annotate FileConverter.xml @ 9:1a186cc82c8d draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5

<?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: [File Handling]-->
<tool id="FileConverter" name="FileConverter" version="2.3.0">
  <description>Converts between different MS file formats.</description>
  <macros>
    <token name="@EXECUTABLE@">FileConverter</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command detect_errors="aggressive"><![CDATA[FileConverter

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_UID_postprocessing:
  -UID_postprocessing
  #if " " in str($adv_opts.param_UID_postprocessing):
    "$adv_opts.param_UID_postprocessing"
  #else
    $adv_opts.param_UID_postprocessing
  #end if
#end if
    #if $adv_opts.param_out_type:
  -out_type
  #if " " in str($adv_opts.param_out_type):
    "$adv_opts.param_out_type"
  #else
    $adv_opts.param_out_type
  #end if
#end if
    #if $adv_opts.param_TIC_DTA2D:
  -TIC_DTA2D
#end if
    #if $adv_opts.param_MGF_compact:
  -MGF_compact
#end if
    #if $adv_opts.param_force_MaxQuant_compatibility:
  -force_MaxQuant_compatibility
#end if
    #if $adv_opts.param_force_TPP_compatibility:
  -force_TPP_compatibility
#end if
    #if $adv_opts.param_write_scan_index:
  -write_scan_index
  #if " " in str($adv_opts.param_write_scan_index):
    "$adv_opts.param_write_scan_index"
  #else
    $adv_opts.param_write_scan_index
  #end if
#end if
    #if $adv_opts.param_lossy_compression:
  -lossy_compression
#end if
    #if $adv_opts.param_lossy_mass_accuracy:
  -lossy_mass_accuracy $adv_opts.param_lossy_mass_accuracy
#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="mzData,mzxml,mzml,cachedMzML,dta,dta2d,mgf,featurexml,consensusxml,ms2,fid,tabular,peplist,kroenik,tabular" optional="False" label="Input file to convert" help="(-in) "/>
    <expand macro="advanced_options">
      <param name="param_UID_postprocessing" display="radio" type="select" optional="False" 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" selected="true">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="cachedMzML">cachedMzML</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_TIC_DTA2D" display="radio" 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" display="radio" 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_force_MaxQuant_compatibility" display="radio" type="boolean" truevalue="-force_MaxQuant_compatibility" falsevalue="" checked="false" optional="True" label="[mzXML output only] Make sure that MaxQuant can read the mzXML and set the msManufacturer to 'Thermo Scientific'" help="(-force_MaxQuant_compatibility) "/>
      <param name="param_force_TPP_compatibility" display="radio" type="boolean" truevalue="-force_TPP_compatibility" falsevalue="" checked="false" optional="True" label="[mXML output only] Make sure that TPP parsers can read the mzML and the precursor ion m/z in the file (otherwise it will be set to zero by the TPP)" help="(-force_TPP_compatibility) "/>
      <param name="param_write_scan_index" display="radio" type="select" optional="False" value="true" label="Append an index when writing mzML or mzXML files" help="(-write_scan_index) Some external tools might rely on it">
        <option value="true" selected="true">true</option>
        <option value="false">false</option>
      </param>
      <param name="param_lossy_compression" display="radio" type="boolean" truevalue="-lossy_compression" falsevalue="" checked="false" optional="True" label="Use numpress compression to achieve optimally small file size (attention: may cause small loss of precision; only for mzML data)" help="(-lossy_compression) "/>
      <param name="param_lossy_mass_accuracy" type="float" value="-1.0" label="Desired (absolute) m/z accuracy for lossy compression (" help="(-lossy_mass_accuracy) e.g. use 0.0001 for a mass accuracy of 0.2 ppm at 500 m/z, default uses -1.0 for maximal accuracy)"/>
      <param name="param_process_lowmemory" display="radio" 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" display="radio" 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" auto_format="true"/>
  </outputs>
  <help>Converts between different MS file formats.


For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_FileConverter.html</help>
</tool>