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comparison searchgui.xml @ 45:5fa8b409599e draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 62699d7e79ddbe3374ed28dfeb9002e8efa4c544
author galaxyp
date Mon, 30 Apr 2018 04:41:50 -0400
parents f35bb9d0c93e
children baeced706dbc
comparison
equal deleted inserted replaced
44:f35bb9d0c93e 45:5fa8b409599e
1 <tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.4"> 1 <tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.0">
2 <description> 2 <description>
3 Perform protein identification using various search engines and prepare results for input to Peptide Shaker 3 Perform protein identification using various search engines and prepare results for input to Peptide Shaker
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
156 -ms_amanda_instrument "${advanced_options.ms_amanda.ms_amanda_instrument}" 156 -ms_amanda_instrument "${advanced_options.ms_amanda.ms_amanda_instrument}"
157 -ms_amanda_max_rank ${advanced_options.ms_amanda.ms_amanda_max_rank} 157 -ms_amanda_max_rank ${advanced_options.ms_amanda.ms_amanda_max_rank}
158 -ms_amanda_mono ${advanced_options.ms_amanda.ms_amanda_mono} 158 -ms_amanda_mono ${advanced_options.ms_amanda.ms_amanda_mono}
159 #end if 159 #end if
160 160
161 #* Not working in tests
162 #if $advanced_options.myrimatch.myrimatch_advanced == "yes" 161 #if $advanced_options.myrimatch.myrimatch_advanced == "yes"
163 -myrimatch_min_pep_length ${advanced_options.myrimatch.myrimatch_min_pep_length} 162 -myrimatch_min_pep_length ${advanced_options.myrimatch.myrimatch_min_pep_length}
164 -myrimatch_max_pep_length ${advanced_options.myrimatch.myrimatch_max_pep_length} 163 -myrimatch_max_pep_length ${advanced_options.myrimatch.myrimatch_max_pep_length}
165 -myrimatch_min_prec_mass ${advanced_options.myrimatch.myrimatch_min_prec_mass} 164 -myrimatch_min_prec_mass ${advanced_options.myrimatch.myrimatch_min_prec_mass}
166 -myrimatch_max_prec_mass ${advanced_options.myrimatch.myrimatch_max_prec_mass} 165 -myrimatch_max_prec_mass ${advanced_options.myrimatch.myrimatch_max_prec_mass}
174 -myrimatch_intensity_classes ${advanced_options.myrimatch.myrimatch_intensity_classes} 173 -myrimatch_intensity_classes ${advanced_options.myrimatch.myrimatch_intensity_classes}
175 -myrimatch_class_multiplier ${advanced_options.myrimatch.myrimatch_class_multiplier} 174 -myrimatch_class_multiplier ${advanced_options.myrimatch.myrimatch_class_multiplier}
176 -myrimatch_num_batches ${advanced_options.myrimatch.myrimatch_num_batches} 175 -myrimatch_num_batches ${advanced_options.myrimatch.myrimatch_num_batches}
177 -myrimatch_max_peak ${advanced_options.myrimatch.myrimatch_max_peak} 176 -myrimatch_max_peak ${advanced_options.myrimatch.myrimatch_max_peak}
178 #end if 177 #end if
179 *# 178
180 179
181 #* Not working in tests 180 #* Not working in tests
182 #if $advanced_options.andromeda.andromeda_advanced == "yes" 181 #if $advanced_options.andromeda.andromeda_advanced == "yes"
183 -andromeda_max_pep_mass ${advanced_options.andromeda.andromeda_max_pep_mass} 182 -andromeda_max_pep_mass ${advanced_options.andromeda.andromeda_max_pep_mass}
184 -andromeda_max_comb ${advanced_options.andromeda.andromeda_max_comb} 183 -andromeda_max_comb ${advanced_options.andromeda.andromeda_max_comb}
454 453
455 <option value="MSGF" selected="True">MS-GF+</option> 454 <option value="MSGF" selected="True">MS-GF+</option>
456 <option value="OMSSA" selected="True">OMSSA</option> 455 <option value="OMSSA" selected="True">OMSSA</option>
457 <option value="Comet">Comet</option> 456 <option value="Comet">Comet</option>
458 <option value="Tide">Tide</option> 457 <option value="Tide">Tide</option>
459 <!-- Not working in tests
460 -->
461 <option value="MyriMatch">MyriMatch</option> 458 <option value="MyriMatch">MyriMatch</option>
462 <option value="MS_Amanda">MS_Amanda</option> 459 <option value="MS_Amanda">MS_Amanda</option>
463 <!-- Windows only 460 <!-- Windows only
464 <option value="Andromeda">Andromeda</option> 461 <option value="Andromeda">Andromeda</option>
465 --> 462 -->
844 841
845 <param name="tide_export" label="TIDE: Output Format" type="select" help="Choose the output format"> 842 <param name="tide_export" label="TIDE: Output Format" type="select" help="Choose the output format">
846 <option value="tide_export_text" selected="True">Text</option> 843 <option value="tide_export_text" selected="True">Text</option>
847 <option value="tide_export_sqt" >SQT</option> 844 <option value="tide_export_sqt" >SQT</option>
848 <option value="tide_export_pepxml" >pepxml</option> 845 <option value="tide_export_pepxml" >pepxml</option>
849 <!-- 846 <option value="tide_export_mzid" >MzIdentML</option>
850 MZidentML and Percolator input file options generates files with the format (ie. if we use a spectrum file called ´qExactive01819´):
851 galaxy/database/jobs_directory/000/88/working/bin/resources/Tide/linux/linux_64bit/crux-output/qExactive01819.tide-search.target.mzid
852 instead of
853 galaxy/database/jobs_directory/000/88/working/bin/resources/Tide/linux/linux_64bit/crux-output/qExactive01819.tide-search.mzid
854 which is the expected one, so current searchgui version gives a "does not exist error".
855 -->
856 <!--
857 <option value="tide_export_mzid" >MzIdentML</option
858 <option value="tide_export_pin" >Percolator input file</option> 847 <option value="tide_export_pin" >Percolator input file</option>
859 -->
860 </param> 848 </param>
861 849
862 <param name="tide_remove_temp" type="boolean" truevalue="1" falsevalue="0" checked="true" 850 <param name="tide_remove_temp" type="boolean" truevalue="1" falsevalue="0" checked="true"
863 label="TIDE: Remove Temp Folders" help="If true, the temp folders are removed when the search is done"/> 851 label="TIDE: Remove Temp Folders" help="If true, the temp folders are removed when the search is done"/>
864 </when> 852 </when>
865 </conditional> 853 </conditional>
866 854
867 855
868 <!-- MyriMatch ADVANCED PARAMETERS --> 856 <!-- MyriMatch ADVANCED PARAMETERS -->
869 <!-- Not working in tests
870 <conditional name="myrimatch"> 857 <conditional name="myrimatch">
871 <param name="myrimatch_advanced" type="select" label="MyriMatch Options"> 858 <param name="myrimatch_advanced" type="select" label="MyriMatch Options">
872 <option value="yes">Advanced</option> 859 <option value="yes">Advanced</option>
873 <option value="no" selected="True">Default</option> 860 <option value="no" selected="True">Default</option>
874 </param> 861 </param>
875 <when value="no" /> 862 <when value="no" />
876 <when value="yes"> 863 <when value="yes">
877 <param name="myrimatch_min_pep_length" type="integer" value="6" 864 <param name="myrimatch_min_pep_length" type="integer" value="8"
878 label="MyriMatch: Minimum Peptide Length" help="Minimum length for a peptide to be considered" /> 865 label="MyriMatch: Minimum Peptide Length" help="Minimum length for a peptide to be considered" />
879 <param name="myrimatch_max_pep_length" type="integer" value="30" 866 <param name="myrimatch_max_pep_length" type="integer" value="30"
880 label="MyriMatch: Maximum Peptide Length" help="Maximum length for a peptide to be considered" /> 867 label="MyriMatch: Maximum Peptide Length" help="Maximum length for a peptide to be considered" />
881 <param name="myrimatch_min_prec_mass" type="float" value="0.0" 868 <param name="myrimatch_min_prec_mass" type="float" value="600.0"
882 label="MyriMatch: Minimum Peptide Mass" help="Minimum 1+ mass of parent ion to be considered" /> 869 label="MyriMatch: Minimum Precursor Mass" help="Minimum precursor mass of parent ion to be considered" />
883 <param name="myrimatch_max_prec_mass" type="float" value="10000.0" 870 <param name="myrimatch_max_prec_mass" type="float" value="5000.0"
884 label="MyriMatch: Maximum Peptide Mass" help="Maximum 1+ mass of parent ion to be considered" /> 871 label="MyriMatch: Maximum Precursor Mass" help="Maximum precursor mass of parent ion to be considered" />
885 <param name="myrimatch_num_matches" type="integer" value="10" 872 <param name="myrimatch_num_matches" type="integer" value="10"
886 label="MyriMatch: Maximum Number of Spectrum Matches" help="Set the value for the maximum number of spectrum matches" /> 873 label="MyriMatch: Maximum Number of Spectrum Matches" help="Set the value for the maximum number of spectrum matches" />
887 <param name="myrimatch_num_ptms" type="integer" value="2" 874 <param name="myrimatch_num_ptms" type="integer" value="2"
888 label="MyriMatch: Number of PTMs" help="Set the number of PTMS allowed per peptide" /> 875 label="MyriMatch: Max Variable PTMs per Peptide" help="Set the number of PTMS allowed per peptide" />
889 <param name="myrimatch_fragmentation" label="MyriMatch: Fragmentation Method" type="select" help="Choose the fragmentation method used (CID: b,y) or (ETD: c, z*)"> 876 <param name="myrimatch_fragmentation" label="MyriMatch: Fragmentation Method" type="select" help="Choose the fragmentation method used (CID: b,y) or (ETD: c, z*)">
890 <option value="CID" selected="True">CID</option> 877 <option value="CID" selected="True">CID</option>
878 <option value="HCD" >HCD</option>
891 <option value="ETD" >ETD</option> 879 <option value="ETD" >ETD</option>
892 </param> 880 </param>
893 <param name="myrimatch_termini" label="MyriMatch: Number of Enzymatic Termini" type="select" help="Select the number of enzymatic termini"> 881 <param name="myrimatch_termini" label="MyriMatch: Enzymatic Terminals" type="select" help="Select the number of enzymatic terminals">
894 <option value="0">non-tryptic</option> 882 <option value="0">None required</option>
895 <option value="1" >semi-tryptic</option> 883 <option value="1">At least one</option>
896 <option value="2" selected="True" >fully-tryptic</option> 884 <option value="2" selected="True" >Both</option>
897 </param> 885 </param>
898 <param name="myrimatch_plus_three" type="boolean" truevalue="1" falsevalue="0" checked="true" 886 <param name="myrimatch_plus_three" type="boolean" truevalue="1" falsevalue="0" checked="true"
899 label="MyriMatch: Smart Plus Three Option" help="Defines what algorithms are used to generate a set of theoretical fragment ions" /> 887 label="MyriMatch: Use Smart Plus Three Option" help="Defines what algorithms are used to generate a set of theoretical fragment ions" />
900 <param name="myrimatch_xcorr" type="boolean" truevalue="1" falsevalue="0" checked="false" 888 <param name="myrimatch_xcorr" type="boolean" truevalue="1" falsevalue="0" checked="false"
901 label="MyriMatch: Xcorr Option" help="a Sequest-like cross correlation score can be calculated for the top ranking hits" /> 889 label="MyriMatch: Compute Xcorr" help="a Sequest-like cross correlation score can be calculated for the top ranking hits" />
902 <param name="myrimatch_tic_cutoff" type="float" value="0.98" 890 <param name="myrimatch_tic_cutoff" type="float" value="0.98"
903 label="MyriMatch: TIC cutoff percentage" help="Cumulative ion current of picked peaks divided by TIC >= this value for peaks to be retained" /> 891 label="MyriMatch: TIC cutoff percentage" help="Cumulative ion current of picked peaks divided by TIC >= this value for peaks to be retained (0.0 - 1.0)" />
904 <param name="myrimatch_intensity_classes" type="integer" value="3" 892 <param name="myrimatch_intensity_classes" type="integer" value="3"
905 label="MyriMatch: Number of Intensity Classes" help="Experimental spectra have their peaks stratified into this number of intensity classed" /> 893 label="MyriMatch: Number of Intensity Classes" help="Experimental spectra have their peaks stratified into this number of intensity classed" />
906 <param name="myrimatch_class_multiplier" type="integer" value="2" 894 <param name="myrimatch_class_multiplier" type="integer" value="2"
907 label="MyriMatch: Class Multiplier" help="Has to do with previous option, this parameter controls the size of each class relative to the class above" /> 895 label="MyriMatch: Class Size Multiplier" help="Has to do with previous option, this parameter controls the size of each class relative to the class above" />
908 <param name="myrimatch_num_batches" type="integer" value="50" 896 <param name="myrimatch_num_batches" type="integer" value="50"
909 label="MyriMatch: Number of Batches" help="The number of batches per node to strive for when usinge the MPI-based parallelization features" /> 897 label="MyriMatch: Number of Batches" help="The number of batches per node to strive for when usinge the MPI-based parallelization features" />
910 <param name="myrimatch_max_peak" type="integer" value="100" 898 <param name="myrimatch_max_peak" type="integer" value="100"
911 label="MyriMatch: Maximum Peak Count" help="Maximum number of peaks to be used from a spectrum" /> 899 label="MyriMatch: Maximum Peak Count" help="Maximum number of peaks to be used from a spectrum" />
912 </when> 900 </when>
913 </conditional> 901 </conditional>
914 --> 902
915 903
916 <!-- Andromeda ADVANCED PARAMETERS --> 904 <!-- Andromeda ADVANCED PARAMETERS -->
917 <!-- Windows only 905 <!-- Windows only
918 <conditional name="andromeda"> 906 <conditional name="andromeda">
919 <param name="andromeda_advanced" type="select" label="Andromeda Options"> 907 <param name="andromeda_advanced" type="select" label="Andromeda Options">