view MascotAdapter.xml @ 6:b4d8885a6cce draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8fcd33df23901e111d6c18f450bd09cd8cb3819e

<?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="MascotAdapter" name="MascotAdapter" version="2.2.0.1">
  <description>Annotates MS/MS spectra using Mascot.</description>
  <macros>
    <token name="@EXECUTABLE@">MascotAdapter</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>MascotAdapter

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_mascot_in:
  -mascot_in
#end if
#if $param_mascot_out:
  -mascot_out
#end if
#if $param_instrument:
  -instrument     "$param_instrument"
#end if
#if $param_precursor_mass_tolerance:
  -precursor_mass_tolerance $param_precursor_mass_tolerance
#end if
#if $param_peak_mass_tolerance:
  -peak_mass_tolerance $param_peak_mass_tolerance
#end if
#if $param_taxonomy:
  -taxonomy
  #if " " in str($param_taxonomy):
    "$param_taxonomy"
  #else
    $param_taxonomy
  #end if
#end if

#if $rep_param_modifications:
-modifications
  #for token in $rep_param_modifications:
    #if " " in str(token):
      "$token.param_modifications"
    #else
      $token.param_modifications
    #end if
  #end for
#end if

#if $rep_param_variable_modifications:
-variable_modifications
  #for token in $rep_param_variable_modifications:
    #if " " in str(token):
      "$token.param_variable_modifications"
    #else
      $token.param_variable_modifications
    #end if
  #end for
#end if

#if $rep_param_charges:
-charges
  #for token in $rep_param_charges:
    #if " " in str(token):
      "$token.param_charges"
    #else
      $token.param_charges
    #end if
  #end for
#end if
#if $param_db:
  -db     "$param_db"
#end if
#if $param_hits:
  -hits     "$param_hits"
#end if
#if $param_cleavage:
  -cleavage
  #if " " in str($param_cleavage):
    "$param_cleavage"
  #else
    $param_cleavage
  #end if
#end if
#if $param_missed_cleavages:
  -missed_cleavages $param_missed_cleavages
#end if
#if $param_sig_threshold:
  -sig_threshold $param_sig_threshold
#end if
#if $param_pep_homol:
  -pep_homol $param_pep_homol
#end if
#if $param_pep_ident:
  -pep_ident $param_pep_ident
#end if
#if $param_pep_rank:
  -pep_rank $param_pep_rank
#end if
#if $param_prot_score:
  -prot_score $param_prot_score
#end if
#if $param_pep_score:
  -pep_score $param_pep_score
#end if
#if $param_pep_exp_z:
  -pep_exp_z $param_pep_exp_z
#end if
#if $param_show_unassigned:
  -show_unassigned $param_show_unassigned
#end if
#if $param_first_dim_rt:
  -first_dim_rt $param_first_dim_rt
#end if
#if $param_boundary:
  -boundary     "$param_boundary"
#end if
#if $param_mass_type:
  -mass_type
  #if " " in str($param_mass_type):
    "$param_mass_type"
  #else
    $param_mass_type
  #end if
#end if
#if $param_mascot_directory:
  -mascot_directory     "$param_mascot_directory"
#end if
#if $param_temp_data_directory:
  -temp_data_directory     "$param_temp_data_directory"
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="txt" label="input file in mzData format" help="(-in) &lt;br&gt;Note: In mode 'mascot_out' a Mascot results file (.mascotXML) is read"/>
    <param name="param_mascot_in" display="radio" type="boolean" truevalue="-mascot_in" falsevalue="" checked="false" optional="True" label="if this flag is set the MascotAdapter will read in mzData and write Mascot generic format" help="(-mascot_in) "/>
    <param name="param_mascot_out" display="radio" type="boolean" truevalue="-mascot_out" falsevalue="" checked="false" optional="True" label="if this flag is set the MascotAdapter will read in a Mascot results file (.mascotXML) and write idXML" help="(-mascot_out) "/>
    <param name="param_instrument" type="text" size="30" value="Default" label="the instrument that was used to measure the spectra" help="(-instrument) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_precursor_mass_tolerance" type="float" value="2.0" label="the precursor mass tolerance" help="(-precursor_mass_tolerance) "/>
    <param name="param_peak_mass_tolerance" type="float" value="1.0" label="the peak mass tolerance" help="(-peak_mass_tolerance) "/>
    <param name="param_taxonomy" type="select" optional="False" value="All entries" label="the taxonomy" help="(-taxonomy) ">
      <option value="All entries" selected="true">All entries</option>
      <option value=". . Archaea (Archaeobacteria)">. . Archaea (Archaeobacteria)</option>
      <option value=". . Eukaryota (eucaryotes)">. . Eukaryota (eucaryotes)</option>
      <option value=". . . . Alveolata (alveolates)">. . . . Alveolata (alveolates)</option>
      <option value=". . . . . . Plasmodium falciparum (malaria parasite)">. . . . . . Plasmodium falciparum (malaria parasite)</option>
      <option value=". . . . . . Other Alveolata">. . . . . . Other Alveolata</option>
      <option value=". . . . Metazoa (Animals)">. . . . Metazoa (Animals)</option>
      <option value=". . . . . . Caenorhabditis elegans">. . . . . . Caenorhabditis elegans</option>
      <option value=". . . . . . Drosophila (fruit flies)">. . . . . . Drosophila (fruit flies)</option>
      <option value=". . . . . . Chordata (vertebrates and relatives)">. . . . . . Chordata (vertebrates and relatives)</option>
      <option value=". . . . . . . . bony vertebrates">. . . . . . . . bony vertebrates</option>
      <option value=". . . . . . . . . . lobe-finned fish and tetrapod clade">. . . . . . . . . . lobe-finned fish and tetrapod clade</option>
      <option value=". . . . . . . . . . . . Mammalia (mammals)">. . . . . . . . . . . . Mammalia (mammals)</option>
      <option value=". . . . . . . . . . . . . . Primates">. . . . . . . . . . . . . . Primates</option>
      <option value=". . . . . . . . . . . . . . . . Homo sapiens (human)">. . . . . . . . . . . . . . . . Homo sapiens (human)</option>
      <option value=". . . . . . . . . . . . . . . . Other primates">. . . . . . . . . . . . . . . . Other primates</option>
      <option value=". . . . . . . . . . . . . . Rodentia (Rodents)">. . . . . . . . . . . . . . Rodentia (Rodents)</option>
      <option value=". . . . . . . . . . . . . . . . Mus.">. . . . . . . . . . . . . . . . Mus.</option>
      <option value=". . . . . . . . . . . . . . . . . . Mus musculus (house mouse)">. . . . . . . . . . . . . . . . . . Mus musculus (house mouse)</option>
      <option value=". . . . . . . . . . . . . . . . Rattus">. . . . . . . . . . . . . . . . Rattus</option>
      <option value=". . . . . . . . . . . . . . . . Other rodentia">. . . . . . . . . . . . . . . . Other rodentia</option>
      <option value=". . . . . . . . . . . . . . Other mammalia">. . . . . . . . . . . . . . Other mammalia</option>
      <option value=". . . . . . . . . . . . Xenopus laevis (African clawed frog)">. . . . . . . . . . . . Xenopus laevis (African clawed frog)</option>
      <option value=". . . . . . . . . . . . Other lobe-finned fish and tetrapod clade">. . . . . . . . . . . . Other lobe-finned fish and tetrapod clade</option>
      <option value=". . . . . . . . . . Actinopterygii (ray-finned fishes)">. . . . . . . . . . Actinopterygii (ray-finned fishes)</option>
      <option value=". . . . . . . . . . . . Takifugu rubripes (Japanese Pufferfish)">. . . . . . . . . . . . Takifugu rubripes (Japanese Pufferfish)</option>
      <option value=". . . . . . . . . . . . Danio rerio (zebra fish)">. . . . . . . . . . . . Danio rerio (zebra fish)</option>
      <option value=". . . . . . . . . . . . Other Actinopterygii">. . . . . . . . . . . . Other Actinopterygii</option>
      <option value=". . . . . . . . Other Chordata">. . . . . . . . Other Chordata</option>
      <option value=". . . . . . Other Metazoa">. . . . . . Other Metazoa</option>
      <option value=". . . . Dictyostelium discoideum">. . . . Dictyostelium discoideum</option>
      <option value=". . . . Fungi">. . . . Fungi</option>
      <option value=". . . . . . Saccharomyces Cerevisiae (baker's yeast)">. . . . . . Saccharomyces Cerevisiae (baker's yeast)</option>
      <option value=". . . . . . Schizosaccharomyces pombe (fission yeast)">. . . . . . Schizosaccharomyces pombe (fission yeast)</option>
      <option value=". . . . . . Pneumocystis carinii">. . . . . . Pneumocystis carinii</option>
      <option value=". . . . . . Other Fungi">. . . . . . Other Fungi</option>
      <option value=". . . . Viridiplantae (Green Plants)">. . . . Viridiplantae (Green Plants)</option>
      <option value=". . . . . . Arabidopsis thaliana (thale cress)">. . . . . . Arabidopsis thaliana (thale cress)</option>
      <option value=". . . . . . Oryza sativa (rice)">. . . . . . Oryza sativa (rice)</option>
      <option value=". . . . . . Other green plants">. . . . . . Other green plants</option>
      <option value=". . . . Other Eukaryota">. . . . Other Eukaryota</option>
      <option value=". . Bacteria (Eubacteria)">. . Bacteria (Eubacteria)</option>
      <option value=". . . . Actinobacteria (class)">. . . . Actinobacteria (class)</option>
      <option value=". . . . . . Mycobacterium tuberculosis complex">. . . . . . Mycobacterium tuberculosis complex</option>
      <option value=". . . . . . Other Actinobacteria (class)">. . . . . . Other Actinobacteria (class)</option>
      <option value=". . . . Firmicutes (gram-positive bacteria)">. . . . Firmicutes (gram-positive bacteria)</option>
      <option value=". . . . . . Bacillus subtilis">. . . . . . Bacillus subtilis</option>
      <option value=". . . . . . Mycoplasma">. . . . . . Mycoplasma</option>
      <option value=". . . . . . Streptococcus Pneumoniae">. . . . . . Streptococcus Pneumoniae</option>
      <option value=". . . . . . Streptomyces coelicolor">. . . . . . Streptomyces coelicolor</option>
      <option value=". . . . . . Other Firmicutes">. . . . . . Other Firmicutes</option>
      <option value=". . . . Proteobacteria (purple bacteria)">. . . . Proteobacteria (purple bacteria)</option>
      <option value=". . . . . . Agrobacterium tumefaciens">. . . . . . Agrobacterium tumefaciens</option>
      <option value=". . . . . . Campylobacter jejuni">. . . . . . Campylobacter jejuni</option>
      <option value=". . . . . . Escherichia coli">. . . . . . Escherichia coli</option>
      <option value=". . . . . . Neisseria meningitidis">. . . . . . Neisseria meningitidis</option>
      <option value=". . . . . . Salmonella">. . . . . . Salmonella</option>
      <option value=". . . . . . Other Proteobacteria">. . . . . . Other Proteobacteria</option>
      <option value=". . . . Other Bacteria">. . . . Other Bacteria</option>
      <option value=". . Viruses">. . Viruses</option>
      <option value=". . . . Hepatitis C virus">. . . . Hepatitis C virus</option>
      <option value=". . . . Other viruses">. . . . Other viruses</option>
      <option value=". . Other (includes plasmids and artificial sequences)">. . Other (includes plasmids and artificial sequences)</option>
      <option value=". . unclassified">. . unclassified</option>
      <option value=". . Species information unavailable">. . Species information unavailable</option>
    </param>
    <repeat name="rep_param_modifications" min="0" max="1" title="param_modifications">
      <param name="param_modifications" type="text" size="30" label="the modifications i.e. Carboxymethyl (C)" help="(-modifications) ">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
    </repeat>
    <repeat name="rep_param_variable_modifications" min="0" max="1" title="param_variable_modifications">
      <param name="param_variable_modifications" type="text" size="30" label="the variable modifications i.e. Carboxymethyl (C)" help="(-variable_modifications) ">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
    </repeat>
    <repeat name="rep_param_charges" min="0" max="1" title="param_charges">
      <param name="param_charges" type="text" size="30" value="1+ 2+ 3+" label="the different charge states" help="(-charges) ">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
    </repeat>
    <param name="param_db" type="text" size="30" value="MSDB" label="the database to search in" help="(-db) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_hits" type="text" size="30" value="AUTO" label="the number of hits to report" help="(-hits) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_cleavage" type="select" optional="False" value="Trypsin" label="The enzyme descriptor to the enzyme used for digestion" help="(-cleavage) (Trypsin is default, None would be best for peptide input or unspecific digestion, for more please refer to your mascot server)">
      <option value="Trypsin" selected="true">Trypsin</option>
      <option value="Arg-C">Arg-C</option>
      <option value="Asp-N">Asp-N</option>
      <option value="Asp-N_ambic">Asp-N_ambic</option>
      <option value="Chymotrypsin">Chymotrypsin</option>
      <option value="CNBr">CNBr</option>
      <option value="CNBr+Trypsin">CNBr+Trypsin</option>
      <option value="Formic_acid">Formic_acid</option>
      <option value="Lys-C">Lys-C</option>
      <option value="Lys-C/P">Lys-C/P</option>
      <option value="PepsinA">PepsinA</option>
      <option value="Tryp-CNBr">Tryp-CNBr</option>
      <option value="TrypChymo">TrypChymo</option>
      <option value="Trypsin/P">Trypsin/P</option>
      <option value="V8-DE">V8-DE</option>
      <option value="V8-E">V8-E</option>
      <option value="semiTrypsin">semiTrypsin</option>
      <option value="LysC+AspN">LysC+AspN</option>
      <option value="None">None</option>
    </param>
    <param name="param_missed_cleavages" type="integer" min="0" optional="True" value="0" label="number of allowed missed cleavages" help="(-missed_cleavages) "/>
    <param name="param_sig_threshold" type="float" value="0.05" label="significance threshold" help="(-sig_threshold) "/>
    <param name="param_pep_homol" type="float" value="1.0" label="peptide homology threshold" help="(-pep_homol) "/>
    <param name="param_pep_ident" type="float" value="1.0" label="peptide ident threshold" help="(-pep_ident) "/>
    <param name="param_pep_rank" type="integer" value="1" label="peptide rank" help="(-pep_rank) "/>
    <param name="param_prot_score" type="float" value="1.0" label="protein score" help="(-prot_score) "/>
    <param name="param_pep_score" type="float" value="1.0" label="peptide score" help="(-pep_score) "/>
    <param name="param_pep_exp_z" type="integer" value="1" label="peptide expected charge" help="(-pep_exp_z) "/>
    <param name="param_show_unassigned" type="integer" value="1" label="show_unassigned" help="(-show_unassigned) "/>
    <param name="param_first_dim_rt" type="float" value="0.0" label="additional information which is added to every peptide identification as metavalue if set &gt; 0" help="(-first_dim_rt) "/>
    <param name="param_boundary" type="text" size="30" label="MIME boundary for mascot output format" help="(-boundary) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_mass_type" display="radio" type="select" optional="False" value="Monoisotopic" label="mass type" help="(-mass_type) ">
      <option value="Monoisotopic" selected="true">Monoisotopic</option>
      <option value="Average">Average</option>
    </param>
    <param name="param_mascot_directory" type="text" size="30" label="the directory in which mascot is located" help="(-mascot_directory) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_temp_data_directory" type="text" size="30" label="a directory in which some temporary files can be stored" help="(-temp_data_directory) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <expand macro="advanced_options">
      <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" format="data"/>
  </outputs>
  <help>Annotates MS/MS spectra using Mascot.


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