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comparison searchgui.xml @ 32:ff592231f118 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 047efcfa1e9f45648e6e81d3776a1a93e2cfe46d
author galaxyp
date Wed, 25 Jan 2017 15:37:43 -0500
parents f3f67aa3123b
children bce45e9e6d70
comparison
equal deleted inserted replaced
31:f3f67aa3123b 32:ff592231f118
1 <tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.0"> 1 <tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.1">
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>
99 #if $omssa.omssa_advanced == "yes" 99 #if $omssa.omssa_advanced == "yes"
100 -omssa_hitlist_length ${omssa.hitlist_length} 100 -omssa_hitlist_length ${omssa.hitlist_length}
101 -omssa_remove_prec ${omssa.remove_precursor} 101 -omssa_remove_prec ${omssa.remove_precursor}
102 -omssa_scale_prec ${omssa.scale_precursor} 102 -omssa_scale_prec ${omssa.scale_precursor}
103 -omssa_estimate_charge ${omssa.estimate_charge} 103 -omssa_estimate_charge ${omssa.estimate_charge}
104
105 -omssa_memory ${omssa.omssa_memory} 104 -omssa_memory ${omssa.omssa_memory}
106 ## -omssa_isotopes ${omssa.omssa_isotopes}
107 -omssa_neutron ${omssa.omssa_neutron} 105 -omssa_neutron ${omssa.omssa_neutron}
108 -omssa_low_intensity "${omssa.omssa_low_intensity}" 106 -omssa_low_intensity "${omssa.omssa_low_intensity}"
109 -omssa_high_intensity ${omssa.omssa_high_intensity} 107 -omssa_high_intensity ${omssa.omssa_high_intensity}
110 -omssa_intensity_incr ${omssa.omssa_intensity_incr} 108 -omssa_intensity_incr ${omssa.omssa_intensity_incr}
111 -omssa_single_window_wd ${omssa.omssa_single_window_wd} 109 -omssa_single_window_wd ${omssa.omssa_single_window_wd}
146 -msgf_instrument ${msgf.msgf_instrument} 144 -msgf_instrument ${msgf.msgf_instrument}
147 -msgf_fragmentation ${msgf.msgf_fragmentation} 145 -msgf_fragmentation ${msgf.msgf_fragmentation}
148 -msgf_protocol ${msgf.msgf_protocol} 146 -msgf_protocol ${msgf.msgf_protocol}
149 -msgf_num_matches ${msgf.msgf_num_matches} 147 -msgf_num_matches ${msgf.msgf_num_matches}
150 -msgf_additional ${msgf.msgf_additional} 148 -msgf_additional ${msgf.msgf_additional}
151 -msgf_isotope_low ${msgf.msgf_isotope_low}
152 -msgf_isotope_high ${msgf.msgf_isotope_high}
153 #end if 149 #end if
154 150
155 #* Not working in tests 151 #* Not working in tests
156 #if $ms_amanda.ms_amanda_advanced == "yes" 152 #if $ms_amanda.ms_amanda_advanced == "yes"
157 -ms_amanda_decoy ${ms_amanda.ms_amanda_decoy} 153 -ms_amanda_decoy ${ms_amanda.ms_amanda_decoy}
166 #if $myrimatch.myrimatch_advanced == "yes" 162 #if $myrimatch.myrimatch_advanced == "yes"
167 -myrimatch_min_pep_length ${myrimatch.myrimatch_min_pep_length} 163 -myrimatch_min_pep_length ${myrimatch.myrimatch_min_pep_length}
168 -myrimatch_max_pep_length ${myrimatch.myrimatch_max_pep_length} 164 -myrimatch_max_pep_length ${myrimatch.myrimatch_max_pep_length}
169 -myrimatch_min_prec_mass ${myrimatch.myrimatch_min_prec_mass} 165 -myrimatch_min_prec_mass ${myrimatch.myrimatch_min_prec_mass}
170 -myrimatch_max_prec_mass ${myrimatch.myrimatch_max_prec_mass} 166 -myrimatch_max_prec_mass ${myrimatch.myrimatch_max_prec_mass}
171 -myrimatch_isotope_low ${myrimatch.myrimatch_isotope_low}
172 -myrimatch_isotope_high ${myrimatch.myrimatch_isotope_high}
173 -myrimatch_num_matches ${myrimatch.myrimatch_num_matches} 167 -myrimatch_num_matches ${myrimatch.myrimatch_num_matches}
174 -myrimatch_num_ptms ${myrimatch.myrimatch_num_ptms} 168 -myrimatch_num_ptms ${myrimatch.myrimatch_num_ptms}
175 -myrimatch_fragmentation ${myrimatch.myrimatch_fragmentation} 169 -myrimatch_fragmentation ${myrimatch.myrimatch_fragmentation}
176 -myrimatch_termini ${myrimatch.myrimatch_termini} 170 -myrimatch_termini ${myrimatch.myrimatch_termini}
177 -myrimatch_plus_three ${myrimatch.myrimatch_plus_three} 171 -myrimatch_plus_three ${myrimatch.myrimatch_plus_three}
579 <param name="scale_precursor" label="OMSSA: Scale Precursor Mass" type="boolean" truevalue="1" falsevalue="0" checked="false"/> 573 <param name="scale_precursor" label="OMSSA: Scale Precursor Mass" type="boolean" truevalue="1" falsevalue="0" checked="false"/>
580 <param name="estimate_charge" label="OMSSA: Estimate Charge" type="boolean" truevalue="1" falsevalue="0" checked="true" /> 574 <param name="estimate_charge" label="OMSSA: Estimate Charge" type="boolean" truevalue="1" falsevalue="0" checked="true" />
581 575
582 <param name="omssa_memory" type="boolean" truevalue="1" falsevalue="0" checked="true" 576 <param name="omssa_memory" type="boolean" truevalue="1" falsevalue="0" checked="true"
583 label="OMSSA: Map Sequences in Memory" help="Use memory mapped sequence libraries" /> 577 label="OMSSA: Map Sequences in Memory" help="Use memory mapped sequence libraries" />
584 <!-- param name="omssa_isotopes" type="integer" value="0" 578 <param name="omssa_neutron" type="float" value="1446.94"
585 label="OMSSA: Number of Isotopes" help="Number of isotopes to use (integer), 0 implies monoisotopic (default)" / -->
586 <param name="omssa_neutron" type="float" value="1446.94"
587 label="OMSSA: Neutron Mass" help="Mass after which OMSSA should consider neutron exact mass" /> 579 label="OMSSA: Neutron Mass" help="Mass after which OMSSA should consider neutron exact mass" />
588 <param name="omssa_low_intensity" type="float" value="0.0" 580 <param name="omssa_low_intensity" type="float" value="0.0"
589 label="OMSSA: Low Intensity Cutoff" help="Low intensity cutoff as a fraction of max peak" /> 581 label="OMSSA: Low Intensity Cutoff" help="Low intensity cutoff as a fraction of max peak" />
590 <param name="omssa_high_intensity" type="float" value="0.2" 582 <param name="omssa_high_intensity" type="float" value="0.2"
591 label="OMSSA: High Intensity Cutoff" help="High intensity cutoff as a fraction of max peak" /> 583 label="OMSSA: High Intensity Cutoff" help="High intensity cutoff as a fraction of max peak" />
710 <param name="msgf_num_matches" label="MSGF: Maximum Number of Spectrum Matches" type="integer" value="1" help="Number of peptide matches per spectrum to report" /> 702 <param name="msgf_num_matches" label="MSGF: Maximum Number of Spectrum Matches" type="integer" value="1" help="Number of peptide matches per spectrum to report" />
711 <param name="msgf_additional" label="MS-GF+ additional features" type="select" help="Additional features to export"> 703 <param name="msgf_additional" label="MS-GF+ additional features" type="select" help="Additional features to export">
712 <option value="0" selected="True">output basic scores only</option> 704 <option value="0" selected="True">output basic scores only</option>
713 <option value="1" >output additional features</option> 705 <option value="1" >output additional features</option>
714 </param> 706 </param>
715 <param name="msgf_isotope_low" label="MSGF: Lower Isotope Error Range" type="integer" value="0" help="Lower isotope error range" />
716 <param name="msgf_isotope_high" label="MSGF: Upper Isotope Error Range" type="integer" value="1" help="Upper isotope errror range" />
717 </when> 707 </when>
718 </conditional> 708 </conditional>
719 709
720 <!-- MS-AMANDA ADVANCED PARAMETERS --> 710 <!-- MS-AMANDA ADVANCED PARAMETERS -->
721 <!-- Not working in tests 711 <!-- Not working in tests
862 label="MyriMatch: Maximum Peptide Length" help="Maximum length for a peptide to be considered" /> 852 label="MyriMatch: Maximum Peptide Length" help="Maximum length for a peptide to be considered" />
863 <param name="myrimatch_min_prec_mass" type="float" value="0.0" 853 <param name="myrimatch_min_prec_mass" type="float" value="0.0"
864 label="MyriMatch: Minimum Peptide Mass" help="Minimum 1+ mass of parent ion to be considered" /> 854 label="MyriMatch: Minimum Peptide Mass" help="Minimum 1+ mass of parent ion to be considered" />
865 <param name="myrimatch_max_prec_mass" type="float" value="10000.0" 855 <param name="myrimatch_max_prec_mass" type="float" value="10000.0"
866 label="MyriMatch: Maximum Peptide Mass" help="Maximum 1+ mass of parent ion to be considered" /> 856 label="MyriMatch: Maximum Peptide Mass" help="Maximum 1+ mass of parent ion to be considered" />
867 <param name="myrimatch_isotope_low" type="integer" value="-1"
868 label="MyriMatch: Lower Isotope Error Range" help="Lower isotope error ragne" />
869 <param name="myrimatch_isotope_high" type="integer" value="2"
870 label="MyriMatch: Upper Isotope Error Range" help="Upper isotope error range" />
871 <param name="myrimatch_num_matches" type="integer" value="10" 857 <param name="myrimatch_num_matches" type="integer" value="10"
872 label="MyriMatch: Maximum Number of Spectrum Matches" help="Set the value for the maximum number of spectrum matches" /> 858 label="MyriMatch: Maximum Number of Spectrum Matches" help="Set the value for the maximum number of spectrum matches" />
873 <param name="myrimatch_num_ptms" type="integer" value="2" 859 <param name="myrimatch_num_ptms" type="integer" value="2"
874 label="MyriMatch: Number of PTMs" help="Set the number of PTMS allowed per peptide" /> 860 label="MyriMatch: Number of PTMs" help="Set the number of PTMS allowed per peptide" />
875 <param name="myrimatch_fragmentation" label="MyriMatch: Fragmentation Method" type="select" help="Choose the fragmentation method used (CID: b,y) or (ETD: c, z*)"> 861 <param name="myrimatch_fragmentation" label="MyriMatch: Fragmentation Method" type="select" help="Choose the fragmentation method used (CID: b,y) or (ETD: c, z*)">
1097 <param name="min_charge" value="1"/> 1083 <param name="min_charge" value="1"/>
1098 <param name="max_charge" value="3"/> 1084 <param name="max_charge" value="3"/>
1099 <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/> 1085 <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/>
1100 <param name="xtandem.xtandem_advanced" value="yes"/> 1086 <param name="xtandem.xtandem_advanced" value="yes"/>
1101 <param name="xtandem_advanced.xtandem_refine_selector" value="yes"/> 1087 <param name="xtandem_advanced.xtandem_refine_selector" value="yes"/>
1102
1103 <output name="output" file="tiny_searchgui_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" /> 1088 <output name="output" file="tiny_searchgui_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" />
1104 </test> 1089 </test>
1105 <!-- Test that search works with MSAmanda --> 1090 <!-- Test that search works with MSAmanda -->
1106 <test> 1091 <test>
1107 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/> 1092 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>
1110 <param name="fixed_modifications" value="carbamidomethyl c"/> 1095 <param name="fixed_modifications" value="carbamidomethyl c"/>
1111 <param name="variable_modifications" value="oxidation of m"/> 1096 <param name="variable_modifications" value="oxidation of m"/>
1112 <param name="min_charge" value="1"/> 1097 <param name="min_charge" value="1"/>
1113 <param name="max_charge" value="3"/> 1098 <param name="max_charge" value="3"/>
1114 <param name="engines" value="MS_Amanda"/> 1099 <param name="engines" value="MS_Amanda"/>
1115
1116 <output name="output" file="tiny_searchgui_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" /> 1100 <output name="output" file="tiny_searchgui_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" />
1117 </test> 1101 </test>
1118 </tests> 1102 </tests>
1119 <help> 1103 <help>
1120 **What it does** 1104 **What it does**