annotate TargetedFileConverter.xml @ 2:9489083b668f draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d4b74e94ddabaccec6b1c5f9540d074c39207600

<?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: [Targeted Experiments]-->
<tool id="TargetedFileConverter" name="TargetedFileConverter" version="2.2.0">
  <description>Converts different transition files for targeted proteomics / metabolomics analysis.</description>
  <macros>
    <token name="@EXECUTABLE@">TargetedFileConverter</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>TargetedFileConverter

#if $param_in:
  -in $param_in
#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 $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_legacy_traml_id:
  -legacy_traml_id
#end if
    #if $adv_opts.param_force:
  -force
#end if
    #if $adv_opts.param_algorithm_retentionTimeInterpretation:
  -algorithm:retentionTimeInterpretation
  #if " " in str($adv_opts.param_algorithm_retentionTimeInterpretation):
    "$adv_opts.param_algorithm_retentionTimeInterpretation"
  #else
    $adv_opts.param_algorithm_retentionTimeInterpretation
  #end if
#end if
    #if $adv_opts.param_algorithm_override_group_label_check:
  -algorithm:override_group_label_check
#end if
    #if $adv_opts.param_algorithm_force_invalid_mods:
  -algorithm:force_invalid_mods
#end if
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="tabular,mrm,pqp,traml" optional="False" label="Input file to convert" help="(-in) &lt;br&gt; See http://www.openms.de/current_doxygen/html/UTILS_TargetedFileConverter.html for format of OpenSWATH transition TSV file or SpectraST MRM file"/>
    <param name="param_out_type" display="radio" 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="tsv">tsv</option>
      <option value="pqp">pqp</option>
      <option value="TraML">TraML</option>
    </param>
    <expand macro="advanced_options">
      <param name="param_legacy_traml_id" display="radio" type="boolean" truevalue="-legacy_traml_id" falsevalue="" checked="false" optional="True" label="PQP to TraML: Should legacy TraML IDs be used?" help="(-legacy_traml_id) "/>
      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
      <param name="param_algorithm_retentionTimeInterpretation" display="radio" type="select" optional="False" value="iRT" label="How to interpret the provided retention time (the retention time column can either be interpreted to be in iRT, minutes or seconds)" help="(-retentionTimeInterpretation) ">
        <option value="iRT" selected="true">iRT</option>
        <option value="seconds">seconds</option>
        <option value="minutes">minutes</option>
      </param>
      <param name="param_algorithm_override_group_label_check" display="radio" type="boolean" truevalue="-algorithm:override_group_label_check" falsevalue="" checked="false" optional="True" label="Override an internal check that assures that all members of the same PeptideGroupLabel have the same PeptideSequence (this ensures that only different isotopic forms of the same peptide can be grouped together in the same label group)" help="(-override_group_label_check) Only turn this off if you know what you are doing"/>
      <param name="param_algorithm_force_invalid_mods" display="radio" type="boolean" truevalue="-algorithm:force_invalid_mods" falsevalue="" checked="false" optional="True" label="Force reading even if invalid modifications are encountered (OpenMS may not recognize the modification)" help="(-force_invalid_mods) "/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" metadata_source="param_in" format="input"/>
  </outputs>
  <help>Converts different transition files for targeted proteomics / metabolomics analysis.


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