Mercurial > repos > jjohnson > peptideshaker

annotate searchgui.xml @ 1:fa76abf69433 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit e09348a0c372d4355c5dda6519e52ff17e0e8621-dirty
author jjohnson
date Fri, 08 Jun 2018 15:58:53 -0400
parents 8b99cb00e1c4
children eea7e945f479
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8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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1 <tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.0">
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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2 <description>
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3 Perform protein identification using various search engines and prepare results for input to Peptide Shaker
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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4 </description>
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5 <macros>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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6 <import>macros_basic.xml</import>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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7 </macros>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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8 <requirements>
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9 <requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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10 <requirement type="package" version="3.0">zip</requirement>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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11 </requirements>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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12 <expand macro="stdio" />
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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13 <command>
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14 <![CDATA[
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15 #from datetime import datetime
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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16 #import json
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17 #import os
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18 #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
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19 #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
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20 #set $temp_stderr = "searchgui_stderr"
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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21 #set $bin_dir = "bin"
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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23 mkdir output;
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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24 mkdir output_reports;
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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25 cwd=`pwd`;
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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26 export HOME=\$cwd;
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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28 ## echo the search engines to run
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29 echo '$search_engines_options.engines';
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31 ##Create a searchgui.properties file for the version, which will be added to the searchgui_results if not already present
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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32 echo "searchgui.version=@SEARCHGUI_VERSION@" >> searchgui.properties;
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34 #for $mgf in $peak_lists:
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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35 #set $input_name = $mgf.display_name.split('/')[-1].replace(".mgf", "") + ".mgf"
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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36 ln -s -f '${mgf}' '${input_name}';
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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37 #set $encoded_id = $__app__.security.encode_id($mgf.id)
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fa76abf69433 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit e09348a0c372d4355c5dda6519e52ff17e0e8621-dirty
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38 echo 'Spectrums:${mgf.display_name}(API:${encoded_id}) ';
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39 #end for
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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41 ## copy the input .par file to the working folder
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42 cp '${input_zip}' './input_par_fasta.zip';
fa76abf69433 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit e09348a0c372d4355c5dda6519e52ff17e0e8621-dirty
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43 echo '-.zip source file:';
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44 echo '${input_zip}';
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45
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46
1
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47 ## Necessary for executing tests. Specific par files need to be uncompressed to be used by the tool.
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48 jar xvf './input_par_fasta.zip' 'Identification_Parameters_default.par' 'searchgui_tinydb1_concatenated_target_decoy.fasta';
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49 jar xvf './input_par_fasta.zip' Identification_Parameters_specific.par searchgui_tinydb1_concatenated_target_decoy.fasta;
fa76abf69433 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit e09348a0c372d4355c5dda6519e52ff17e0e8621-dirty
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50 if [ -f ./Identification_Parameters_default.par ];then
fa76abf69433 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit e09348a0c372d4355c5dda6519e52ff17e0e8621-dirty
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51 mv ./Identification_Parameters_default.par ./SEARCHGUI_IdentificationParameters.par;
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52 fi;
fa76abf69433 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit e09348a0c372d4355c5dda6519e52ff17e0e8621-dirty
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53 if [ -f ./Identification_Parameters_specific.par ];then
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54 mv './Identification_Parameters_specific.par' './SEARCHGUI_IdentificationParameters.par';
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55 fi;
0
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56
1
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57 ## By default we will always try to uncompress SEARCHGUI_IdentificationParameters.par and input_database.fasta
fa76abf69433 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit e09348a0c372d4355c5dda6519e52ff17e0e8621-dirty
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58 jar xvf './input_par_fasta.zip' SEARCHGUI_IdentificationParameters.par input_database.fasta;
0
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59
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61 ################
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62 ## Search CLI ##
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63 ################
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64 (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI
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65 --exec_dir="\$cwd/${bin_dir}"
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66 -temp_folder `pwd`
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67 -spectrum_files \$cwd
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68 -output_folder \$cwd/output
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69 -id_params ./SEARCHGUI_IdentificationParameters.par
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71 -threads "\${GALAXY_SLOTS:-12}"
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73 #if $searchgui_advanced.searchgui_advanced_selector == 'advanced'
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74 -correct_titles "${searchgui_advanced.correct_titles}"
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75 $searchgui_advanced.missing_titles
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76 -mgf_splitting "${searchgui_advanced.mgf_splitting}"
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77 -mgf_spectrum_count "${searchgui_advanced.mgf_spectrum_count}"
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78 #end if
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8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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parents:
diff changeset
80 ## Turn of the protein tree generation as it can produce errors if the search is finished before the tree is created
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
81 ## the tree is generated afterwards in PeptideShaker
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
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82 ## -protein_index 0
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
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83
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
84 ##-makeblastdb_folder \$BLAST_ROOT_DIR
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
85
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
86 #set $engines_list = str($search_engines_options.engines).split(',')
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
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87 #if 'X!Tandem' in $engines_list:
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
88 -xtandem 1
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
89 #else
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
diff changeset
90 -xtandem 0
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
parents:
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91 #end if
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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92
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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93 #if 'MyriMatch' in $engines_list:
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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diff changeset
94 -myrimatch 1
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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95 #else
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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96 -myrimatch 0
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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97 #end if
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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98
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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99 #if 'MSGF' in $engines_list:
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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100 -msgf 1
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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101 #else
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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102 -msgf 0
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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103 #end if
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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104
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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105 #if 'OMSSA' in $engines_list:
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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106 -omssa 1
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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107 #else
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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108 -omssa 0
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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109 #end if
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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110
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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111 #if 'Comet' in $engines_list:
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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112 -comet 1
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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113 #else
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114 -comet 0
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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115 #end if
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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116
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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117 #if 'Tide' in $engines_list:
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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118 -tide 1
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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119 #else
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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120 -tide 0
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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121 #end if
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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122
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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123 #if 'MS_Amanda' in $engines_list:
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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124 -ms_amanda 1
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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125 #else
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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126 -ms_amanda 0
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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127 #end if
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128
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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129 #if 'Andromeda' in $engines_list:
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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130 -andromeda 1
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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131 #else
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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132 -andromeda 0
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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133 #end if
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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134
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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135 #if 'Novor' in $engines_list:
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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136 -novor 1
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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137 #else
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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138 -novor 0
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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139 #end if
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140
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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141 #if 'DirecTag' in $engines_list:
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142 -directag 1
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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143 #else
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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144 -directag 0
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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145 #end if
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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146
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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147 ## single zip file
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148 -output_option 0
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149
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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150 ## mgf and database in output
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151 -output_data 1
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152
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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153 2>> $temp_stderr)
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154
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155 &&
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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156
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
jjohnson
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157 (mv output/searchgui_out.zip searchgui_out.zip 2>> $temp_stderr)
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158
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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159 &&
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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160
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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161 (zip -u searchgui_out.zip searchgui.properties 2>> $temp_stderr);
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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162
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163 exit_code_for_galaxy=\$?;
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164 cat $temp_stderr 2>&1;
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165 (exit \$exit_code_for_galaxy)
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166 ]]>
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167 </command>
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168 <inputs>
1
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169 <param format="zip" name="input_zip" type="data" label="Identification Parameters and fasta file"
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170 help="Select a zip file with Identification Parameters (.par) and a fasta file from history"/>
0
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171
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172 <param name="peak_lists" format="mgf" type="data" multiple="true" label="Input Peak Lists (mgf)"
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173 help="Select appropriate MGF dataset(s) from history" />
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174
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175 <!-- Search Engine Selection -->
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176 <section name="search_engines_options" expanded="true" title="Search Engine Options">
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177 <param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines">
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178 <help>Comet and Tide shouldn't both be selected since they use a similar algoritm.</help>
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179 <option value="X!Tandem" selected="True">X!Tandem</option>
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180 <option value="MSGF" selected="True">MS-GF+</option>
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181 <option value="OMSSA" selected="True">OMSSA</option>
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182 <option value="Comet">Comet</option>
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183 <option value="Tide">Tide</option>
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184 <option value="MyriMatch">MyriMatch</option>
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185 <option value="MS_Amanda">MS_Amanda</option>
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186 <!-- Windows only
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187 <option value="Andromeda">Andromeda</option>
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188 -->
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189 <!-- New with version 3.0
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190 -->
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191 <!--working in tests
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192 -->
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193 <option value="DirecTag">DirecTag</option>
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194 <option value="Novor">Novor (Select for non-commercial use only)</option>
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195 <validator type="no_options" message="Please select at least one output file" />
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196 </param>
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197 </section>
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198
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199 <conditional name="searchgui_advanced">
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200 <param name="searchgui_advanced_selector" type="select" label="SearchGUI Options">
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201 <option value="basic" selected="True">Default</option>
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202 <option value="advanced">Advanced</option>
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203 </param>
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204 <when value="basic" />
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205 <when value="advanced">
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206 <param name="correct_titles" type="select" label="How should PeptideShaker deal with duplicate spectra?"
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207 help="Unless you suspect some input files to be genuine duplicates then rename spectra is the safest option">
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208 <option value="0">no correction</option>
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209 <option value="1" selected="True">rename spectra</option>
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210 <option value="2">delete spectra</option>
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211 </param>
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212
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213 <param name="missing_titles" type="boolean" checked="false" truevalue="-missing_titles 1" falsevalue="-missing_titles 0"
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214 label="Add missing spectrum titles" help="(-missing_titles)"/>
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215
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216 <param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf"
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217 help="Choose a smaller value if you are running on a machine with limited memory"/>
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218
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219 <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting"
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220 help="Choose a smaller value if you are running on a machine with limited memory"/>
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221 </when>
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222 </conditional>
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223
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224 </inputs>
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225 <outputs>
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226 <data name="searchgui_results" format="searchgui_archive" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" />
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227 </outputs>
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228 <tests>
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229
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230 <!-- Test that specifying non-default search engines works -->
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231 <test>
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232 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>
1
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233 <!-- <param name="input_par" value="Identification_Parameters_specific.par"/>-->
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234 <param name="input_zip" value="IdentificationParametersAndFastaSpecific.zip" ftype="zip" />
0
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235 <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/>
1
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236 <output name="searchgui_results" file="tiny_searchgui_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" />
0
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237 </test>
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238 <!-- Test that search works with MSAmanda -->
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239 <test>
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240 <param name="peak_lists" value="searchgui_smallspectra.mgf"/>
1
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241 <!-- <param name="input_par" value="Identification_Parameters_default.par"/>-->
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242 <param name="input_zip" value="IdentificationParametersAndFastaDefault.zip" ftype="zip" />
0
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243 <param name="engines" value="MS_Amanda"/>
1
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244 <output name="searchgui_results" file="smallsearch_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" />
0
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245 </test>
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246
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247 </tests>
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248 <help>
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249 **What it does**
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250
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251 Runs multiple search engines on any number of MGF peak lists using the SearchGUI.
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252
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253 Default: X! Tandem, OMSSA and MS-GF+ are executed.
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254
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255 Optional: MyriMatch, MS-Amanda, Comet and Tide can be executed.
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256
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257 </help>
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258 <expand macro="citations" />
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259 </tool>