comparison MSGFPlusAdapter.xml @ 15:bb971f471df8 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5

14:0bef374d6c41

<?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="MSGFPlusAdapter" name="MSGFPlusAdapter" version="2.2.0">
  <description>MS/MS database search using MS-GF+.</description>
  <macros>
    <token name="@EXECUTABLE@">MSGFPlusAdapter</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command><![CDATA[

 ## check input file type
 #set $in_type = $param_in.ext

 ## create the symlinks to set the proper file extension, since msgf uses them to choose how to handle the input files

#end if
    #if $adv_opts.param_force:
  -force
#end if
#end if
]]>
</command>
  <inputs>
    <param name="param_in" type="data" format="mzml,mzxml,mgf,ms2" optional="False" label="Input file (MS-GF+ parameter '-s')" help="(-in) "/>
    <param name="param_database" type="data" format="fasta" optional="False" label="Protein sequence database (FASTA file; MS-GF+ parameter '-d')" help="(-database) Non-existing relative filenames are looked up via 'OpenMS.ini:id_db_dir'"/>
    <param name="param_add_decoys" display="radio" type="boolean" truevalue="-add_decoys" falsevalue="" checked="false" optional="True" label="Create decoy proteins (reversed sequences) and append them to the database for the search (MS-GF+ parameter '-tda')" help="(-add_decoys) This allows the calculation of FDRs, but should only be used if the database does not already contain decoys"/>
    <param name="param_precursor_mass_tolerance" type="float" value="20.0" label="Precursor monoisotopic mass tolerance (MS-GF+ parameter '-t')" help="(-precursor_mass_tolerance) "/>
    <param name="param_precursor_error_units" display="radio" type="select" optional="False" value="ppm" label="Unit of precursor mass tolerance (MS-GF+ parameter '-t')" help="(-precursor_error_units) ">
      <option value="Da">Da</option>
      <option value="ppm" selected="true">ppm</option>
    </param>
    <param name="param_isotope_error_range" type="text" size="30" value="0,1" label="Range of allowed isotope peak errors (MS-GF+ parameter '-ti')" help="(-isotope_error_range) Takes into account the error introduced by choosing a non-monoisotopic peak for fragmentation. Combined with 'precursor_mass_tolerance'/'precursor_error_units', this determines the actual precursor mass tolerance. E.g. for experimental mass 'exp' and calculated mass 'calc', '-precursor_mass_tolerance 20 -precursor_error_units ppm -isotope_error_range -1,2' tests '|exp - calc - n * 1.00335 Da| &lt; 20 ppm' for n = -1, 0, 1, 2">

      <option value="low_res" selected="true">low_res</option>
      <option value="high_res">high_res</option>
      <option value="TOF">TOF</option>
      <option value="Q_Exactive">Q_Exactive</option>
    </param>
    <param name="param_enzyme" type="select" optional="False" value="trypsin" label="Enzyme used for digestion, or type of cleavage (MS-GF+ parameter '-e')" help="(-enzyme) ">
      <option value="unspecific">unspecific</option>
      <option value="trypsin" selected="true">trypsin</option>
      <option value="chymotrypsin">chymotrypsin</option>
      <option value="LysC">LysC</option>
      <option value="LysN">LysN</option>
      <option value="GluC">GluC</option>
      <option value="ArgC">ArgC</option>
      <option value="AspN">AspN</option>
      <option value="alphaLP">alphaLP</option>
      <option value="no_cleavage">no_cleavage</option>
    </param>
    <param name="param_protocol" type="select" optional="False" value="none" label="Labeling or enrichment protocol used, if any (MS-GF+ parameter '-p')" help="(-protocol) ">
      <option value="none" selected="true">none</option>
      <option value="phospho">phospho</option>
      <option value="iTRAQ">iTRAQ</option>

      <param name="param_legacy_conversion" display="radio" type="boolean" truevalue="-legacy_conversion" falsevalue="" checked="false" optional="True" label="Use the indirect conversion of MS-GF+ results to idXML via export to TSV" help="(-legacy_conversion) Try this only if the default conversion takes too long or uses too much memory"/>
      <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="idxml"/>
    <data name="param_mzid_out" format="mzid"/>
  </outputs>
  <help>MS/MS database search using MS-GF+.


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

15:bb971f471df8

<?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="MSGFPlusAdapter" name="MSGFPlusAdapter" version="2.3.0">
  <description>MS/MS database search using MS-GF+.</description>
  <macros>
    <token name="@EXECUTABLE@">MSGFPlusAdapter</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
<command detect_errors="aggressive"><![CDATA[

 ## check input file type
 #set $in_type = $param_in.ext

 ## create the symlinks to set the proper file extension, since msgf uses them to choose how to handle the input files

#end if
    #if $adv_opts.param_force:
  -force
#end if
#end if
-threads "\${GALAXY_SLOTS:-1}"
 ]]>
</command>
  <inputs>
    <param name="param_in" type="data" format="mzml,mzxml,mgf,ms2" optional="False" label="Input file (MS-GF+ parameter '-s')" help="(-in) "/>
    <param name="param_database" type="data" format="fasta" optional="False" label="Protein sequence database (FASTA file; MS-GF+ parameter '-d')" help="(-database) Non-existing relative filenames are looked up via 'OpenMS.ini:id_db_dir'"/>
    <param name="param_add_decoys" display="radio" type="boolean" truevalue="-add_decoys" falsevalue="" checked="false" optional="True" label="Create decoy proteins (reversed sequences) and append them to the database for the search (MS-GF+ parameter '-tda')" help="(-add_decoys) This allows the calculation of FDRs, but should only be used if the database does not already contain decoys. Decoys are marked by the prefix XXX_"/>
    <param name="param_precursor_mass_tolerance" type="float" value="10.0" label="Precursor monoisotopic mass tolerance (MS-GF+ parameter '-t')" help="(-precursor_mass_tolerance) "/>
    <param name="param_precursor_error_units" display="radio" type="select" optional="False" value="ppm" label="Unit of precursor mass tolerance (MS-GF+ parameter '-t')" help="(-precursor_error_units) ">
      <option value="Da">Da</option>
      <option value="ppm" selected="true">ppm</option>
    </param>
    <param name="param_isotope_error_range" type="text" size="30" value="0,1" label="Range of allowed isotope peak errors (MS-GF+ parameter '-ti')" help="(-isotope_error_range) Takes into account the error introduced by choosing a non-monoisotopic peak for fragmentation. Combined with 'precursor_mass_tolerance'/'precursor_error_units', this determines the actual precursor mass tolerance. E.g. for experimental mass 'exp' and calculated mass 'calc', '-precursor_mass_tolerance 20 -precursor_error_units ppm -isotope_error_range -1,2' tests '|exp - calc - n * 1.00335 Da| &lt; 20 ppm' for n = -1, 0, 1, 2">

      <option value="low_res" selected="true">low_res</option>
      <option value="high_res">high_res</option>
      <option value="TOF">TOF</option>
      <option value="Q_Exactive">Q_Exactive</option>
    </param>
    <param name="param_enzyme" type="select" optional="False" value="Trypsin/P" label="Enzyme used for digestion, or type of cleavage" help="(-enzyme) Note: MS-GF+ does not support blocking rules. (MS-GF+ parameter '-e')">
      <option value="Alpha-lytic protease">Alpha-lytic protease</option>
      <option value="Arg-C/P">Arg-C/P</option>
      <option value="Asp-N/B">Asp-N/B</option>
      <option value="Chymotrypsin/P">Chymotrypsin/P</option>
      <option value="Lys-C/P">Lys-C/P</option>
      <option value="Lys-N">Lys-N</option>
      <option value="Trypsin/P" selected="true">Trypsin/P</option>
      <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
      <option value="no cleavage">no cleavage</option>
      <option value="unspecific cleavage">unspecific cleavage</option>
    </param>
    <param name="param_protocol" type="select" optional="False" value="none" label="Labeling or enrichment protocol used, if any (MS-GF+ parameter '-p')" help="(-protocol) ">
      <option value="none" selected="true">none</option>
      <option value="phospho">phospho</option>
      <option value="iTRAQ">iTRAQ</option>

      <param name="param_legacy_conversion" display="radio" type="boolean" truevalue="-legacy_conversion" falsevalue="" checked="false" optional="True" label="Use the indirect conversion of MS-GF+ results to idXML via export to TSV" help="(-legacy_conversion) Try this only if the default conversion takes too long or uses too much memory"/>
      <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="idxml" label="${tool.name} on ${on_string}: idxml"/>
    <data name="param_mzid_out" format="mzid" label=" ${tool.name} on ${on_string}: mzid"/>
  </outputs>
  <help>MS/MS database search using MS-GF+.


For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_MSGFPlusAdapter.html</help>
</tool>