annotate MzMLSplitter.xml @ 0:60b83eb38cd4 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8

<?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.-->
<!--Proposed Tool Section: [Utilities]-->
<tool id="MzMLSplitter" name="MzMLSplitter" version="2.1.0">
  <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="stdio"/>
  <expand macro="requirements"/>
  <command>MzMLSplitter

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out     "$param_out"
#end if
#if $param_parts:
  -parts $param_parts
#end if
#if $param_size:
  -size $param_size
#end if
#if $param_unit:
  -unit $param_unit
#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
&gt; $param_stdout
</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>
    <data name="param_stdout" format="text" label="Output from stdout"/>
  </outputs>
  <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>
</tool>