diff QCEmbedder.xml @ 14:815e502a2288 draft default tip

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

--- a/QCEmbedder.xml	Thu Dec 01 19:04:55 2022 +0000
+++ b/QCEmbedder.xml	Fri Jun 14 21:33:20 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="QCEmbedder" name="QCEmbedder" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Attaches a table or an image to a given qc parameter.</description>
+  <description>Attaches a table or an image to a given qc parameter</description>
   <macros>
     <token name="@EXECUTABLE@">QCEmbedder</token>
     <import>macros.xml</import>
@@ -16,19 +15,19 @@
 ## Preprocessing
 #if $in:
   mkdir in &&
-  ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+  cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
 #end if
 #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
 #if $plot:
   mkdir plot &&
-  ln -s '$plot' 'plot/${re.sub("[^\w\-_]", "_", $plot.element_identifier)}.$gxy2omsext($plot.ext)' &&
+  cp '$plot' 'plot/${re.sub("[^\w\-_]", "_", $plot.element_identifier)}.$gxy2omsext($plot.ext)' &&
 #end if
 #if $table:
   mkdir table &&
-  ln -s '$table' 'table/${re.sub("[^\w\-_]", "_", $table.element_identifier)}.$gxy2omsext($table.ext)' &&
+  cp '$table' 'table/${re.sub("[^\w\-_]", "_", $table.element_identifier)}.$gxy2omsext($table.ext)' &&
 #end if
 mkdir out &&
 
@@ -71,7 +70,7 @@
     <param argument="-qp_att_acc" type="text" optional="true" value="" label="Defines the qp cv accession of the qp to which the table/image is attached" help="">
       <expand macro="list_string_san" name="qp_att_acc"/>
     </param>
-    <param argument="-cv_acc" type="text" optional="false" value="" label="Defines the cv accession of the attachment" help="">
+    <param argument="-cv_acc" type="text" value="" label="Defines the cv accession of the attachment" help="">
       <expand macro="list_string_san" name="cv_acc"/>
     </param>
     <param argument="-run" type="data" format="mzml" optional="true" label="The file that defined the run under which the qp for the attachment is aggregated as mzML file" help="The file is only used to extract the run name from the file name select mzml data sets(s)"/>
@@ -82,7 +81,7 @@
     <param argument="-table" type="data" format="csv" optional="true" label="If a table is to be attached to a qp, this has to be specified here" help=" select csv 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>
@@ -96,11 +95,12 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!--TODO-->
-</tests>
+  <tests>
+    <!--TODO-->
+  </tests>
   <help><![CDATA[Attaches a table or an image to a given qc parameter.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_QCEmbedder.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_QCEmbedder.html]]></help>
   <expand macro="references"/>
 </tool>