annotate DTAExtractor.xml @ 4:22d30860be71 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d2b76821e22b13ed6e21795ac1b82446d8f594c6

<?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: [File Handling]-->
<tool id="DTAExtractor" name="DTAExtractor" version="2.2.0.1">
  <description>Extracts spectra of an MS run file to several files in DTA format.</description>
  <macros>
    <token name="@EXECUTABLE@">DTAExtractor</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>DTAExtractor

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out     "$param_out"
#end if
#if $param_mz:
  -mz     "$param_mz"
#end if
#if $param_rt:
  -rt     "$param_rt"
#end if
#if $param_level:
  -level     "$param_level"
#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="base name of DTA output files (RT, m/z and extension are appended)" help="(-out) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_mz" type="text" size="30" value=":" label="m/z range of precursor peaks to extract" help="(-mz) &lt;br&gt;This option is ignored for MS level 1">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_rt" type="text" size="30" value=":" label="retention time range of spectra to extract" help="(-rt) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_level" type="text" size="30" value="1,2,3" label="MS levels to extract" help="(-level) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <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="txt" label="Output from stdout"/>
  </outputs>
  <help>Extracts spectra of an MS run file to several files in DTA format.


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_DTAExtractor.html</help>
</tool>