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comparison searchgui.xml @ 46:baeced706dbc draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 57426db0c017009ac7ab0498f8580efc453398c8
author galaxyp
date Wed, 11 Jul 2018 08:14:23 -0400
parents 5fa8b409599e
children 44ca2967218c
comparison
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45:5fa8b409599e 46:baeced706dbc
1090 <!-- Test that specifying non-default search engines works --> 1090 <!-- Test that specifying non-default search engines works -->
1091 <test> 1091 <test>
1092 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/> 1092 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>
1093 <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/> 1093 <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
1094 <param name="precursor_ion_tol" value="100"/> 1094 <param name="precursor_ion_tol" value="100"/>
1095 <param name="fixed_modifications" value="carbamidomethyl c"/>
1096 <param name="variable_modifications" value="oxidation of m"/>
1097 <param name="min_charge" value="1"/> 1095 <param name="min_charge" value="1"/>
1098 <param name="max_charge" value="3"/> 1096 <param name="max_charge" value="3"/>
1099 <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/> 1097 <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/>
1100 <param name="xtandem.xtandem_advanced" value="yes"/> 1098 <param name="xtandem.xtandem_advanced" value="yes"/>
1101 <param name="xtandem_advanced.xtandem_refine_selector" value="yes"/> 1099 <param name="xtandem_advanced.xtandem_refine_selector" value="yes"/>
1104 <!-- Test that search works with MSAmanda --> 1102 <!-- Test that search works with MSAmanda -->
1105 <test> 1103 <test>
1106 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/> 1104 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>
1107 <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/> 1105 <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
1108 <param name="precursor_ion_tol" value="100"/> 1106 <param name="precursor_ion_tol" value="100"/>
1107 <param name="min_charge" value="1"/>
1108 <param name="max_charge" value="3"/>
1109 <param name="engines" value="MS_Amanda"/>
1110 <output name="output" file="tiny_searchgui_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" />
1111 </test>
1112
1113 <!-- Test that specifying non-default search engines works using modifications -->
1114 <!--
1115 <test>
1116 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>
1117 <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
1118 <param name="precursor_ion_tol" value="100"/>
1119 <param name="fixed_modifications" value="carbamidomethyl c"/>
1120 <param name="variable_modifications" value="oxidation of m"/>
1121 <param name="min_charge" value="1"/>
1122 <param name="max_charge" value="3"/>
1123 <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/>
1124 <param name="xtandem.xtandem_advanced" value="yes"/>
1125 <param name="xtandem_advanced.xtandem_refine_selector" value="yes"/>
1126 <output name="output" file="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" />
1127 </test>
1128 -->
1129 <!-- Test that search works with MSAmanda - with modifications -->
1130 <!--
1131 <test>
1132 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>
1133 <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
1134 <param name="precursor_ion_tol" value="100"/>
1109 <param name="fixed_modifications" value="carbamidomethyl c"/> 1135 <param name="fixed_modifications" value="carbamidomethyl c"/>
1110 <param name="variable_modifications" value="oxidation of m"/> 1136 <param name="variable_modifications" value="oxidation of m"/>
1111 <param name="min_charge" value="1"/> 1137 <param name="min_charge" value="1"/>
1112 <param name="max_charge" value="3"/> 1138 <param name="max_charge" value="3"/>
1113 <param name="engines" value="MS_Amanda"/> 1139 <param name="engines" value="MS_Amanda"/>
1114 <output name="output" file="tiny_searchgui_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" /> 1140 <output name="output" file="tiny_searchgui_modifications_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" />
1115 </test> 1141 </test>
1142 -->
1116 </tests> 1143 </tests>
1117 <help> 1144 <help>
1118 **What it does** 1145 **What it does**
1119 1146
1120 Runs multiple search engines on any number of MGF peak lists using the SearchGUI. 1147 Runs multiple search engines on any number of MGF peak lists using the SearchGUI.