diff MzMLSplitter.xml @ 13:609bc5efdcc9 draft default tip

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

--- a/MzMLSplitter.xml	Thu Dec 01 19:14:47 2022 +0000
+++ b/MzMLSplitter.xml	Fri Jun 14 21:45:37 2024 +0000
@@ -1,6 +1,5 @@
-<?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: [File Filtering / Extraction / Merging]-->
 <tool id="MzMLSplitter" name="MzMLSplitter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
   <description>Splits an mzML file into multiple parts</description>
   <macros>
@@ -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
@@ -38,10 +37,10 @@
     <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
   </configfiles>
   <inputs>
-    <param argument="-in" type="data" format="mzml" optional="false" label="Input file" help=" select mzml data sets(s)"/>
-    <param argument="-parts" type="integer" optional="true" min="1" value="1" label="Number of parts to split into (takes precedence over 'size' if set)" help=""/>
-    <param argument="-size" type="integer" optional="true" min="0" value="0" label="Approximate upper limit for resulting file sizes (in 'unit')" help=""/>
-    <param argument="-unit" type="select" optional="true" label="Unit for 'size' (base 1024)" help="">
+    <param argument="-in" type="data" format="mzml" label="Input file" help=" select mzml data sets(s)"/>
+    <param argument="-parts" type="integer" min="1" value="1" label="Number of parts to split into (takes precedence over 'size' if set)" help=""/>
+    <param argument="-size" type="integer" min="0" value="0" label="Approximate upper limit for resulting file sizes (in 'unit')" help=""/>
+    <param argument="-unit" type="select" label="Unit for 'size' (base 1024)" help="">
       <option value="KB">KB</option>
       <option value="MB" selected="true">MB</option>
       <option value="GB">GB</option>
@@ -51,7 +50,7 @@
     <param argument="-no_spec" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove spectra, keep only chromatograms" 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>
@@ -67,54 +66,55 @@
       <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
     </data>
   </outputs>
-  <tests><!-- UTILS_MzMLSplitter_1 -->
-    <!-- UTILS_MzMLSplitter_2 -->
-  <test expect_num_outputs="2">
-  <section name="adv_opts">
-    <param name="test" value="true"/>
-  </section>
-  <param name="in" value="FileFilter_1_input.mzML"/>
-  <param name="parts" value="2"/>
-  <param name="size" value="0"/>
-  <param name="unit" value="MB"/>
-  <param name="no_chrom" value="false"/>
-  <param name="no_spec" value="false"/>
-  <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-  <output name="ctd_out" ftype="xml">
-    <assert_contents>
-      <is_valid_xml/>
-    </assert_contents>
-  </output>
-  <output_collection name="out" type="list" count="2">
-    <element name="part1of2" file="MzMLSplitter_1_output_part1of2.mzML" ftype="mzml"/>
-    <element name="part2of2" file="MzMLSplitter_1_output_part2of2.mzML" ftype="mzml"/>
-  </output_collection>
-</test>
-<test expect_num_outputs="2">
-  <section name="adv_opts">
-    <param name="test" value="true"/>
-  </section>
-  <param name="in" value="FileFilter_1_input.mzML"/>
-  <param name="parts" value="1"/>
-  <param name="size" value="40"/>
-  <param name="unit" value="KB"/>
-  <param name="no_chrom" value="false"/>
-  <param name="no_spec" value="false"/>
-  <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
-  <output name="ctd_out" ftype="xml">
-    <assert_contents>
-      <is_valid_xml/>
-    </assert_contents>
-  </output>
-  <output_collection name="out" type="list" count="2">
-    <element name="part1of2" file="MzMLSplitter_2_output_part1of2.mzML" ftype="mzml"/>
-    <element name="part2of2" file="MzMLSplitter_2_output_part2of2.mzML" ftype="mzml"/>
-  </output_collection>
-</test>
-</tests>
+  <tests>
+    <!-- TOPP_MzMLSplitter_1 -->
+    <!-- TOPP_MzMLSplitter_2 -->
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="FileFilter_1_input.mzML"/>
+      <param name="parts" value="2"/>
+      <param name="size" value="0"/>
+      <param name="unit" value="MB"/>
+      <param name="no_chrom" value="false"/>
+      <param name="no_spec" value="false"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+      <output_collection name="out" type="list" count="2">
+        <element name="part1of2" file="MzMLSplitter_1_output_part1of2.mzML" ftype="mzml"/>
+        <element name="part2of2" file="MzMLSplitter_1_output_part2of2.mzML" ftype="mzml"/>
+      </output_collection>
+    </test>
+    <test expect_num_outputs="2">
+      <section name="adv_opts">
+        <param name="test" value="true"/>
+      </section>
+      <param name="in" value="FileFilter_1_input.mzML"/>
+      <param name="parts" value="1"/>
+      <param name="size" value="40"/>
+      <param name="unit" value="KB"/>
+      <param name="no_chrom" value="false"/>
+      <param name="no_spec" value="false"/>
+      <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
+      <output name="ctd_out" ftype="xml">
+        <assert_contents>
+          <is_valid_xml/>
+        </assert_contents>
+      </output>
+      <output_collection name="out" type="list" count="2">
+        <element name="part1of2" file="MzMLSplitter_2_output_part1of2.mzML" ftype="mzml"/>
+        <element name="part2of2" file="MzMLSplitter_2_output_part2of2.mzML" ftype="mzml"/>
+      </output_collection>
+    </test>
+  </tests>
   <help><![CDATA[Splits an mzML file into multiple parts
 
 
-For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_MzMLSplitter.html]]></help>
+For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MzMLSplitter.html]]></help>
   <expand macro="references"/>
 </tool>