Mercurial > repos > galaxyp > openms_msfraggeradapter

annotate MSFraggerAdapter.xml @ 2:6bcc338b9dc6 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 20:09:43 +0000
parents 5a9c3e827da5
children e133b5c8878f
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52a0856534d9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
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3 <!--Proposed Tool Section: [Utilities]-->
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4 <tool id="MSFraggerAdapter" name="MSFraggerAdapter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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5 <description>Peptide Identification with MSFragger</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">MSFraggerAdapter</token>
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8 <import>macros.xml</import>
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9 <import>macros_autotest.xml</import>
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10 <import>macros_test.xml</import>
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11 </macros>
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12 <expand macro="requirements"/>
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13 <expand macro="stdio"/>
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14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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15 @EXT_FOO@
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16 #import re
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17
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18 ## Preprocessing
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19 mkdir in &&
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20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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21 mkdir out &&
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22 #if "opt_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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23 mkdir opt_out &&
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24 #end if
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25 mkdir database &&
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26 ln -s '$database' 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)' &&
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27
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28 ## Main program call
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29
52a0856534d9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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30 set -o pipefail &&
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31 @EXECUTABLE@ -write_ctd ./ &&
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32 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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33 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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34 -in
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35 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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36 -out
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37 'out/output.${gxy2omsext("idxml")}'
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38 #if "opt_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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39 -opt_out
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40 'opt_out/output.${gxy2omsext("pepxml")}'
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41 #end if
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42 -database
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43 'database/${re.sub("[^\w\-_]", "_", $database.element_identifier)}.$gxy2omsext($database.ext)'
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44 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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45 | tee '$stdout'
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46 #end if
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47
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48 ## Postprocessing
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49 && mv 'out/output.${gxy2omsext("idxml")}' '$out'
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50 #if "opt_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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51 && mv 'opt_out/output.${gxy2omsext("pepxml")}' '$opt_out'
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52 #end if
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53 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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54 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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55 #end if]]></command>
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56 <configfiles>
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57 <inputs name="args_json" data_style="paths"/>
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58 <configfile name="hardcoded_json"><![CDATA[{"java_executable": "java", "executable": "/home/berntm/Downloads/MSFragger-20171106/MSFragger-20171106.jar", "log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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59 </configfiles>
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60 <inputs>
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61 <param name="java_heapmemory" argument="-java_heapmemory" type="integer" optional="true" value="3500" label="Maximum Java heap size (in MB)" help=""/>
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62 <param name="in" argument="-in" type="data" format="mzml,mzxml" optional="false" label="Input File with specta for MSFragge" help=" select mzml,mzxml data sets(s)"/>
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63 <param name="database" argument="-database" type="data" format="fasta" optional="false" label="Protein FASTA database file path" help=" select fasta data sets(s)"/>
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64 <section name="tolerance" title="Search Tolerances" help="" expanded="false">
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65 <param name="precursor_mass_tolerance" argument="-tolerance:precursor_mass_tolerance" type="float" optional="true" min="0.0" value="20.0" label="Precursor mass tolerance (window is +/- this value)" help=""/>
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66 <param name="precursor_mass_unit" argument="-tolerance:precursor_mass_unit" display="radio" type="select" optional="false" label="Unit of precursor mass tolerance" help="">
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67 <option value="Da">Da</option>
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68 <option value="ppm" selected="true">ppm</option>
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69 <expand macro="list_string_san"/>
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70 </param>
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71 <param name="precursor_true_tolerance" argument="-tolerance:precursor_true_tolerance" type="float" optional="true" min="0.0" value="0.0" label="True precursor mass tolerance (window is +/- this value)" help="Used for tie breaker of results (in spectrally ambiguous cases) and zero bin boosting in open searches (0 disables these features). This option is STRONGLY recommended for open searches"/>
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72 <param name="precursor_true_unit" argument="-tolerance:precursor_true_unit" display="radio" type="select" optional="false" label="Unit of precursor true tolerance" help="">
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73 <option value="Da">Da</option>
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74 <option value="ppm" selected="true">ppm</option>
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75 <expand macro="list_string_san"/>
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76 </param>
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77 <param name="fragment_mass_tolerance" argument="-tolerance:fragment_mass_tolerance" type="float" optional="true" min="0.0" value="20.0" label="Fragment mass tolerance (window is +/- this value)" help=""/>
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78 <param name="fragment_mass_unit" argument="-tolerance:fragment_mass_unit" display="radio" type="select" optional="false" label="Unit of fragment mass tolerance" help="">
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79 <option value="Da">Da</option>
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80 <option value="ppm" selected="true">ppm</option>
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81 <expand macro="list_string_san"/>
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parents:
diff changeset
82 </param>
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galaxyp
parents:
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83 <param name="isotope_error" argument="-tolerance:isotope_error" display="radio" type="select" optional="false" label="Isotope correction for MS/MS events triggered on isotopic peaks" help="Should be set to 0 (disabled) for open search or 0/1/2 for correction of narrow window searches. Shifts the precursor mass window to multiples of this value multiplied by the mass of C13-C12">
52a0856534d9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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parents:
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84 <option value="0" selected="true">0</option>
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galaxyp
parents:
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85 <option value="1">1</option>
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galaxyp
parents:
diff changeset
86 <option value="2">2</option>
52a0856534d9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
87 <expand macro="list_string_san"/>
52a0856534d9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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parents:
diff changeset
88 </param>
52a0856534d9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
diff changeset
89 </section>
52a0856534d9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
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90 <section name="digest" title="In-Silico Digestion Parameters" help="" expanded="false">
52a0856534d9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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parents:
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91 <param name="search_enzyme_name" argument="-digest:search_enzyme_name" type="select" optional="false" label="Name of the enzyme to be written to the pepXML file" help="">
2
6bcc338b9dc6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
galaxyp
parents: 1
diff changeset
92 <option value="staphylococcal protease/D">staphylococcal protease/D</option>
6bcc338b9dc6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
galaxyp
parents: 1
diff changeset
93 <option value="proline-endopeptidase/HKR">proline-endopeptidase/HKR</option>
6bcc338b9dc6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
galaxyp
parents: 1
diff changeset
94 <option value="Glu-C+P">Glu-C+P</option>
0
52a0856534d9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
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95 <option value="PepsinA + P">PepsinA + P</option>
52a0856534d9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
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96 <option value="cyanogen-bromide">cyanogen-bromide</option>
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galaxyp
parents:
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97 <option value="Clostripain/P">Clostripain/P</option>
52a0856534d9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
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98 <option value="elastase-trypsin-chymotrypsin">elastase-trypsin-chymotrypsin</option>
52a0856534d9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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parents:
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99 <option value="no cleavage">no cleavage</option>
52a0856534d9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents:
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100 <option value="unspecific cleavage">unspecific cleavage</option>
2
6bcc338b9dc6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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parents: 1
diff changeset
101 <option value="Arg-C">Arg-C</option>
6bcc338b9dc6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
galaxyp
parents: 1
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102 <option value="Arg-C/P">Arg-C/P</option>
6bcc338b9dc6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
galaxyp
parents: 1
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103 <option value="Lys-C">Lys-C</option>
6bcc338b9dc6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
galaxyp
parents: 1
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104 <option value="Lys-N">Lys-N</option>
6bcc338b9dc6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
galaxyp
parents: 1
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105 <option value="Lys-C/P">Lys-C/P</option>
6bcc338b9dc6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
galaxyp
parents: 1
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106 <option value="PepsinA">PepsinA</option>
6bcc338b9dc6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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parents: 1
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107 <option value="TrypChymo">TrypChymo</option>
6bcc338b9dc6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
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parents: 1
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108 <option value="Trypsin/P">Trypsin/P</option>
6bcc338b9dc6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
galaxyp
parents: 1
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109 <option value="V8-DE">V8-DE</option>
6bcc338b9dc6 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
galaxyp
parents: 1
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110 <option value="V8-E">V8-E</option>
1
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galaxyp
parents: 0
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111 <option value="leukocyte elastase">leukocyte elastase</option>
5a9c3e827da5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f5fcdd54599554099fb00b1973cc91a766ad246a"
galaxyp
parents: 0
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112 <option value="proline endopeptidase">proline endopeptidase</option>
5a9c3e827da5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f5fcdd54599554099fb00b1973cc91a766ad246a"
galaxyp
parents: 0
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113 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option>
5a9c3e827da5 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f5fcdd54599554099fb00b1973cc91a766ad246a"
galaxyp
parents: 0
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114 <option value="Alpha-lytic protease">Alpha-lytic protease</option>
0
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galaxyp
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115 <option value="2-iodobenzoate">2-iodobenzoate</option>
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galaxyp
parents:
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116 <option value="iodosobenzoate">iodosobenzoate</option>
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galaxyp
parents:
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117 <option value="Asp-N">Asp-N</option>
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galaxyp
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118 <option value="Asp-N/B">Asp-N/B</option>
52a0856534d9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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119 <option value="Asp-N_ambic">Asp-N_ambic</option>
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120 <option value="Chymotrypsin">Chymotrypsin</option>
52a0856534d9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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121 <option value="Chymotrypsin/P">Chymotrypsin/P</option>
52a0856534d9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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122 <option value="CNBr">CNBr</option>
52a0856534d9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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123 <option value="Formic_acid">Formic_acid</option>
52a0856534d9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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124 <option value="Trypsin" selected="true">Trypsin</option>
52a0856534d9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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125 <expand macro="list_string_san"/>
52a0856534d9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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126 </param>
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127 <param name="search_enzyme_cutafter" argument="-digest:search_enzyme_cutafter" type="text" optional="true" value="KR" label="Residues after which the enzyme cuts (specified as a string of amino acids)" help="">
52a0856534d9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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128 <expand macro="list_string_san"/>
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129 </param>
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galaxyp
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130 <param name="search_enzyme_nocutbefore" argument="-digest:search_enzyme_nocutbefore" type="text" optional="true" value="P" label="Residues that the enzyme will not cut before" help="">
52a0856534d9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
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131 <expand macro="list_string_san"/>
52a0856534d9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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132 </param>
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133 <param name="num_enzyme_termini" argument="-digest:num_enzyme_termini" display="radio" type="select" optional="false" label="Number of enzyme termini (non-enzymatic (0), semi (1), fully (2)" help="">
52a0856534d9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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134 <option value="non-enzymatic">non-enzymatic</option>
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135 <option value="semi">semi</option>
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136 <option value="fully" selected="true">fully</option>
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137 <expand macro="list_string_san"/>
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138 </param>
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139 <param name="allowed_missed_cleavage" argument="-digest:allowed_missed_cleavage" type="select" optional="false" label="Allowed number of missed cleavages" help="">
52a0856534d9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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140 <option value="0">0</option>
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141 <option value="1">1</option>
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142 <option value="2" selected="true">2</option>
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143 <option value="3">3</option>
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144 <option value="4">4</option>
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145 <option value="5">5</option>
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146 <expand macro="list_string_san"/>
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147 </param>
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148 <param name="min_length" argument="-digest:min_length" type="integer" optional="true" min="0" value="7" label="Minimum length of peptides to be generated during in-silico digestion" help=""/>
52a0856534d9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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149 <param name="max_length" argument="-digest:max_length" type="integer" optional="true" min="0" value="64" label="Maximum length of peptides to be generated during in-silico digestion" help=""/>
52a0856534d9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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150 <param name="mass_range_min" argument="-digest:mass_range_min" type="float" optional="true" min="0.0" value="500.0" label="Min mass of peptides to be generated (Da)" help=""/>
52a0856534d9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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151 <param name="mass_range_max" argument="-digest:mass_range_max" type="float" optional="true" min="0.0" value="5000.0" label="Max mass of peptides to be generated (Da)" help=""/>
52a0856534d9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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152 </section>
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153 <section name="varmod" title="Variable Modification Parameters" help="" expanded="false">
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154 <param name="clip_nterm_m" argument="-varmod:clip_nterm_m" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Specifies the trimming of a protein N-terminal methionine as a variable modification" help=""/>
52a0856534d9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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155 <param name="masses" argument="-varmod:masses" type="text" optional="true" value="" label="Masses for variable modifications" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
52a0856534d9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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156 <expand macro="list_float_valsan"/>
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157 </param>
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158 <param name="syntaxes" argument="-varmod:syntaxes" type="text" optional="true" value="" label="Syntax Strings for variable modifications" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
52a0856534d9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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159 <expand macro="list_string_val"/>
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160 <expand macro="list_string_san"/>
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161 </param>
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162 <param name="enable_common" argument="-varmod:enable_common" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Enable common variable modifications (15.9949 M and 42.0106 [^)" help=""/>
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163 <param name="not_allow_multiple_variable_mods_on_residue" argument="-varmod:not_allow_multiple_variable_mods_on_residue" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not allow any one amino acid to be modified by multiple variable modifications" help=""/>
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164 <param name="max_variable_mods_per_mod" argument="-varmod:max_variable_mods_per_mod" type="select" optional="false" label="Maximum number of residues that can be occupied by each variable modification" help="">
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165 <option value="0">0</option>
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166 <option value="1">1</option>
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167 <option value="2" selected="true">2</option>
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168 <option value="3">3</option>
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169 <option value="4">4</option>
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170 <option value="5">5</option>
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171 <expand macro="list_string_san"/>
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172 </param>
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173 <param name="max_variable_mods_combinations" argument="-varmod:max_variable_mods_combinations" type="integer" optional="true" min="0" max="65534" value="5000" label="Maximum allowed number of modified variably modified peptides from each peptide sequence, (maximum of 65534)" help="If a greater number than the maximum is generated, only the unmodified peptide is considered"/>
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174 </section>
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175 <section name="spectrum" title="Spectrum Processing Parameters" help="" expanded="false">
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176 <param name="minimum_peaks" argument="-spectrum:minimum_peaks" type="integer" optional="true" min="0" value="10" label="Minimum number of peaks in experimental spectrum for matching" help=""/>
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177 <param name="use_topn_peaks" argument="-spectrum:use_topn_peaks" type="integer" optional="true" min="0" value="50" label="Pre-process experimental spectrum to only use top N peaks" help=""/>
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178 <param name="minimum_ratio" argument="-spectrum:minimum_ratio" type="float" optional="true" min="0.0" max="1.0" value="0.0" label="Filters out all peaks in experimental spectrum less intense than this multiple of the base peak intensity" help=""/>
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179 <param name="clear_mz_range_min" argument="-spectrum:clear_mz_range_min" type="float" optional="true" min="0.0" value="0.0" label="Removes peaks in this m/z range prior to matching (minimum value)" help="Useful for iTRAQ/TMT experiments (i.e. 0.0 150.0)"/>
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180 <param name="clear_mz_range_max" argument="-spectrum:clear_mz_range_max" type="float" optional="true" min="0.0" value="0.0" label="Removes peaks in this m/z range prior to matching (maximum value)" help="Useful for iTRAQ/TMT experiments (i.e. 0.0 150.0)"/>
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181 <param name="max_fragment_charge" argument="-spectrum:max_fragment_charge" display="radio" type="select" optional="false" label="Maximum charge state for theoretical fragments to match" help="">
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182 <option value="1">1</option>
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183 <option value="2" selected="true">2</option>
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184 <option value="3">3</option>
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185 <option value="4">4</option>
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186 <expand macro="list_string_san"/>
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187 </param>
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188 <param name="override_charge" argument="-spectrum:override_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Ignores precursor charge and uses charge state specified in precursor_charge range (parameters: spectrum:precursor_charge_min and spectrum:precursor_charge_max)" help=""/>
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189 <param name="precursor_charge_min" argument="-spectrum:precursor_charge_min" type="integer" optional="true" min="0" value="1" label="Min charge of precursor charge range to conside" help="If specified, also spectrum:override_charge must be set)"/>
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190 <param name="precursor_charge_max" argument="-spectrum:precursor_charge_max" type="integer" optional="true" min="0" value="4" label="Max charge of precursor charge range to conside" help="If specified, also spectrum:override_charge must be set)"/>
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191 </section>
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192 <section name="search" title="Open Search Features" help="" expanded="false">
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193 <param name="track_zero_topn" argument="-search:track_zero_topn" type="integer" optional="true" min="0" value="0" label="Track top N unmodified peptide results separately from main results internally for boosting features" help="Should be set to a number greater than search:output_report_topN if zero bin boosting is desired"/>
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194 <param name="zero_bin_accept_expect" argument="-search:zero_bin_accept_expect" type="float" optional="true" min="0.0" value="0.0" label="Ranks a zero-bin hit above all non-zero-bin hit if it has expectation less than this value" help=""/>
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195 <param name="zero_bin_mult_expect" argument="-search:zero_bin_mult_expect" type="float" optional="true" min="0.0" value="1.0" label="Multiplies expect value of PSMs in the zero-bin during results ordering (set to less than 1 for boosting)" help=""/>
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196 <param name="add_topn_complementary" argument="-search:add_topn_complementary" type="integer" optional="true" min="0" value="0" label="Inserts complementary ions corresponding to the top N most intense fragments in each experimental spectrum" help="Useful for recovery of modified peptides near C-terminus in open search. 0 disables this option"/>
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197 <param name="min_fragments_modeling" argument="-search:min_fragments_modeling" type="integer" optional="true" min="0" value="3" label="Minimum number of matched peaks in PSM for inclusion in statistical modeling" help=""/>
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198 <param name="min_matched_fragments" argument="-search:min_matched_fragments" type="integer" optional="true" min="0" value="4" label="Minimum number of matched peaks for PSM to be reported" help="MSFragger recommends a minimum of 4 for narrow window searching and 6 for open searches"/>
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199 <param name="output_report_topn" argument="-search:output_report_topn" type="integer" optional="true" min="0" value="1" label="Reports top N PSMs per input spectrum" help=""/>
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200 <param name="output_max_expect" argument="-search:output_max_expect" type="float" optional="true" min="0.0" value="50.0" label="Suppresses reporting of PSM if top hit has expectation greater than this threshold" help=""/>
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201 </section>
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202 <section name="statmod" title="Static Modification Parameters" help="" expanded="false">
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203 <param name="add_cterm_peptide" argument="-statmod:add_cterm_peptide" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass in Da to C-terminal of peptide" help=""/>
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204 <param name="add_nterm_peptide" argument="-statmod:add_nterm_peptide" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass in Da to N-terminal of peptide" help=""/>
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205 <param name="add_cterm_protein" argument="-statmod:add_cterm_protein" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass in Da to C-terminal of protein" help=""/>
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206 <param name="add_nterm_protein" argument="-statmod:add_nterm_protein" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass in Da to N-terminal of protein" help=""/>
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207 <param name="add_G_glycine" argument="-statmod:add_G_glycine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to glycine" help=""/>
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208 <param name="add_A_alanine" argument="-statmod:add_A_alanine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to alanine" help=""/>
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209 <param name="add_S_serine" argument="-statmod:add_S_serine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to serine" help=""/>
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210 <param name="add_P_proline" argument="-statmod:add_P_proline" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to proline" help=""/>
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211 <param name="add_V_valine" argument="-statmod:add_V_valine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to valine" help=""/>
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212 <param name="add_T_threonine" argument="-statmod:add_T_threonine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to threonine" help=""/>
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213 <param name="add_C_cysteine" argument="-statmod:add_C_cysteine" type="float" optional="true" min="0.0" value="57.021464" label="Statically add mass to cysteine" help=""/>
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214 <param name="add_L_leucine" argument="-statmod:add_L_leucine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to leucine" help=""/>
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215 <param name="add_I_isoleucine" argument="-statmod:add_I_isoleucine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to isoleucine" help=""/>
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216 <param name="add_N_asparagine" argument="-statmod:add_N_asparagine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to asparagine" help=""/>
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217 <param name="add_D_aspartic_acid" argument="-statmod:add_D_aspartic_acid" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to aspartic_acid" help=""/>
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218 <param name="add_Q_glutamine" argument="-statmod:add_Q_glutamine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to glutamine" help=""/>
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219 <param name="add_K_lysine" argument="-statmod:add_K_lysine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to lysine" help=""/>
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220 <param name="add_E_glutamic_acid" argument="-statmod:add_E_glutamic_acid" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to glutamic_acid" help=""/>
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221 <param name="add_M_methionine" argument="-statmod:add_M_methionine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to methionine" help=""/>
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222 <param name="add_H_histidine" argument="-statmod:add_H_histidine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to histidine" help=""/>
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223 <param name="add_F_phenylalanine" argument="-statmod:add_F_phenylalanine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to phenylalanine" help=""/>
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224 <param name="add_R_arginine" argument="-statmod:add_R_arginine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to arginine" help=""/>
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225 <param name="add_Y_tyrosine" argument="-statmod:add_Y_tyrosine" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to tyrosine" help=""/>
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226 <param name="add_W_tryptophan" argument="-statmod:add_W_tryptophan" type="float" optional="true" min="0.0" value="0.0" label="Statically add mass to tryptophan" help=""/>
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227 </section>
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228 <expand macro="adv_opts_macro">
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229 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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230 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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231 <expand macro="list_string_san"/>
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232 </param>
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233 </expand>
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234 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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235 <option value="opt_out_FLAG">opt_out (MSFragger optional output file)</option>
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236 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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237 </param>
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238 </inputs>
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239 <outputs>
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240 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
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241 <data name="opt_out" label="${tool.name} on ${on_string}: opt_out" format="pepxml">
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242 <filter>OPTIONAL_OUTPUTS is not None and "opt_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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243 </data>
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244 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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245 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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246 </data>
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247 </outputs>
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248 <tests>
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249 <expand macro="autotest_MSFraggerAdapter"/>
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250 <expand macro="manutest_MSFraggerAdapter"/>
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251 </tests>
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252 <help><![CDATA[Peptide Identification with MSFragger
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253
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254
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255 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_MSFraggerAdapter.html]]></help>
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256 <expand macro="references"/>
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257 </tool>