Mercurial > repos > galaxyp > peptideshaker

comparison searchgui.xml @ 49:58a3e6cb2598 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4
author galaxyp
date Fri, 12 Oct 2018 08:56:06 -0400
parents 64e3a8cc8ffb
children 864bd76db767
comparison
equal deleted inserted replaced
48:64e3a8cc8ffb 49:58a3e6cb2598
1 <tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.1"> 1 <tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@">
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>
21 mkdir output; 21 mkdir output;
22 mkdir output_reports; 22 mkdir output_reports;
23 cwd=`pwd`; 23 cwd=`pwd`;
24 export HOME=\$cwd; 24 export HOME=\$cwd;
25 25
26 echo "" > $temp_stderr &&
27
26 ## echo the search engines to run (single quotes important because X!Tandem) 28 ## echo the search engines to run (single quotes important because X!Tandem)
27 echo '$search_engines_options.engines'; 29 echo '$search_engines_options.engines';
28 echo 'DB: ${input_database.element_identifier} sequences: ${input_database.metadata.sequences}'; 30 echo 'DB: ${input_database.element_identifier} sequences: ${input_database.metadata.sequences}';
29 31
30 ##Create a searchgui.properties file for the version, which will be added to the searchgui_results if not already present 32 ##Create a searchgui.properties file for the version, which will be added to the searchgui_results if not already present
41 43
42 ########################################### 44 ###########################################
43 #### Set paths #### 45 #### Set paths ####
44 ########################################### 46 ###########################################
45 echo 'Setting paths' && 47 echo 'Setting paths' &&
46 searchgui eu.isas.searchgui.cmd.PathSettingsCLI 48 searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.PathSettingsCLI
47 --exec_dir="\$cwd/${bin_dir}" 49 --exec_dir="\$cwd/${bin_dir}"
48 -temp_folder \$cwd 50 -temp_folder \$cwd
49 -log \$cwd/searchgui.log 2>> $temp_stderr && 51 -log \$cwd/searchgui.log 2>> $temp_stderr &&
50 52
51 ########################################### 53 ###########################################
52 #### Creating decoy database #### 54 #### Creating decoy database ####
53 ########################################### 55 ###########################################
54 #if $protein_database_options.create_decoy: 56 #if $protein_database_options.create_decoy:
55 echo 'Creating decoy database.' && 57 echo 'Creating decoy database.' &&
56 searchgui eu.isas.searchgui.cmd.FastaCLI 58 searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.FastaCLI
57 --exec_dir="\$cwd/${bin_dir}" 59 --exec_dir="\$cwd/${bin_dir}"
58 -in input_database.fasta 60 -in input_database.fasta
59 -decoy 2>> $temp_stderr && 61 -decoy 2>> $temp_stderr &&
60 rm input_database.fasta && 62 rm input_database.fasta &&
61 cp input_database_concatenated_target_decoy.fasta input_database.fasta && 63 cp input_database_concatenated_target_decoy.fasta input_database.fasta &&
64 66
65 ##################################################### 67 #####################################################
66 ## generate IdentificationParameters for SearchGUI ## 68 ## generate IdentificationParameters for SearchGUI ##
67 ##################################################### 69 #####################################################
68 echo 'setting identification parameters' && 70 echo 'setting identification parameters' &&
69 (searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI 71 (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.IdentificationParametersCLI
70 --exec_dir="\$cwd/${bin_dir}" 72 --exec_dir="\$cwd/${bin_dir}"
71 -out SEARCHGUI_IdentificationParameters.par 73 -out SEARCHGUI_IdentificationParameters.par
72 74
73 @GENERAL_PARAMETERS@ 75 @GENERAL_PARAMETERS@
74 76
433 435
434 && 436 &&
435 437
436 (zip -u searchgui_out.zip searchgui.properties 2>> $temp_stderr); 438 (zip -u searchgui_out.zip searchgui.properties 2>> $temp_stderr);
437 439
438 exit_code_for_galaxy=\$?;
439 cat $temp_stderr 2>&1; 440 cat $temp_stderr 2>&1;
440 (exit \$exit_code_for_galaxy)
441 ]]> 441 ]]>
442 </command> 442 </command>
443 <inputs> 443 <inputs>
444 444
445 <param format="fasta" name="input_database" type="data" label="Protein Database" 445 <param format="fasta" name="input_database" type="data" label="Protein Database"
1106 <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/> 1106 <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
1107 <param name="precursor_ion_tol" value="100"/> 1107 <param name="precursor_ion_tol" value="100"/>
1108 <param name="min_charge" value="1"/> 1108 <param name="min_charge" value="1"/>
1109 <param name="max_charge" value="3"/> 1109 <param name="max_charge" value="3"/>
1110 <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/> 1110 <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/>
1111 <param name="xtandem.xtandem_advanced" value="yes"/> 1111 <param name="xtandem|xtandem_advanced" value="yes"/>
1112 <param name="xtandem_advanced.xtandem_refine_selector" value="yes"/> 1112 <param name="xtandem|xtandem_advanced|xtandem_refine_selector" value="yes"/>
1113 <output name="searchgui_results" file="tiny_searchgui_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" /> 1113 <output name="searchgui_results" file="tiny_searchgui_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" />
1114 </test> 1114 </test>
1115 <!-- Test that search works with MSAmanda --> 1115 <!-- Test that search works with MSAmanda -->
1116 <test> 1116 <test>
1117 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/> 1117 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>
1122 <param name="engines" value="MS_Amanda"/> 1122 <param name="engines" value="MS_Amanda"/>
1123 <output name="searchgui_results" file="tiny_searchgui_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" /> 1123 <output name="searchgui_results" file="tiny_searchgui_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" />
1124 </test> 1124 </test>
1125 1125
1126 <!-- Test that specifying non-default search engines works using modifications --> 1126 <!-- Test that specifying non-default search engines works using modifications -->
1127 <!--
1128 <test> 1127 <test>
1129 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/> 1128 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>
1130 <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/> 1129 <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
1131 <param name="precursor_ion_tol" value="100"/> 1130 <param name="precursor_ion_tol" value="100"/>
1132 <param name="fixed_modifications" value="carbamidomethyl c"/> 1131 <param name="fixed_modifications" value="carbamidomethyl c"/>
1133 <param name="variable_modifications" value="oxidation of m"/> 1132 <param name="variable_modifications" value="oxidation of m"/>
1134 <param name="min_charge" value="1"/> 1133 <param name="min_charge" value="1"/>
1135 <param name="max_charge" value="3"/> 1134 <param name="max_charge" value="3"/>
1136 <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/> 1135 <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/>
1137 <param name="xtandem.xtandem_advanced" value="yes"/> 1136 <param name="xtandem|xtandem_advanced" value="yes"/>
1138 <param name="xtandem_advanced.xtandem_refine_selector" value="yes"/> 1137 <param name="xtandem|xtandem_advanced|xtandem_refine_selector" value="yes"/>
1139 <output name="output" file="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" /> 1138 <output name="searchgui_results" file="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" />
1140 </test> 1139 </test>
1141 -->
1142 <!-- Test that search works with MSAmanda - with modifications --> 1140 <!-- Test that search works with MSAmanda - with modifications -->
1143 <!--
1144 <test> 1141 <test>
1145 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/> 1142 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>
1146 <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/> 1143 <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
1147 <param name="precursor_ion_tol" value="100"/> 1144 <param name="precursor_ion_tol" value="100"/>
1148 <param name="fixed_modifications" value="carbamidomethyl c"/> 1145 <param name="fixed_modifications" value="carbamidomethyl c"/>
1149 <param name="variable_modifications" value="oxidation of m"/> 1146 <param name="variable_modifications" value="oxidation of m"/>
1150 <param name="min_charge" value="1"/> 1147 <param name="min_charge" value="1"/>
1151 <param name="max_charge" value="3"/> 1148 <param name="max_charge" value="3"/>
1152 <param name="engines" value="MS_Amanda"/> 1149 <param name="engines" value="MS_Amanda"/>
1153 <output name="output" file="tiny_searchgui_modifications_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" /> 1150 <output name="searchgui_results" file="tiny_searchgui_modifications_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" />
1154 </test> 1151 </test>
1155 -->
1156 </tests> 1152 </tests>
1157 <help> 1153 <help>
1158 **What it does** 1154 **What it does**
1159 1155
1160 Runs multiple search engines on any number of MGF peak lists using the SearchGUI. 1156 Runs multiple search engines on any number of MGF peak lists using the SearchGUI.