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annotate searchgui.xml @ 0:8b99cb00e1c4 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
author jjohnson
date Tue, 15 May 2018 14:50:35 -0400
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children fa76abf69433
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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>
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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>
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11 <requirement type="package">JQ</requirement>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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12 </requirements>
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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13 <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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14 <command>
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15 <![CDATA[
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16 #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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17 #import json
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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18 #import os;
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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19 #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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20 #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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21 #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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22 #set $bin_dir = "bin"
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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23
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24 mkdir output;
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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25 mkdir output_reports;
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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26 cwd=`pwd`;
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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27 export HOME=\$cwd;
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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29 ## echo the search engines to run
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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30 echo "$search_engines_options.engines";
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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31
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32 ##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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33 echo "searchgui.version=@SEARCHGUI_VERSION@" >> searchgui.properties;
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34
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35 #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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36 #set $input_name = $mgf.display_name.split('/')[-1].replace(".mgf", "") + ".mgf"
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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37 ln -s -f '${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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38 #set $encoded_id = $__app__.security.encode_id($mgf.id)
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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39 echo "Spectrums:${mgf.display_name}(API:${encoded_id}) ";
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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40 #end for
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43
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44 ## Necessary for executing tests. The FASTA file has to be manually copied from the test-data folder to the working directory in order it can be found when using the PAR file.
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45 cp '$__tool_directory__/test-data/searchgui_tinydb1_concatenated_target_decoy.fasta' "\$cwd/searchgui_tinydb1_concatenated_target_decoy.fasta";
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46
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47
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48
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49 ## copy the input .par file to the working folder
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50 cp "${input_par}" "\$cwd/SEARCHGUI_IdentificationParameters.par";
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51 echo "-.par source file:";
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52 echo "${input_par}";
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53
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54 ## (local) PAR file points to a FASTA file with .dat extension, which gives problems with many search engines. We should rename it to a .fasta file before passing it to SearchGUI
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55 #set $par_target_path = "$cwd/SEARCHGUI_IdentificationParameters.par";
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56 echo "-.par target file:";
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57 echo $par_target_path;
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58
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59 ## reading from the original .par file the path of the source .dat (fasta) file to be used
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60 content_par_target_path=`cat $par_target_path`;
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61 dat_path=`jq -r '.searchParameters.fastaFile.path' <<< "\$content_par_target_path"`;
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62 echo "-.dat file path from target .par: ";
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63 echo "\$dat_path";
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64
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65 ## copy original .data fasta file to a local .fasta file
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66 new_fasta_file_path="\$cwd/input_database.fasta";
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67 cp "\$dat_path" "\$new_fasta_file_path";
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68 echo "-new .fasta file path copied from source .dat file: ";
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69 echo "\$new_fasta_file_path";
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70
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71 ## modifying the .par file!!
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72 ## First we establish the new content for the path: .searchParameters.fastaFile.path
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73 new_content_par_target_path=`jq '.searchParameters.fastaFile.path = \$newVal' --arg newVal "\$new_fasta_file_path" <<< "\$content_par_target_path"`;
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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74 ## Secondly, for .proteinInferencePreferences.proteinSequenceDatabase.path
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75 new_content_par_target_path=`jq '.proteinInferencePreferences.proteinSequenceDatabase.path = \$newVal' --arg newVal "\$new_fasta_file_path" <<< "\$new_content_par_target_path"`;
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76
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77 ## we generate a new .par file filled with the new fasta path.
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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78 #set $new_par_target_path = "$cwd/SEARCHGUI_IdentificationParameters_new.par";
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79 echo "\$new_content_par_target_path" >> $new_par_target_path;
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80 echo "-new par target path: ";
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81 echo $new_par_target_path;
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82
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83 ## As PeptideShaker waits for "SEARCHGUI_IdentificationParameters.par" name, we overwrite the original file with the "_new" file
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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84 ##mv "\$cwd/SEARCHGUI_IdentificationParameters_new.par" "\$cwd/SEARCHGUI_IdentificationParameters.par"
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85 rm $par_target_path;
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86 mv $new_par_target_path $par_target_path;
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87
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88
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89 ################
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90 ## Search CLI ##
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91 ################
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92 (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI
8b99cb00e1c4 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 3c83b8f8ca60d6399bc5dd7096b830ca1f1c457e-dirty
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93 --exec_dir="\$cwd/${bin_dir}"
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94 -temp_folder `pwd`
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95 -spectrum_files \$cwd
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96 -output_folder \$cwd/output
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97 -id_params $par_target_path
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98
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99 -threads "\${GALAXY_SLOTS:-12}"
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100
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101 #if $searchgui_advanced.searchgui_advanced_selector == 'advanced'
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102 -correct_titles "${searchgui_advanced.correct_titles}"
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103 $searchgui_advanced.missing_titles
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104 -mgf_splitting "${searchgui_advanced.mgf_splitting}"
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105 -mgf_spectrum_count "${searchgui_advanced.mgf_spectrum_count}"
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106 #end if
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107
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108 ## Turn of the protein tree generation as it can produce errors if the search is finished before the tree is created
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109 ## the tree is generated afterwards in PeptideShaker
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110 ## -protein_index 0
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111
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112 ##-makeblastdb_folder \$BLAST_ROOT_DIR
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113
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114 #set $engines_list = str($search_engines_options.engines).split(',')
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115 #if 'X!Tandem' in $engines_list:
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116 -xtandem 1
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117 #else
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118 -xtandem 0
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119 #end if
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120
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121 #if 'MyriMatch' in $engines_list:
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122 -myrimatch 1
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123 #else
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124 -myrimatch 0
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125 #end if
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126
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127 #if 'MSGF' in $engines_list:
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128 -msgf 1
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129 #else
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130 -msgf 0
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131 #end if
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132
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133 #if 'OMSSA' in $engines_list:
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134 -omssa 1
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135 #else
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136 -omssa 0
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137 #end if
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138
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139 #if 'Comet' in $engines_list:
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140 -comet 1
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141 #else
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142 -comet 0
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143 #end if
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144
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145 #if 'Tide' in $engines_list:
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146 -tide 1
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147 #else
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148 -tide 0
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149 #end if
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150
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151 #if 'MS_Amanda' in $engines_list:
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152 -ms_amanda 1
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153 #else
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154 -ms_amanda 0
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155 #end if
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156
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157 #if 'Andromeda' in $engines_list:
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158 -andromeda 1
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159 #else
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160 -andromeda 0
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161 #end if
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162
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163 #if 'Novor' in $engines_list:
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164 -novor 1
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165 #else
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166 -novor 0
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167 #end if
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168
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169 #if 'DirecTag' in $engines_list:
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170 -directag 1
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171 #else
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172 -directag 0
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173 #end if
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174
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175 ## single zip file
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176 -output_option 0
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177
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178 ## mgf and database in output
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179 -output_data 1
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180
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181 2>> $temp_stderr)
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182
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183 &&
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184
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185 (mv output/searchgui_out.zip searchgui_out.zip 2>> $temp_stderr)
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186
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187 &&
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188
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189 (zip -u searchgui_out.zip searchgui.properties 2>> $temp_stderr);
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190
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191 exit_code_for_galaxy=\$?;
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192 cat $temp_stderr 2>&1;
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193 (exit \$exit_code_for_galaxy)
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194 ]]>
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195 </command>
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196 <inputs>
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197 <param format="par" name="input_par" type="data" label="Identification Parameters file"
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198 help="Select PAR file from history"/>
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199
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200 <param name="peak_lists" format="mgf" type="data" multiple="true" label="Input Peak Lists (mgf)"
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201 help="Select appropriate MGF dataset(s) from history" />
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202
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203 <!-- Search Engine Selection -->
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204 <section name="search_engines_options" expanded="true" title="Search Engine Options">
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205 <param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines">
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206 <help>Comet and Tide shouldn't both be selected since they use a similar algoritm.</help>
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207 <option value="X!Tandem" selected="True">X!Tandem</option>
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208 <option value="MSGF" selected="True">MS-GF+</option>
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209 <option value="OMSSA" selected="True">OMSSA</option>
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210 <option value="Comet">Comet</option>
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211 <option value="Tide">Tide</option>
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212 <option value="MyriMatch">MyriMatch</option>
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213 <option value="MS_Amanda">MS_Amanda</option>
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214 <!-- Windows only
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215 <option value="Andromeda">Andromeda</option>
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216 -->
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217 <!-- New with version 3.0
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218 -->
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219 <!--working in tests
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220 -->
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221 <option value="DirecTag">DirecTag</option>
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222 <option value="Novor">Novor (Select for non-commercial use only)</option>
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223 <validator type="no_options" message="Please select at least one output file" />
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224 </param>
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225 </section>
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226
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227 <conditional name="searchgui_advanced">
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228 <param name="searchgui_advanced_selector" type="select" label="SearchGUI Options">
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229 <option value="basic" selected="True">Default</option>
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230 <option value="advanced">Advanced</option>
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231 </param>
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232 <when value="basic" />
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233 <when value="advanced">
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234 <param name="correct_titles" type="select" label="How should PeptideShaker deal with duplicate spectra?"
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235 help="Unless you suspect some input files to be genuine duplicates then rename spectra is the safest option">
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236 <option value="0">no correction</option>
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237 <option value="1" selected="True">rename spectra</option>
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238 <option value="2">delete spectra</option>
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239 </param>
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240
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241 <param name="missing_titles" type="boolean" checked="false" truevalue="-missing_titles 1" falsevalue="-missing_titles 0"
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242 label="Add missing spectrum titles" help="(-missing_titles)"/>
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243
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244 <param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf"
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245 help="Choose a smaller value if you are running on a machine with limited memory"/>
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246
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247 <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting"
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248 help="Choose a smaller value if you are running on a machine with limited memory"/>
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249 </when>
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250 </conditional>
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251
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252 </inputs>
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253 <outputs>
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254 <data name="searchgui_results" format="searchgui_archive" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" />
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255 </outputs>
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256 <tests>
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257
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258 <!-- Test that specifying non-default search engines works -->
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259 <test>
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260 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>
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261 <param name="input_par" value="Identification_Parameters_specific.par"/>
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262 <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/>
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263 <output name="output" file="tiny_searchgui_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" />
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264 </test>
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265 <!-- Test that search works with MSAmanda -->
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266 <test>
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267 <param name="peak_lists" value="searchgui_smallspectra.mgf"/>
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268 <param name="input_par" value="Identification_Parameters_default.par"/>
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269 <param name="engines" value="MS_Amanda"/>
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270 <output name="output" file="smallsearch_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" />
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271 </test>
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272
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273 </tests>
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274 <help>
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275 **What it does**
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276
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277 Runs multiple search engines on any number of MGF peak lists using the SearchGUI.
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278
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279 Default: X! Tandem, OMSSA and MS-GF+ are executed.
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280
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281 Optional: MyriMatch, MS-Amanda, Comet and Tide can be executed.
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282
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283 </help>
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284 <expand macro="citations" />
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285 </tool>