Mercurial > repos > galaxyp > peptideshaker
comparison searchgui.xml @ 39:f63401dd6cbb draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 57426db0c017009ac7ab0498f8580efc453398c8
| author | galaxyp |
|---|---|
| date | Wed, 11 Jul 2018 08:14:05 -0400 |
| parents | 263440bb1900 |
| children | fec15a483a5c |
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| 38:263440bb1900 | 39:f63401dd6cbb |
|---|---|
| 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. |