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

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

<!--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: [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>
    <token name="@EXECUTABLE@">MzMLSplitter</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <expand macro="stdio"/>
  <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
@EXT_FOO@
#import re

## Preprocessing
mkdir in &&
cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
mkdir out &&

## Main program call

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 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>
      <expand macro="list_string_san" name="unit"/>
    </param>
    <param argument="-no_chrom" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove chromatograms, keep only spectra" help=""/>
    <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" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
        <expand macro="list_string_san" name="test"/>
      </param>
    </expand>
    <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
      <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
    </param>
  </inputs>
  <outputs>
    <collection type="list" name="out" label="${tool.name} on ${on_string}: out">
      <discover_datasets directory="out" recurse="true" format="mzml" pattern="_?(?P&lt;designation&gt;.*)\.[^.]*"/>
    </collection>
    <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
      <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
    </data>
  </outputs>
  <tests>
    <!-- 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 https://openms.de/doxygen/release/3.1.0/html/TOPP_MzMLSplitter.html]]></help>
  <expand macro="references"/>
</tool>