comparison XTandemAdapter.xml @ 6:b09039836cb1 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b

5:c8b225c69a7f

<?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: [Identification]-->
<tool id="XTandemAdapter" name="XTandemAdapter" version="2.2.0.1">
  <description>Annotates MS/MS spectra using X! Tandem.</description>
  <macros>
    <token name="@EXECUTABLE@">XTandemAdapter</token>
    <import>macros.xml</import>
  </macros>

      <option value="ppm">ppm</option>
      <option value="Da" selected="true">Da</option>
    </param>
    <param name="param_max_precursor_charge" type="integer" min="0" optional="True" value="4" label="Maximum precursor charge ('0' to use X! Tandem default)" help="(-max_precursor_charge) "/>
    <param name="param_no_isotope_error" display="radio" type="boolean" truevalue="-no_isotope_error" falsevalue="" checked="false" optional="True" label="By default, misassignment to the first and second isotopic 13C peak are also considered" help="(-no_isotope_error) Set this flag to disable"/>
    <repeat name="rep_param_fixed_modifications" min="0"  title="param_fixed_modifications">
      <param name="param_fixed_modifications" type="select" optional="True" label="Fixed modifications, specified using Unimod (www.unimod.org) terms," help="(-fixed_modifications) e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
        <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
        <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
        <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option>
        <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option>

        <option value="trifluoro (L)">trifluoro (L)</option>
      </param>
    </repeat>
    <param name="param_minimum_fragment_mz" type="float" value="150.0" label="Minimum fragment mz" help="(-minimum_fragment_mz) "/>
    <param name="param_enzyme" type="select" optional="False" value="Trypsin" label="The enzyme used for peptide digestion" help="(-enzyme) ">
      <option value="CNBr">CNBr</option>
      <option value="Formic_acid">Formic_acid</option>
      <option value="TrypChymo">TrypChymo</option>
      <option value="PepsinA">PepsinA</option>
      <option value="2-iodobenzoate">2-iodobenzoate</option>
      <option value="Asp-N">Asp-N</option>
      <option value="Arg-C">Arg-C</option>
      <option value="V8-E">V8-E</option>
      <option value="Lys-C">Lys-C</option>
      <option value="V8-DE">V8-DE</option>
      <option value="leukocyte elastase">leukocyte elastase</option>
      <option value="Asp-N_ambic">Asp-N_ambic</option>
      <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
      <option value="Chymotrypsin">Chymotrypsin</option>
      <option value="Trypsin/P">Trypsin/P</option>
      <option value="Trypsin" selected="true">Trypsin</option>
      <option value="unspecific cleavage">unspecific cleavage</option>
      <option value="Lys-C/P">Lys-C/P</option>
    </param>
    <param name="param_missed_cleavages" type="integer" value="1" label="Number of possible cleavage sites missed by the enzyme" help="(-missed_cleavages) "/>
    <param name="param_semi_cleavage" display="radio" type="boolean" truevalue="-semi_cleavage" falsevalue="" checked="false" optional="True" label="Require only peptide end to have a valid cleavage site, not both" help="(-semi_cleavage) "/>
    <param name="param_output_results" display="radio" type="select" optional="False" value="all" label="Which hits should be reported" help="(-output_results) All, valid ones (passing the E-Value threshold), or stochastic (failing the threshold)">
      <option value="all" selected="true">all</option>

6:b09039836cb1

<?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: [Identification]-->
<tool id="XTandemAdapter" name="XTandemAdapter" version="2.3.0">
  <description>Annotates MS/MS spectra using X! Tandem.</description>
  <macros>
    <token name="@EXECUTABLE@">XTandemAdapter</token>
    <import>macros.xml</import>
  </macros>

      <option value="ppm">ppm</option>
      <option value="Da" selected="true">Da</option>
    </param>
    <param name="param_max_precursor_charge" type="integer" min="0" optional="True" value="4" label="Maximum precursor charge ('0' to use X! Tandem default)" help="(-max_precursor_charge) "/>
    <param name="param_no_isotope_error" display="radio" type="boolean" truevalue="-no_isotope_error" falsevalue="" checked="false" optional="True" label="By default, misassignment to the first and second isotopic 13C peak are also considered" help="(-no_isotope_error) Set this flag to disable"/>
    <repeat name="rep_param_fixed_modifications" min="0" title="param_fixed_modifications">
      <param name="param_fixed_modifications" type="select" optional="True" label="Fixed modifications, specified using Unimod (www.unimod.org) terms," help="(-fixed_modifications) e.g. 'Carbamidomethyl (C)' or 'Oxidation (M)'">
        <option value="15N-oxobutanoic (N-term C)">15N-oxobutanoic (N-term C)</option>
        <option value="2-dimethylsuccinyl (C)">2-dimethylsuccinyl (C)</option>
        <option value="2-monomethylsuccinyl (C)">2-monomethylsuccinyl (C)</option>
        <option value="2-nitrobenzyl (Y)">2-nitrobenzyl (Y)</option>

        <option value="trifluoro (L)">trifluoro (L)</option>
      </param>
    </repeat>
    <param name="param_minimum_fragment_mz" type="float" value="150.0" label="Minimum fragment mz" help="(-minimum_fragment_mz) "/>
    <param name="param_enzyme" type="select" optional="False" value="Trypsin" label="The enzyme used for peptide digestion" help="(-enzyme) ">
      <option value="Trypsin/P">Trypsin/P</option>
      <option value="2-iodobenzoate">2-iodobenzoate</option>
      <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
      <option value="Trypsin" selected="true">Trypsin</option>
      <option value="leukocyte elastase">leukocyte elastase</option>
      <option value="Asp-N">Asp-N</option>
      <option value="Arg-C">Arg-C</option>
      <option value="V8-DE">V8-DE</option>
      <option value="Arg-C/P">Arg-C/P</option>
      <option value="Alpha-lytic protease">Alpha-lytic protease</option>
      <option value="unspecific cleavage">unspecific cleavage</option>
      <option value="Lys-C">Lys-C</option>
      <option value="CNBr">CNBr</option>
      <option value="Chymotrypsin/P">Chymotrypsin/P</option>
      <option value="Lys-C/P">Lys-C/P</option>
      <option value="PepsinA">PepsinA</option>
      <option value="TrypChymo">TrypChymo</option>
      <option value="Asp-N_ambic">Asp-N_ambic</option>
      <option value="Asp-N/B">Asp-N/B</option>
      <option value="Chymotrypsin">Chymotrypsin</option>
      <option value="Lys-N">Lys-N</option>
      <option value="Formic_acid">Formic_acid</option>
      <option value="V8-E">V8-E</option>
    </param>
    <param name="param_missed_cleavages" type="integer" value="1" label="Number of possible cleavage sites missed by the enzyme" help="(-missed_cleavages) "/>
    <param name="param_semi_cleavage" display="radio" type="boolean" truevalue="-semi_cleavage" falsevalue="" checked="false" optional="True" label="Require only peptide end to have a valid cleavage site, not both" help="(-semi_cleavage) "/>
    <param name="param_output_results" display="radio" type="select" optional="False" value="all" label="Which hits should be reported" help="(-output_results) All, valid ones (passing the E-Value threshold), or stochastic (failing the threshold)">
      <option value="all" selected="true">all</option>