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comparison searchgui.xml @ 52:864bd76db767 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 9dc7c9c3ebd64f14c0ce95a0dc190361a90fa4fb
author galaxyp
date Wed, 16 Jan 2019 08:18:39 -0500
parents 58a3e6cb2598
children bb0130ff73ce
comparison
equal deleted inserted replaced
51:66690eb50a32 52:864bd76db767
1 <tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@"> 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>
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 && 26 echo "" > $temp_stderr &&
27 27
28 ## echo the search engines to run (single quotes important because X!Tandem) 28 ## echo the search engines to run (single quotes important because X!Tandem)
29 echo '$search_engines_options.engines'; 29 echo '$search_engines_options.engines';
30 echo 'DB: ${input_database.element_identifier} sequences: ${input_database.metadata.sequences}'; 30 echo 'DB: ${input_database.element_identifier} sequences: ${input_database.metadata.sequences}';
31 31
44 ########################################### 44 ###########################################
45 #### Set paths #### 45 #### Set paths ####
46 ########################################### 46 ###########################################
47 echo 'Setting paths' && 47 echo 'Setting paths' &&
48 searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.PathSettingsCLI 48 searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.PathSettingsCLI
49 --exec_dir="\$cwd/${bin_dir}" 49 --exec_dir="\$cwd/${bin_dir}"
50 -temp_folder \$cwd 50 -temp_folder \$cwd
51 -log \$cwd/searchgui.log 2>> $temp_stderr && 51 -log \$cwd/searchgui.log 2>> $temp_stderr &&
52 52
53 ########################################### 53 ###########################################
54 #### Creating decoy database #### 54 #### Creating decoy database ####
55 ########################################### 55 ###########################################
56 #if $protein_database_options.create_decoy: 56 #if $protein_database_options.create_decoy:
57 echo 'Creating decoy database.' && 57 echo 'Creating decoy database.' &&
58 searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.FastaCLI 58 searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.FastaCLI
59 --exec_dir="\$cwd/${bin_dir}" 59 --exec_dir="\$cwd/${bin_dir}"
60 -in input_database.fasta 60 -in input_database.fasta
61 -decoy 2>> $temp_stderr && 61 -decoy 2>> $temp_stderr &&
62 rm input_database.fasta && 62 rm input_database.fasta &&
63 cp input_database_concatenated_target_decoy.fasta input_database.fasta && 63 cp input_database_concatenated_target_decoy.fasta input_database.fasta &&
64 ## ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta; 64 ## ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta;
1126 <!-- Test that specifying non-default search engines works using modifications --> 1126 <!-- Test that specifying non-default search engines works using modifications -->
1127 <test> 1127 <test>
1128 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/> 1128 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>
1129 <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/> 1129 <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
1130 <param name="precursor_ion_tol" value="100"/> 1130 <param name="precursor_ion_tol" value="100"/>
1131 <param name="fixed_modifications" value="carbamidomethyl c"/> 1131 <param name="fixed_modifications" value="Carbamidomethylation of C"/>
1132 <param name="variable_modifications" value="oxidation of m"/> 1132 <param name="variable_modifications" value="Oxidation of M"/>
1133 <param name="min_charge" value="1"/> 1133 <param name="min_charge" value="1"/>
1134 <param name="max_charge" value="3"/> 1134 <param name="max_charge" value="3"/>
1135 <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/> 1135 <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/>
1136 <param name="xtandem|xtandem_advanced" value="yes"/> 1136 <param name="xtandem|xtandem_advanced" value="yes"/>
1137 <param name="xtandem|xtandem_advanced|xtandem_refine_selector" value="yes"/> 1137 <param name="xtandem|xtandem_advanced|xtandem_refine_selector" value="yes"/>
1140 <!-- Test that search works with MSAmanda - with modifications --> 1140 <!-- Test that search works with MSAmanda - with modifications -->
1141 <test> 1141 <test>
1142 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/> 1142 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>
1143 <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/> 1143 <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
1144 <param name="precursor_ion_tol" value="100"/> 1144 <param name="precursor_ion_tol" value="100"/>
1145 <param name="fixed_modifications" value="carbamidomethyl c"/> 1145 <param name="fixed_modifications" value="Carbamidomethylation of C"/>
1146 <param name="variable_modifications" value="oxidation of m"/> 1146 <param name="variable_modifications" value="Oxidation of M"/>
1147 <param name="min_charge" value="1"/> 1147 <param name="min_charge" value="1"/>
1148 <param name="max_charge" value="3"/> 1148 <param name="max_charge" value="3"/>
1149 <param name="engines" value="MS_Amanda"/> 1149 <param name="engines" value="MS_Amanda"/>
1150 <output name="searchgui_results" 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" />
1151 </test> 1151 </test>