view FileConverter.xml @ 0:3d84209d3178 draft

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<?xml version='1.0' encoding='UTF-8'?>
<tool id="FileConverter" name="FileConverter" version="1.12.0">
  <description>Converts between different MS file formats.</description>
  <macros>
    <token name="@EXECUTABLE@">FileConverter</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>FileConverter

-in ${param_in}
-in_type ${param_in_type}
-UID_postprocessing ${param_UID_postprocessing}
-out ${param_out}
-out_type ${param_out_type}
${param_write_mzML_index}
-threads \${GALAXY_SLOTS:-24} 
#if $adv_opts.adv_opts_selector=='advanced':
    ${adv_opts.param_TIC_DTA2D}
    ${adv_opts.param_MGF_compact}
    ${adv_opts.param_process_lowmemory}
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="mzXML,mzML,mgf,featureXML,consensusXML" optional="False" label="Input file to convert." help="(-in)"/>
    <param name="param_in_type" type="select" optional="True" label="Input file type -- default: determined from file extension or content#br#" help="(-in_type)">
      <option value="mzData">mzData</option>
      <option value="mzXML">mzXML</option>
      <option value="mzML">mzML</option>
      <option value="dta">dta</option>
      <option value="dta2d">dta2d</option>
      <option value="mgf">mgf</option>
      <option value="featureXML">featureXML</option>
      <option value="consensusXML">consensusXML</option>
      <option value="ms2">ms2</option>
      <option value="fid">fid</option>
      <option value="tsv">tsv</option>
      <option value="peplist">peplist</option>
      <option value="kroenik">kroenik</option>
      <option value="edta">edta</option>
    </param>
    <param name="param_UID_postprocessing" type="select" optional="True" value="ensure" label="unique ID post-processing for output data.#br#'none' keeps current IDs even if invalid.#br#'ensure' keeps current IDs but reassigns invalid ones.#br#'reassign' assigns new unique IDs." help="(-UID_postprocessing)">
      <option value="none">none</option>
      <option value="ensure">ensure</option>
      <option value="reassign">reassign</option>
    </param>
    <param name="param_out_type" type="select" optional="True" label="Output file type -- default: determined from file extension or content#br#Note: that not all conversion paths work or make sense." help="(-out_type)">
      <option value="mzData">mzData</option>
      <option value="mzXML">mzXML</option>
      <option value="mzML">mzML</option>
      <option value="dta2d">dta2d</option>
      <option value="mgf">mgf</option>
      <option value="featureXML">featureXML</option>
      <option value="consensusXML">consensusXML</option>
      <option value="edta">edta</option>
      <option value="csv">csv</option>
    </param>
    <param name="param_write_mzML_index" type="boolean" truevalue="-write_mzML_index true" falsevalue="-write_mzML_index false" checked="false" optional="True" label="Whether to add an index to the file when writing mzML files" help="(-write_mzML_index)"/>
    <expand macro="advanced_options">
      <param name="param_TIC_DTA2D" type="boolean" truevalue="-TIC_DTA2D true" falsevalue="-TIC_DTA2D false" checked="false" optional="True" label="Export the TIC instead of the entire experiment in mzML/mzData/mzXML -&gt; DTA2D conversions." help="(-TIC_DTA2D)"/>
      <param name="param_MGF_compact" type="boolean" truevalue="-MGF_compact true" falsevalue="-MGF_compact false" checked="false" optional="True" label="Use a more compact format when writing MGF (no zero-intensity peaks, limited number of decimal places)" help="(-MGF_compact)"/>
      <param name="param_process_lowmemory" type="boolean" truevalue="-process_lowmemory true" falsevalue="-process_lowmemory false" checked="false" optional="True" label="Whether to process the file on the fly without loading the whole file into memory first (only for conversions of mzXML/mzML to mzML).#br#Note: this flag will prevent conversion from spectra to chromatograms." help="(-process_lowmemory)"/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" label="Output file" format="tabular">
      <change_format>
        <when input="param_out_type" value="mzXML" format="mzXML"/>
        <when input="param_out_type" value="mzML" format="mzML"/>
        <when input="param_out_type" value="mgf" format="mgf"/>
        <when input="param_out_type" value="featureXML" format="featureXML"/>
        <when input="param_out_type" value="consensusXML" format="consensusXML"/>
      </change_format>
    </data>
  </outputs>
  <help>**What it does**

Converts between different MS file formats.


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileConverter.html

@REFERENCES@
</help>
</tool>