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comparison searchgui.xml @ 47:44ca2967218c draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 69b2ae0ff05482e85ee086005462e7859b383064
author galaxyp
date Sat, 15 Sep 2018 08:51:12 -0400
parents baeced706dbc
children 64e3a8cc8ffb
comparison
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46:baeced706dbc 47:44ca2967218c
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 </macros> 7 </macros>
8 <requirements> 8 <requirements>
9 <requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement> 9 <requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement>
10 <requirement type="package" version="3.0">zip</requirement> 10 <requirement type="package" version="3.0">zip</requirement>
11 </requirements> 11 </requirements>
12 <expand macro="stdio" /> 12 <expand macro="stdio" />
13 <command> 13 <command use_shared_home="false">
14 <![CDATA[ 14 <![CDATA[
15 #from datetime import datetime 15 #from datetime import datetime
16 #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s") 16 #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
17 #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s") 17 #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
18 #set $temp_stderr = "searchgui_stderr" 18 #set $temp_stderr = "searchgui_stderr"
21 mkdir output; 21 mkdir output;
22 mkdir output_reports; 22 mkdir output_reports;
23 cwd=`pwd`; 23 cwd=`pwd`;
24 export HOME=\$cwd; 24 export HOME=\$cwd;
25 25
26 ## echo the search engines to run 26 ## echo the search engines to run (single quotes important because X!Tandem)
27 echo "$search_engines_options.engines"; 27 echo '$search_engines_options.engines';
28 echo "DB: ${input_database.display_name} sequences: ${input_database.metadata.sequences}"; 28 echo 'DB: ${input_database.display_name} sequences: ${input_database.metadata.sequences}';
29 29
30 ##Create a searchgui.properties file for the version, which will be added to the searchgui_results if not already present 30 ##Create a searchgui.properties file for the version, which will be added to the searchgui_results if not already present
31 echo "searchgui.version=@SEARCHGUI_VERSION@" >> searchgui.properties; 31 echo 'searchgui.version=@SEARCHGUI_VERSION@' >> searchgui.properties;
32 32
33 #for $mgf in $peak_lists: 33 #for $mgf in $peak_lists:
34 #set $input_name = $mgf.display_name.split('/')[-1].replace(".mgf", "") + ".mgf" 34 #set $input_name = $mgf.display_name.split('/')[-1].replace(".mgf", "") + ".mgf"
35 ln -s -f '${mgf}' '${input_name}'; 35 ln -s -f '${mgf}' '${input_name}';
36 #set $encoded_id = $__app__.security.encode_id($mgf.id) 36 #set $encoded_id = $__app__.security.encode_id($mgf.id)
37 echo "Spectrums:${mgf.display_name}(API:${encoded_id}) "; 37 echo 'Spectrums:${mgf.display_name}(API:${encoded_id})';
38 #end for 38 #end for
39 ##ln -s "${input_database}" input_database.fasta; 39 ##ln -s "${input_database}" input_database.fasta;
40 cp "${input_database}" input_database.fasta; 40 cp "${input_database}" input_database.fasta;
41
42 ###########################################
43 #### Set paths ####
44 ###########################################
45 echo 'Setting paths' &&
46 searchgui eu.isas.searchgui.cmd.PathSettingsCLI
47 --exec_dir="\$cwd/${bin_dir}"
48 -temp_folder \$cwd
49 -log \$cwd/searchgui.log 2>> $temp_stderr &&
41 50
42 ########################################### 51 ###########################################
43 #### Creating decoy database #### 52 #### Creating decoy database ####
44 ########################################### 53 ###########################################
45 #if $protein_database_options.create_decoy: 54 #if $protein_database_options.create_decoy:
46 echo "Creating decoy database."; 55 echo 'Creating decoy database.' &&
47 searchgui eu.isas.searchgui.cmd.FastaCLI --exec_dir="\$cwd/${bin_dir}" -in input_database.fasta -decoy && 56 searchgui eu.isas.searchgui.cmd.FastaCLI
57 --exec_dir="\$cwd/${bin_dir}"
58 -in input_database.fasta
59 -decoy 2>> $temp_stderr &&
48 rm input_database.fasta && 60 rm input_database.fasta &&
49 cp input_database_concatenated_target_decoy.fasta input_database.fasta && 61 cp input_database_concatenated_target_decoy.fasta input_database.fasta &&
50 ## ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta; 62 ## ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta;
51 #end if 63 #end if
52 64
53 ##################################################### 65 #####################################################
54 ## generate IdentificationParameters for SearchGUI ## 66 ## generate IdentificationParameters for SearchGUI ##
55 ##################################################### 67 #####################################################
68 echo 'setting identification parameters' &&
56 (searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI 69 (searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI
57 --exec_dir="\$cwd/${bin_dir}" 70 --exec_dir="\$cwd/${bin_dir}"
58 -out SEARCHGUI_IdentificationParameters.par 71 -out SEARCHGUI_IdentificationParameters.par
59 72
60 @GENERAL_PARAMETERS@ 73 @GENERAL_PARAMETERS@
321 && 334 &&
322 335
323 ################ 336 ################
324 ## Search CLI ## 337 ## Search CLI ##
325 ################ 338 ################
339 echo 'running search gui' &&
326 (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI 340 (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI
327 --exec_dir="\$cwd/${bin_dir}" 341 --exec_dir="\$cwd/${bin_dir}"
328 -temp_folder `pwd`
329 -spectrum_files \$cwd 342 -spectrum_files \$cwd
330 -output_folder \$cwd/output 343 -output_folder \$cwd/output
331 -id_params SEARCHGUI_IdentificationParameters.par 344 -id_params SEARCHGUI_IdentificationParameters.par
332 345
333 -threads "\${GALAXY_SLOTS:-12}" 346 -threads "\${GALAXY_SLOTS:-12}"
1095 <param name="min_charge" value="1"/> 1108 <param name="min_charge" value="1"/>
1096 <param name="max_charge" value="3"/> 1109 <param name="max_charge" value="3"/>
1097 <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/> 1110 <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/>
1098 <param name="xtandem.xtandem_advanced" value="yes"/> 1111 <param name="xtandem.xtandem_advanced" value="yes"/>
1099 <param name="xtandem_advanced.xtandem_refine_selector" value="yes"/> 1112 <param name="xtandem_advanced.xtandem_refine_selector" value="yes"/>
1100 <output name="output" 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" />
1101 </test> 1114 </test>
1102 <!-- Test that search works with MSAmanda --> 1115 <!-- Test that search works with MSAmanda -->
1103 <test> 1116 <test>
1104 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/> 1117 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>
1105 <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/> 1118 <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
1106 <param name="precursor_ion_tol" value="100"/> 1119 <param name="precursor_ion_tol" value="100"/>
1107 <param name="min_charge" value="1"/> 1120 <param name="min_charge" value="1"/>
1108 <param name="max_charge" value="3"/> 1121 <param name="max_charge" value="3"/>
1109 <param name="engines" value="MS_Amanda"/> 1122 <param name="engines" value="MS_Amanda"/>
1110 <output name="output" 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" />
1111 </test> 1124 </test>
1112 1125
1113 <!-- Test that specifying non-default search engines works using modifications --> 1126 <!-- Test that specifying non-default search engines works using modifications -->
1114 <!-- 1127 <!--
1115 <test> 1128 <test>