comparison MzMLSplitter.xml @ 8:a2bf6f5def91 draft

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

7:ab079a6757c1

<?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">
  <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="aggressive"><![CDATA[
mkdir parts/ &&

MzMLSplitter

#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>
  <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) ">
      <option value="KB">KB</option>
      <option value="MB" selected="true">MB</option>
      <option value="GB">GB</option>
    </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) "/>
    </expand>
  </inputs>
  <outputs>
    <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 https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_MzMLSplitter.html</help>
<expand macro="references"/>
</tool>

8:a2bf6f5def91

<?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="@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="exit_code"><![CDATA[@QUOTE_FOO@
@EXT_FOO@
#import re

## Preprocessing
mkdir in &&
ln -s '$in' 'in/${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 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="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 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>
    <expand macro="autotest_MzMLSplitter"/>
    <expand macro="manutest_MzMLSplitter"/>
  </tests>
  <help><![CDATA[Splits an mzML file into multiple parts


For more information, visit http://www.openms.de/documentation/UTILS_MzMLSplitter.html]]></help>
  <expand macro="references"/>
</tool>