Mercurial > repos > galaxyp > openms_msgfplusadapter
comparison MSGFPlusAdapter.xml @ 7:f0761deada39 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 981be1bde91d6d565693cd691553f77465e653bb
author | galaxyp |
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date | Tue, 20 Mar 2018 15:08:17 -0400 |
parents | 2244cc0ac5cd |
children | 1ed1f9f53857 |
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6:2244cc0ac5cd | 7:f0761deada39 |
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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 -threads "\${GALAXY_SLOTS:-1}" | |
146 ]]> | 147 ]]> |
147 </command> | 148 </command> |
148 <inputs> | 149 <inputs> |
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_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'"/> | 151 <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"/> | 152 <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_"/> |
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_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) "> | 154 <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> | 155 <option value="Da">Da</option> |
155 <option value="ppm" selected="true">ppm</option> | 156 <option value="ppm" selected="true">ppm</option> |
156 </param> | 157 </param> |
5275 <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"/> | 5276 <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"/> |
5276 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> | 5277 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> |
5277 </expand> | 5278 </expand> |
5278 </inputs> | 5279 </inputs> |
5279 <outputs> | 5280 <outputs> |
5280 <data name="param_out" format="idxml"/> | 5281 <data name="param_out" format="idxml" label="${tool.name} on ${on_string}: idxml"/> |
5281 <data name="param_mzid_out" format="mzid"/> | 5282 <data name="param_mzid_out" format="mzid" label=" ${tool.name} on ${on_string}: mzid"/> |
5282 </outputs> | 5283 </outputs> |
5283 <help>MS/MS database search using MS-GF+. | 5284 <help>MS/MS database search using MS-GF+. |
5284 | 5285 |
5285 | 5286 |
5286 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MSGFPlusAdapter.html</help> | 5287 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MSGFPlusAdapter.html</help> |