comparison PeptideIndexer.xml @ 5:fc6ccd403439 draft

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

4:e039cc5c7aed

<?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: [ID Processing]-->
<tool id="PeptideIndexer" name="PeptideIndexer" version="2.2.0">
  <description>Refreshes the protein references for all peptide hits.</description>
  <macros>
    <token name="@EXECUTABLE@">PeptideIndexer</token>
    <import>macros.xml</import>
  </macros>

    <param name="param_mismatches_max" type="integer" min="0" optional="True" value="0" label="[tolerant search only] Maximal number of real mismatches (will be used after checking for ambiguous AA's (see 'aaa_max' option)" help="(-mismatches_max) In general this param should only be changed if you want to look for other potential origins of a peptide which might have unknown SNPs or the like"/>
    <param name="param_IL_equivalent" display="radio" type="boolean" truevalue="-IL_equivalent" falsevalue="" checked="false" optional="True" label="Treat the isobaric amino acids isoleucine ('I') and leucine ('L') as equivalent (indistinguishable)" help="(-IL_equivalent) "/>
    <param name="param_filter_aaa_proteins" display="radio" type="boolean" truevalue="-filter_aaa_proteins" falsevalue="" checked="false" optional="True" label="In the tolerant search for matches to proteins with ambiguous amino acids (AAAs), rebuild the search database to only consider proteins with AAAs" help="(-filter_aaa_proteins) This may save time if most proteins don't contain AAAs and if there is a significant number of peptides that enter the tolerant search"/>
    <param name="param_enzyme_name" type="select" optional="False" value="Trypsin" label="Enzyme which determines valid cleavage sites -" help="(-name) e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P)">
      <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
      <option value="CNBr">CNBr</option>
      <option value="Asp-N_ambic">Asp-N_ambic</option>
      <option value="Trypsin" selected="true">Trypsin</option>
      <option value="Formic_acid">Formic_acid</option>
      <option value="TrypChymo">TrypChymo</option>
      <option value="proline endopeptidase">proline endopeptidase</option>
      <option value="Lys-C/P">Lys-C/P</option>
      <option value="Chymotrypsin">Chymotrypsin</option>
      <option value="Arg-C">Arg-C</option>
      <option value="PepsinA">PepsinA</option>
      <option value="Asp-N">Asp-N</option>
      <option value="Trypsin/P">Trypsin/P</option>
      <option value="Lys-C">Lys-C</option>
      <option value="no cleavage">no cleavage</option>
      <option value="unspecific cleavage">unspecific cleavage</option>
      <option value="2-iodobenzoate">2-iodobenzoate</option>
      <option value="V8-E">V8-E</option>
      <option value="leukocyte elastase">leukocyte elastase</option>
      <option value="V8-DE">V8-DE</option>
    </param>
    <param name="param_enzyme_specificity" display="radio" type="select" optional="False" value="full" label="Specificity of the enzyme" help="(-specificity) &lt;br&gt;  'full': both internal cleavage sites must match. &lt;br&gt;  'semi': one of two internal cleavage sites must match. &lt;br&gt;  'none': allow all peptide hits no matter their context. Therefore, the enzyme chosen does not play a role here">
      <option value="full" selected="true">full</option>
      <option value="semi">semi</option>
      <option value="none">none</option>

5:fc6ccd403439

<?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: [ID Processing]-->
<tool id="PeptideIndexer" name="PeptideIndexer" version="2.3.0">
  <description>Refreshes the protein references for all peptide hits.</description>
  <macros>
    <token name="@EXECUTABLE@">PeptideIndexer</token>
    <import>macros.xml</import>
  </macros>

    <param name="param_mismatches_max" type="integer" min="0" optional="True" value="0" label="[tolerant search only] Maximal number of real mismatches (will be used after checking for ambiguous AA's (see 'aaa_max' option)" help="(-mismatches_max) In general this param should only be changed if you want to look for other potential origins of a peptide which might have unknown SNPs or the like"/>
    <param name="param_IL_equivalent" display="radio" type="boolean" truevalue="-IL_equivalent" falsevalue="" checked="false" optional="True" label="Treat the isobaric amino acids isoleucine ('I') and leucine ('L') as equivalent (indistinguishable)" help="(-IL_equivalent) "/>
    <param name="param_filter_aaa_proteins" display="radio" type="boolean" truevalue="-filter_aaa_proteins" falsevalue="" checked="false" optional="True" label="In the tolerant search for matches to proteins with ambiguous amino acids (AAAs), rebuild the search database to only consider proteins with AAAs" help="(-filter_aaa_proteins) This may save time if most proteins don't contain AAAs and if there is a significant number of peptides that enter the tolerant search"/>
    <param name="param_enzyme_name" type="select" optional="False" value="Trypsin" label="Enzyme which determines valid cleavage sites -" help="(-name) e.g. trypsin cleaves after lysine (K) or arginine (R), but not before proline (P)">
      <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
      <option value="TrypChymo">TrypChymo</option>
      <option value="unspecific cleavage">unspecific cleavage</option>
      <option value="Trypsin/P">Trypsin/P</option>
      <option value="Alpha-lytic protease">Alpha-lytic protease</option>
      <option value="V8-DE">V8-DE</option>
      <option value="V8-E">V8-E</option>
      <option value="PepsinA">PepsinA</option>
      <option value="Asp-N">Asp-N</option>
      <option value="2-iodobenzoate">2-iodobenzoate</option>
      <option value="Lys-N">Lys-N</option>
      <option value="Asp-N_ambic">Asp-N_ambic</option>
      <option value="CNBr">CNBr</option>
      <option value="Asp-N/B">Asp-N/B</option>
      <option value="Formic_acid">Formic_acid</option>
      <option value="Chymotrypsin">Chymotrypsin</option>
      <option value="Lys-C">Lys-C</option>
      <option value="Trypsin" selected="true">Trypsin</option>
      <option value="Arg-C">Arg-C</option>
      <option value="Arg-C/P">Arg-C/P</option>
      <option value="Lys-C/P">Lys-C/P</option>
      <option value="no cleavage">no cleavage</option>
      <option value="leukocyte elastase">leukocyte elastase</option>
      <option value="proline endopeptidase">proline endopeptidase</option>
      <option value="Chymotrypsin/P">Chymotrypsin/P</option>
    </param>
    <param name="param_enzyme_specificity" display="radio" type="select" optional="False" value="full" label="Specificity of the enzyme" help="(-specificity) &lt;br&gt;  'full': both internal cleavage sites must match. &lt;br&gt;  'semi': one of two internal cleavage sites must match. &lt;br&gt;  'none': allow all peptide hits no matter their context. Therefore, the enzyme chosen does not play a role here">
      <option value="full" selected="true">full</option>
      <option value="semi">semi</option>
      <option value="none">none</option>