diff MzMLSplitter.xml @ 13:de4558451cad draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
author galaxyp
date Wed, 15 May 2019 06:55:05 -0400
parents d77557781bfa
children dd3c80c9f138
line wrap: on
line diff
--- a/MzMLSplitter.xml	Mon Feb 12 08:59:57 2018 -0500
+++ b/MzMLSplitter.xml	Wed May 15 06:55:05 2019 -0400
@@ -1,22 +1,26 @@
 <?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 CTD2Galaxy.-->
+<!--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]-->
-<tool id="MzMLSplitter" name="MzMLSplitter" version="2.2.0.1">
+<tool id="MzMLSplitter" name="MzMLSplitter" version="2.3.0">
   <description>Splits an mzML file into multiple parts</description>
   <macros>
     <token name="@EXECUTABLE@">MzMLSplitter</token>
     <import>macros.xml</import>
   </macros>
-  <expand macro="references"/>
+  <expand macro="requirements"/>
   <expand macro="stdio"/>
-  <expand macro="requirements"/>
-  <command>MzMLSplitter
+  <command detect_errors="aggressive"><![CDATA[
+mkdir parts/ &&
+
+MzMLSplitter
 
 #if $param_in:
   -in $param_in
 #end if
 #if $param_out:
-  -out     "$param_out"
+  -out "parts/$param_out"
+#else
+  -out "parts/MzML"
 #end if
 #if $param_parts:
   -parts $param_parts
@@ -43,8 +47,8 @@
   -force
 #end if
 #end if
-&gt; $param_stdout
-</command>
+-threads "\${GALAXY_SLOTS:-1}"
+]]></command>
   <inputs>
     <param name="param_in" type="data" format="mzml" optional="False" label="Input file" help="(-in) "/>
     <param name="param_out" type="text" size="30" label="Prefix for output files ('_part1of2.mzML' etc" help="(-out) will be appended; default: same as 'in' without the file extension)">
@@ -69,10 +73,23 @@
     </expand>
   </inputs>
   <outputs>
-    <data name="param_stdout" format="txt" label="Output from stdout"/>
+    <collection name="parts" type="list">
+      <discover_datasets pattern="__name_and_ext__" format="mzml"  directory="parts" />
+    </collection>
   </outputs>
+  <tests>
+    <test>
+      <param name="param_in" value="FileFilter_1_input.mzML"/>
+      <param name="param_parts" value="2" />
+      <output_collection name="parts" type="list">
+        <element name="MzML_part1of2" file="MzMLSplitter_output_part1.mzML" ftype="mzml" />
+        <element name="MzML_part2of2" file="MzMLSplitter_output_part2.mzML" ftype="mzml" />
+      </output_collection>
+    </test>
+  </tests>
   <help>Splits an mzML file into multiple parts
 
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MzMLSplitter.html</help>
+For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_MzMLSplitter.html</help>
+<expand macro="references"/>
 </tool>