comparison FileInfo.xml @ 0:3d84209d3178 draft

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0:3d84209d3178

<?xml version='1.0' encoding='UTF-8'?>
<tool id="FileInfo" name="FileInfo" version="1.12.0">
  <description>Shows basic information about the file, such as data ranges and file type.</description>
  <macros>
    <token name="@EXECUTABLE@">FileInfo</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>FileInfo

-in ${param_in}
-in_type ${param_in_type}
-out ${param_out}
${param_m}
${param_p}
${param_s}
${param_d}
${param_c}
${param_v}
${param_i}
-threads \${GALAXY_SLOTS:-24} 
#if $adv_opts.adv_opts_selector=='advanced':
    -out_tsv ${adv_opts.param_out_tsv}
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="mzXML,mzML,mgf,featureXML,consensusXML,idXML,pepXML" optional="False" label="input file " help="(-in)"/>
    <param name="param_in_type" type="select" optional="True" label="input file type -- default: determined from file extension or content" 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="idXML">idXML</option>
      <option value="pepXML">pepXML</option>
      <option value="fid">fid</option>
    </param>
    <param name="param_m" type="boolean" truevalue="-m true" falsevalue="-m false" checked="false" optional="True" label="Show meta information about the whole experiment" help="(-m)"/>
    <param name="param_p" type="boolean" truevalue="-p true" falsevalue="-p false" checked="false" optional="True" label="Shows data processing information" help="(-p)"/>
    <param name="param_s" type="boolean" truevalue="-s true" falsevalue="-s false" checked="false" optional="True" label="Computes a five-number statistics of intensities, qualities, and widths" help="(-s)"/>
    <param name="param_d" type="boolean" truevalue="-d true" falsevalue="-d false" checked="false" optional="True" label="Show detailed listing of all spectra and chromatograms (peak files only)" help="(-d)"/>
    <param name="param_c" type="boolean" truevalue="-c true" falsevalue="-c false" checked="false" optional="True" label="Check for corrupt data in the file (peak files only)" help="(-c)"/>
    <param name="param_v" type="boolean" truevalue="-v true" falsevalue="-v false" checked="false" optional="True" label="Validate the file only (for mzML, mzData, mzXML, featureXML, idXML, consensusXML, pepXML)" help="(-v)"/>
    <param name="param_i" type="boolean" truevalue="-i true" falsevalue="-i false" checked="false" optional="True" label="Check whether a given mzML file contains valid indices (conforming to the indexedmzML standard)" help="(-i)"/>
  </inputs>
  <outputs>
    <data name="param_out" label="Optional output file. If left out, the output is written to the command line." format="txt"/>
    <data name="param_out_tsv" label="Second optional output file. Tab separated flat text file." format="tabular"/>
  </outputs>
  <help>**What it does**

Shows basic information about the file, such as data ranges and file type.


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

@REFERENCES@
</help>
</tool>