comparison FileConverter.xml @ 0:3070d71e0e5c draft

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0:3070d71e0e5c

<?xml version='1.0' encoding='UTF-8'?>
<tool id="FileConverter" name="FileConverter" version="2.0.0">
  <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

#if $param_in:
  -in $param_in
#end if
#if $param_UID_postprocessing:
  -UID_postprocessing
  #if " " in str($param_UID_postprocessing):
    "$param_UID_postprocessing"
  #else
    $param_UID_postprocessing
  #end if
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_out_type:
  -out_type
  #if " " in str($param_out_type):
    "$param_out_type"
  #else
    $param_out_type
  #end if
#end if
#if $param_write_mzML_index:
  -write_mzML_index
#end if
-threads \${GALAXY_SLOTS:-24} 
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_TIC_DTA2D:
  -TIC_DTA2D
#end if
    #if $adv_opts.param_MGF_compact:
  -MGF_compact
#end if
    #if $adv_opts.param_process_lowmemory:
  -process_lowmemory
#end if
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="mgf,mzml,mzxml,tabular,featurexml,consensusxml" optional="False" label="Input file to convert" help="(-in) "/>
    <param name="param_UID_postprocessing" type="select" optional="True" value="ensure" label="unique ID post-processing for output data" help="(-UID_postprocessing) &lt;br&gt;'none' keeps current IDs even if invalid. &lt;br&gt;'ensure' keeps current IDs but reassigns invalid ones. &lt;br&gt;'reassign' assigns new unique IDs">
      <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 &lt;br&gt;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" falsevalue="" checked="false" optional="True" label="Add an index to the file when writing mzML files (default: no index)" help="(-write_mzML_index) "/>
    <expand macro="advanced_options">
      <param name="param_TIC_DTA2D" type="boolean" truevalue="-TIC_DTA2D" falsevalue="" 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" falsevalue="" 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" falsevalue="" 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)" help="(-process_lowmemory) &lt;br&gt;Note: this flag will prevent conversion from spectra to chromatograms"/>
      <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" metadata_source="param_in" format="input"/>
  </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</help>
  <expand macro="references"/>
</tool>