+    </test>
+  </tests>
   <help><![CDATA[This application is used to remove the verbose table attachments from a qcml file that are not needed anymore, e.g. for a final report.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_QCShrinker.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_QCShrinker.html]]></help>
   <expand macro="references"/>
 </tool>