diff MzMLSplitter.xml @ 8:a2bf6f5def91 draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"

--- a/MzMLSplitter.xml	Fri May 17 10:22:12 2019 -0400
+++ b/MzMLSplitter.xml	Thu Aug 27 19:35:53 2020 -0400
@@ -1,95 +1,81 @@
 <?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]-->
-<tool id="MzMLSplitter" name="MzMLSplitter" version="2.3.0">
+<tool id="MzMLSplitter" name="MzMLSplitter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
   <description>Splits an mzML file into multiple parts</description>
   <macros>
     <token name="@EXECUTABLE@">MzMLSplitter</token>
     <import>macros.xml</import>
+    <import>macros_autotest.xml</import>
+    <import>macros_test.xml</import>
   </macros>
   <expand macro="requirements"/>
   <expand macro="stdio"/>
-  <command detect_errors="aggressive"><![CDATA[
-mkdir parts/ &&
+  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
+@EXT_FOO@
+#import re
 
-MzMLSplitter
+## Preprocessing
+mkdir in &&
+ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
+mkdir out &&
+
+## Main program call
 
-#if $param_in:
-  -in $param_in
-#end if
-#if $param_out:
-  -out "parts/$param_out"
-#else
-  -out "parts/MzML"
-#end if
-#if $param_parts:
-  -parts $param_parts
-#end if
-#if $param_size:
-  -size $param_size
-#end if
-#if $param_unit:
-  -unit
-  #if " " in str($param_unit):
-    "$param_unit"
-  #else
-    $param_unit
-  #end if
-#end if
-#if $param_no_chrom:
-  -no_chrom
-#end if
-#if $param_no_spec:
-  -no_spec
-#end if
-#if $adv_opts.adv_opts_selector=='advanced':
-    #if $adv_opts.param_force:
-  -force
-#end if
-#end if
--threads "\${GALAXY_SLOTS:-1}"
-]]></command>
+set -o pipefail &&
+@EXECUTABLE@ -write_ctd ./ &&
+python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
+@EXECUTABLE@ -ini @EXECUTABLE@.ctd
+-in
+'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
+-out
+out/
+
+## Postprocessing
+#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
+  && mv '@EXECUTABLE@.ctd' '$ctd_out'
+#end if]]></command>
+  <configfiles>
+    <inputs name="args_json" data_style="paths"/>
+    <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
+  </configfiles>
   <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)">
-      <sanitizer>
-        <valid initial="string.printable">
-          <remove value="'"/>
-          <remove value="&quot;"/>
-        </valid>
-      </sanitizer>
-    </param>
-    <param name="param_parts" type="integer" min="1" optional="True" value="1" label="Number of parts to split into (takes precedence over 'size' if set)" help="(-parts) "/>
-    <param name="param_size" type="integer" min="0" optional="True" value="0" label="Approximate upper limit for resulting file sizes (in 'unit')" help="(-size) "/>
-    <param name="param_unit" display="radio" type="select" optional="False" value="MB" label="Unit for 'size' (base 1024)" help="(-unit) ">
+    <param name="in" argument="-in" type="data" format="mzml" optional="false" label="Input file" help=" select mzml data sets(s)"/>
+    <param name="parts" 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 name="size" argument="-size" type="integer" optional="true" min="0" value="0" label="Approximate upper limit for resulting file sizes (in 'unit')" help=""/>
+    <param name="unit" argument="-unit" display="radio" type="select" optional="false" label="Unit for 'size' (base 1024)" help="">
       <option value="KB">KB</option>
       <option value="MB" selected="true">MB</option>
       <option value="GB">GB</option>
+      <expand macro="list_string_san"/>
     </param>
-    <param name="param_no_chrom" display="radio" type="boolean" truevalue="-no_chrom" falsevalue="" checked="false" optional="True" label="Remove chromatograms, keep only spectra" help="(-no_chrom) "/>
-    <param name="param_no_spec" display="radio" type="boolean" truevalue="-no_spec" falsevalue="" checked="false" optional="True" label="Remove spectra, keep only chromatograms" help="(-no_spec) "/>
-    <expand macro="advanced_options">
-      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
+    <param name="no_chrom" argument="-no_chrom" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove chromatograms, keep only spectra" help=""/>
+    <param name="no_spec" argument="-no_spec" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove spectra, keep only chromatograms" help=""/>
+    <expand macro="adv_opts_macro">
+      <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
+      <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
+        <expand macro="list_string_san"/>
+      </param>
     </expand>
+    <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
+      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
+    </param>
   </inputs>
   <outputs>
-    <collection name="parts" type="list">
-      <discover_datasets pattern="__name_and_ext__" format="mzml"  directory="parts" />
+    <collection type="list" name="out" label="${tool.name} on ${on_string}: out">
+      <discover_datasets directory="out" format="mzml" pattern="_?(?P&lt;designation&gt;.*)\.[^.]*"/>
     </collection>
+    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
+      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
+    </data>
   </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>
+    <expand macro="autotest_MzMLSplitter"/>
+    <expand macro="manutest_MzMLSplitter"/>
   </tests>
-  <help>Splits an mzML file into multiple parts
+  <help><![CDATA[Splits an mzML file into multiple parts
 
 
-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"/>
+For more information, visit http://www.openms.de/documentation/UTILS_MzMLSplitter.html]]></help>
+  <expand macro="references"/>
 </tool>