Mercurial > repos > galaxyp > openms_msgfplusadapter
comparison MSGFPlusAdapter.xml @ 6:2244cc0ac5cd draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
author | galaxyp |
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date | Mon, 12 Feb 2018 13:05:04 -0500 |
parents | 708c31c03d4f |
children | f0761deada39 |
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5:a407b6790342 | 6:2244cc0ac5cd |
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1 <?xml version='1.0' encoding='UTF-8'?> | 1 <?xml version='1.0' encoding='UTF-8'?> |
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> | 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> |
3 <!--Proposed Tool Section: [Identification]--> | 3 <!--Proposed Tool Section: [Identification]--> |
4 <tool id="MSGFPlusAdapter" name="MSGFPlusAdapter" version="2.2.0"> | 4 <tool id="MSGFPlusAdapter" name="MSGFPlusAdapter" version="2.3.0"> |
5 <description>MS/MS database search using MS-GF+.</description> | 5 <description>MS/MS database search using MS-GF+.</description> |
6 <macros> | 6 <macros> |
7 <token name="@EXECUTABLE@">MSGFPlusAdapter</token> | 7 <token name="@EXECUTABLE@">MSGFPlusAdapter</token> |
8 <import>macros.xml</import> | 8 <import>macros.xml</import> |
9 </macros> | 9 </macros> |
10 <expand macro="references"/> | 10 <expand macro="references"/> |
11 <expand macro="stdio"/> | 11 <expand macro="stdio"/> |
12 <expand macro="requirements"/> | 12 <expand macro="requirements"/> |
13 <command><![CDATA[ | 13 <command><![CDATA[ |
14 | 14 |
15 ## check input file type | 15 ## check input file type |
16 #set $in_type = $param_in.ext | 16 #set $in_type = $param_in.ext |
17 | 17 |
18 ## create the symlinks to set the proper file extension, since msgf uses them to choose how to handle the input files | 18 ## create the symlinks to set the proper file extension, since msgf uses them to choose how to handle the input files |
141 #end if | 141 #end if |
142 #if $adv_opts.param_force: | 142 #if $adv_opts.param_force: |
143 -force | 143 -force |
144 #end if | 144 #end if |
145 #end if | 145 #end if |
146 ]]> | 146 ]]> |
147 </command> | 147 </command> |
148 <inputs> | 148 <inputs> |
149 <param name="param_in" type="data" format="mzml,mzxml,mgf,ms2" optional="False" label="Input file (MS-GF+ parameter '-s')" help="(-in) "/> | 149 <param name="param_in" type="data" format="mzml,mzxml,mgf,ms2" optional="False" label="Input file (MS-GF+ parameter '-s')" help="(-in) "/> |
150 <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'"/> | 150 <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'"/> |
151 <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"/> | 151 <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"/> |
152 <param name="param_precursor_mass_tolerance" type="float" value="20.0" label="Precursor monoisotopic mass tolerance (MS-GF+ parameter '-t')" help="(-precursor_mass_tolerance) "/> | 152 <param name="param_precursor_mass_tolerance" type="float" value="10.0" label="Precursor monoisotopic mass tolerance (MS-GF+ parameter '-t')" help="(-precursor_mass_tolerance) "/> |
153 <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) "> | 153 <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) "> |
154 <option value="Da">Da</option> | 154 <option value="Da">Da</option> |
155 <option value="ppm" selected="true">ppm</option> | 155 <option value="ppm" selected="true">ppm</option> |
156 </param> | 156 </param> |
157 <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| < 20 ppm' for n = -1, 0, 1, 2"> | 157 <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| < 20 ppm' for n = -1, 0, 1, 2"> |
172 <option value="low_res" selected="true">low_res</option> | 172 <option value="low_res" selected="true">low_res</option> |
173 <option value="high_res">high_res</option> | 173 <option value="high_res">high_res</option> |
174 <option value="TOF">TOF</option> | 174 <option value="TOF">TOF</option> |
175 <option value="Q_Exactive">Q_Exactive</option> | 175 <option value="Q_Exactive">Q_Exactive</option> |
176 </param> | 176 </param> |
177 <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) "> | 177 <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')"> |
178 <option value="unspecific">unspecific</option> | 178 <option value="Alpha-lytic protease">Alpha-lytic protease</option> |
179 <option value="trypsin" selected="true">trypsin</option> | 179 <option value="Arg-C/P">Arg-C/P</option> |
180 <option value="chymotrypsin">chymotrypsin</option> | 180 <option value="Asp-N/B">Asp-N/B</option> |
181 <option value="LysC">LysC</option> | 181 <option value="Chymotrypsin/P">Chymotrypsin/P</option> |
182 <option value="LysN">LysN</option> | 182 <option value="Lys-C/P">Lys-C/P</option> |
183 <option value="GluC">GluC</option> | 183 <option value="Lys-N">Lys-N</option> |
184 <option value="ArgC">ArgC</option> | 184 <option value="Trypsin/P" selected="true">Trypsin/P</option> |
185 <option value="AspN">AspN</option> | 185 <option value="glutamyl endopeptidase">glutamyl endopeptidase</option> |
186 <option value="alphaLP">alphaLP</option> | 186 <option value="no cleavage">no cleavage</option> |
187 <option value="no_cleavage">no_cleavage</option> | 187 <option value="unspecific cleavage">unspecific cleavage</option> |
188 </param> | 188 </param> |
189 <param name="param_protocol" type="select" optional="False" value="none" label="Labeling or enrichment protocol used, if any (MS-GF+ parameter '-p')" help="(-protocol) "> | 189 <param name="param_protocol" type="select" optional="False" value="none" label="Labeling or enrichment protocol used, if any (MS-GF+ parameter '-p')" help="(-protocol) "> |
190 <option value="none" selected="true">none</option> | 190 <option value="none" selected="true">none</option> |
191 <option value="phospho">phospho</option> | 191 <option value="phospho">phospho</option> |
192 <option value="iTRAQ">iTRAQ</option> | 192 <option value="iTRAQ">iTRAQ</option> |