comparison CompNovoCID.xml @ 9:e06fcd216b76 draft

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

8:9b0d7aae8094

<?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="CompNovoCID" name="CompNovoCID" version="2.2.0">
  <description>Performs a de novo peptide identification using the CompNovo engine.</description>
  <macros>
    <token name="@EXECUTABLE@">CompNovoCID</token>
    <import>macros.xml</import>
  </macros>

    <param name="param_algorithm_number_of_hits" type="integer" value="100" label="maximal number of hits which are reported per spectrum" help="(-number_of_hits) "/>
    <param name="param_algorithm_estimate_precursor_mz" display="radio" type="select" optional="False" value="true" label="If set to true, the precursor charge will be estimated," help="(-estimate_precursor_mz) e.g. from the precursor peaks of the ETD spectrum. &lt;br&gt;The input is believed otherwise">
      <option value="true" selected="true">true</option>
      <option value="false">false</option>
    </param>
    <repeat name="rep_param_algorithm_fixed_modifications" min="0" max="1" title="param_algorithm_fixed_modifications">
      <param name="param_algorithm_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="sulfo+amino (Y)">sulfo+amino (Y)</option>
        <option value="thioacylPA (K)">thioacylPA (K)</option>
        <option value="trifluoro (L)">trifluoro (L)</option>
      </param>
    </repeat>
    <repeat name="rep_param_algorithm_variable_modifications" min="0" max="1" title="param_algorithm_variable_modifications">
      <param name="param_algorithm_variable_modifications" type="select" optional="True" label="variable modifications, specified using UniMod (www.unimod.org) terms," help="(-variable_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>

9:e06fcd216b76

<?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="CompNovoCID" name="CompNovoCID" version="2.3.0">
  <description>Performs a de novo peptide identification using the CompNovo engine.</description>
  <macros>
    <token name="@EXECUTABLE@">CompNovoCID</token>
    <import>macros.xml</import>
  </macros>

    <param name="param_algorithm_number_of_hits" type="integer" value="100" label="maximal number of hits which are reported per spectrum" help="(-number_of_hits) "/>
    <param name="param_algorithm_estimate_precursor_mz" display="radio" type="select" optional="False" value="true" label="If set to true, the precursor charge will be estimated," help="(-estimate_precursor_mz) e.g. from the precursor peaks of the ETD spectrum. &lt;br&gt;The input is believed otherwise">
      <option value="true" selected="true">true</option>
      <option value="false">false</option>
    </param>
    <repeat name="rep_param_algorithm_fixed_modifications" min="0" title="param_algorithm_fixed_modifications">
      <param name="param_algorithm_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="sulfo+amino (Y)">sulfo+amino (Y)</option>
        <option value="thioacylPA (K)">thioacylPA (K)</option>
        <option value="trifluoro (L)">trifluoro (L)</option>
      </param>
    </repeat>
    <repeat name="rep_param_algorithm_variable_modifications" min="0" title="param_algorithm_variable_modifications">
      <param name="param_algorithm_variable_modifications" type="select" optional="True" label="variable modifications, specified using UniMod (www.unimod.org) terms," help="(-variable_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>