diff OpenSwathDIAPreScoring.xml @ 12:986d14ec9394 draft default tip

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

--- a/OpenSwathDIAPreScoring.xml	Thu Dec 01 19:20:01 2022 +0000
+++ b/OpenSwathDIAPreScoring.xml	Fri Jun 14 21:34:43 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: [Targeted Experiments]-->
+<!--Proposed Tool Section: [Targeted Experiments and OpenSWATH]-->
 <tool id="OpenSwathDIAPreScoring" name="OpenSwathDIAPreScoring" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
-  <description>Scoring spectra using the DIA scores.</description>
+  <description>Scoring spectra using the DIA scores</description>
   <macros>
     <token name="@EXECUTABLE@">OpenSwathDIAPreScoring</token>
     <import>macros.xml</import>
@@ -15,13 +14,13 @@
 
 ## Preprocessing
 mkdir tr &&
-ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
+cp '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
 mkdir swath_files_cond.swath_files &&
 #if $swath_files_cond.swath_files_select == "no"
 mkdir ${' '.join(["'swath_files_cond.swath_files/%s'" % (i) for i, f in enumerate($swath_files_cond.swath_files) if f])} && 
-${' '.join(["ln -s '%s' 'swath_files_cond.swath_files/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($swath_files_cond.swath_files) if f])}
+${' '.join(["cp '%s' 'swath_files_cond.swath_files/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($swath_files_cond.swath_files) if f])}
 #else
-ln -s '$swath_files_cond.swath_files' 'swath_files_cond.swath_files/${re.sub("[^\w\-_]", "_", $swath_files_cond.swath_files.element_identifier)}.$gxy2omsext($swath_files_cond.swath_files.ext)' &&
+cp '$swath_files_cond.swath_files' 'swath_files_cond.swath_files/${re.sub("[^\w\-_]", "_", $swath_files_cond.swath_files.element_identifier)}.$gxy2omsext($swath_files_cond.swath_files.ext)' &&
 #end if
 mkdir output_files &&
 mkdir ${' '.join(["'output_files/%s'" % (i) for i, f in enumerate($swath_files_cond.swath_files) if f])} && 
@@ -53,23 +52,23 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-tr" type="data" format="traml" optional="false" label="transition file" help=" select traml data sets(s)"/>
+    <param argument="-tr" type="data" format="traml" label="transition file" help=" select traml data sets(s)"/>
     <conditional name="swath_files_cond">
       <param name="swath_files_select" type="select" label="Run tool in batch mode for -swath_files">
         <option value="no">No: process all datasets jointly</option>
         <option value="yes">Yes: process each dataset in an independent job</option>
       </param>
       <when value="no">
-        <param argument="-swath_files" type="data" format="mzml" multiple="true" optional="false" label="Swath files that were used to extract the transitions" help="If present, SWATH specific scoring will be applied select mzml data sets(s)"/>
+        <param argument="-swath_files" type="data" format="mzml" multiple="true" label="Swath files that were used to extract the transitions" help="If present, SWATH specific scoring will be applied select mzml data sets(s)"/>
       </when>
       <when value="yes">
-        <param argument="-swath_files" type="data" format="mzml" multiple="false" optional="false" label="Swath files that were used to extract the transitions" help="If present, SWATH specific scoring will be applied select mzml data sets(s)"/>
+        <param argument="-swath_files" type="data" format="mzml" label="Swath files that were used to extract the transitions" help="If present, SWATH specific scoring will be applied select mzml data sets(s)"/>
       </when>
     </conditional>
-    <param argument="-min_upper_edge_dist" type="float" optional="true" value="0.0" label="Minimal distance to the edge to still consider a precursor, in Thomson (only in SWATH)" help=""/>
+    <param argument="-min_upper_edge_dist" type="float" value="0.0" label="Minimal distance to the edge to still consider a precursor, in Thomson (only in SWATH)" 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>
@@ -85,27 +84,28 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- data from a test that included all the needed test files -->
-  <test>
-    <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
-    <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
-    <output_collection name="output_files" count="1">
-      <element name="OpenSwathAnalyzer_2_swathfile_mzML" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/>
-    </output_collection>
-  </test>
-  <!-- test with two inputs (actually the same file .. symlinked) -->
-  <test>
-    <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
-    <param name="swath_files" value="OpenSwathDIAPreScoring_in1.mzML,OpenSwathDIAPreScoring_in2.mzML"/>
-    <output_collection name="output_files" count="2">
-      <element name="OpenSwathDIAPreScoring_in1_mzML" file="OpenSwathDIAPreScoring_2_1.tsv" ftype="tabular"/>
-      <element name="OpenSwathDIAPreScoring_in2_mzML" file="OpenSwathDIAPreScoring_2_2.tsv" ftype="tabular"/>
-    </output_collection>
-  </test>
-</tests>
+  <tests>
+    <!-- data from a test that included all the needed test files -->
+    <test expect_num_outputs="1">
+      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
+      <param name="swath_files" value="OpenSwathAnalyzer_2_swathfile.mzML"/>
+      <output_collection name="output_files" count="1">
+        <element name="OpenSwathAnalyzer_2_swathfile_mzML" file="OpenSwathDIAPreScoring.tsv" ftype="tabular"/>
+      </output_collection>
+    </test>
+    <!-- test with two inputs (actually the same file .. symlinked) -->
+    <test expect_num_outputs="1">
+      <param name="tr" value="OpenSwathWorkflow_1_input.TraML"/>
+      <param name="swath_files" value="OpenSwathDIAPreScoring_in1.mzML,OpenSwathDIAPreScoring_in2.mzML"/>
+      <output_collection name="output_files" count="2">
+        <element name="OpenSwathDIAPreScoring_in1_mzML" file="OpenSwathDIAPreScoring_2_1.tsv" ftype="tabular"/>
+        <element name="OpenSwathDIAPreScoring_in2_mzML" file="OpenSwathDIAPreScoring_2_2.tsv" ftype="tabular"/>
+      </output_collection>
+    </test>
+  </tests>
   <help><![CDATA[Scoring spectra using the DIA scores.
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_OpenSwathDIAPreScoring.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_OpenSwathDIAPreScoring.html]]></help>
   <expand macro="references"/>
 </tool>