comparison ConvertTSVToTraML.xml @ 4:6ead64a594bd draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty

3:ec62782f6c68

<?xml version='1.0' encoding='UTF-8'?>
<tool id="ConvertTSVToTraML" name="ConvertTSVToTraML" version="1.12.0">
  <description>Converts an OpenSWATH transition TSV file to a TraML file</description>
  <macros>
    <token name="@EXECUTABLE@">ConvertTSVToTraML</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>ConvertTSVToTraML

-in ${param_in}
-in_type ${param_in_type}
-out ${param_out}
-threads \${GALAXY_SLOTS:-24} 
#if $adv_opts.adv_opts_selector=='advanced':
    -algorithm:retentionTimeInterpretation ${adv_opts.param_retentionTimeInterpretation}
    ${adv_opts.param_override_group_label_check}
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="tabular" optional="False" label="Input OpenSWATH transition TSV file or SpectraST MRM file.#br# See http://www.openms.de/current_doxygen/html/UTILS_ConvertTSVToTraML.html for format." help="(-in)"/>
    <param name="param_in_type" type="select" optional="True" label="input file type -- default: determined from file extension or content#br#" help="(-in_type)">
      <option value="tsv">tsv</option>
      <option value="csv">csv</option>
      <option value="mrm">mrm</option>
    </param>
    <expand macro="advanced_options">
      <param name="param_retentionTimeInterpretation" type="select" optional="True" 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">iRT</option>
        <option value="seconds">seconds</option>
        <option value="minutes">minutes</option>
      </param>
      <param name="param_override_group_label_check" type="boolean" truevalue="-algorithm:override_group_label_check true" falsevalue="-algorithm:override_group_label_check false" 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). Only turn this off if you know what you are doing." help="(-override_group_label_check)"/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" label="Output TraML file" format="data"/>
  </outputs>
  <help>**What it does**

Converts an OpenSWATH transition TSV file to a TraML file


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

@REFERENCES@
</help>
</tool>

4:6ead64a594bd

<?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="ConvertTSVToTraML" name="ConvertTSVToTraML" version="2.0.0">
    <description>Converts an OpenSWATH transition TSV file to a TraML file</description>
    <macros>
      <token name="@EXECUTABLE@">ConvertTSVToTraML</token>
      <import>macros.xml</import>
    </macros>
    <expand macro="references"/>
    <expand macro="stdio"/>
    <expand macro="requirements"/>
    <command>ConvertTSVToTraML

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
-threads \${GALAXY_SLOTS:-24}
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
    #if $adv_opts.param_algorithm_retentionTimeInterpretation:
  -algorithm:retentionTimeInterpretation
  #if &quot; &quot; in str($adv_opts.param_algorithm_retentionTimeInterpretation):
    &quot;$adv_opts.param_algorithm_retentionTimeInterpretation&quot;
  #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
#end if
</command>
    <inputs>
      <param format="tabular" help="(-in) &lt;br&gt; See http://www.openms.de/current_doxygen/html/UTILS_ConvertTSVToTraML.html for format" label="Input OpenSWATH transition TSV file or SpectraST MRM file" name="param_in" optional="False" type="data"/>
      <expand macro="advanced_options">
        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
        <param help="(-retentionTimeInterpretation) " label="How to interpret the provided retention time (the retention time column can either be interpreted to be in iRT, minutes or seconds)" name="param_algorithm_retentionTimeInterpretation" optional="True" type="select" value="iRT">
          <option value="iRT">iRT</option>
          <option value="seconds">seconds</option>
          <option value="minutes">minutes</option>
        </param>
        <param checked="false" falsevalue="" help="(-override_group_label_check) Only turn this off if you know what you are doing" 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)" name="param_algorithm_override_group_label_check" optional="True" truevalue="-algorithm:override_group_label_check" type="boolean"/>
      </expand>
    </inputs>
    <outputs>
      <data format="traml" name="param_out"/>
    </outputs>
    <help>Converts an OpenSWATH transition TSV file to a TraML file


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