Mercurial > repos > galaxyp > peptideshaker

annotate searchgui.xml @ 61:3ec27b4cee7c draft default tip

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit fc2810c412d9954fa584ae74497562b986c52764"
author galaxyp
date Thu, 12 Aug 2021 14:06:52 +0000
parents a6ff76e057fd
children
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da885ca16cb2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1"
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1 <tool id="search_gui"
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2 name="Search GUI"
da885ca16cb2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1"
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3 version="@SEARCHGUI_VERSION@+galaxy@SEARCHGUI_VERSION_SUFFIX@"
da885ca16cb2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1"
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4 profile="20.01"
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5 >
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6 <description>
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7 Perform protein identification using various search engines and prepare results for input to Peptide Shaker
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8 </description>
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9 <macros>
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10 <import>macros_basic.xml</import>
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11 </macros>
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12 <requirements>
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13 <requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement>
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14 <requirement type="package" version="3.0">zip</requirement>
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15 </requirements>
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16 <expand macro="stdio" />
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17 <command use_shared_home="false">
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19 <![CDATA[
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
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20 #from datetime import datetime
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21 #import json
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22 #import os
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23 #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
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24 #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
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25 #set $bin_dir = "bin"
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27 mkdir output;
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28 mkdir output_reports;
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29 mkdir temp_folder;
1beff3ddce58 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f2f9adb0e2389a95599d651b4eecab6b10244c75"
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30 mkdir log_folder;
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31 trap ">&2 cat log_folder/*.log" EXIT;
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33 cwd=`pwd`;
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34 export HOME=\$cwd;
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36 ## echo the search engines to run (single quotes important because X!Tandem)
44ca2967218c planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 69b2ae0ff05482e85ee086005462e7859b383064
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37 echo '$search_engines_options.engines';
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38 echo 'DB: ${input_fasta_file.element_identifier} sequences: ${input_fasta_file.metadata.sequences}';
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40 ##Create a searchgui.properties file for the version, which will be added to the searchgui_results if not already present
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41 echo 'searchgui.version=@SEARCHGUI_VERSION@' >> searchgui.properties;
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43 #for $peak_list_file in $peak_lists_files:
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44 #set $input_name = ""
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45 #if $peak_list_file.is_of_type("mgf"):
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46 #set $input_name = $peak_list_file.element_identifier.split('/')[-1].replace(".mgf", "") + ".mgf"
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47 #else if $peak_list_file.is_of_type("mzml"):
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48 #set $input_name = $peak_list_file.element_identifier.split('/')[-1].replace(".mzml", "") + ".mzml"
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49 #end if
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50 ln -s -f '${peak_list_file}' '${input_name}';
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51 #set $encoded_id = $__app__.security.encode_id($peak_list_file.id)
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52 echo 'Spectrums:${peak_list_file.element_identifier}(API:${encoded_id})';
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53 #end for
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54
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55 ## copy the input .par file to the working folder
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56 cp '${input_parameters_file}' './SEARCHGUI_IdentificationParameters.par';
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58 ## copy the input .fasta file to the working folder
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59 cp '${input_fasta_file}' './input_fasta_file.fasta';
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62 ################
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63 ## Search CLI ##
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64 ################
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65 echo 'running search gui' &&
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66 searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI
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67 --exec_dir="\$cwd/${bin_dir}"
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68 -use_log_folder 0
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69 -spectrum_files \$cwd
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70 -fasta_file "\$cwd/input_fasta_file.fasta"
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71 -output_folder \$cwd/output
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72 -id_params ./SEARCHGUI_IdentificationParameters.par
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73 -temp_folder \$cwd/temp_folder
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74 -log \$cwd/log_folder
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75 -threads "\${GALAXY_SLOTS:-12}"
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76
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77 #if $searchgui_advanced.searchgui_advanced_selector == 'advanced'
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78 -correct_titles "${searchgui_advanced.correct_titles}"
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79 $searchgui_advanced.missing_titles
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80 -mgf_splitting "${searchgui_advanced.mgf_splitting}"
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81 -mgf_spectrum_count "${searchgui_advanced.mgf_spectrum_count}"
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82 -output_gzip "${searchgui_advanced.output_gzip}"
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83 #end if
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
84
33
bce45e9e6d70 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 32
diff changeset
85 #set $engines_list = str($search_engines_options.engines).split(',')
21
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
86 #if 'X!Tandem' in $engines_list:
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
87 -xtandem 1
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
88 #else
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
89 -xtandem 0
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
90 #end if
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
91
21
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
92 #if 'MyriMatch' in $engines_list:
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
93 -myrimatch 1
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
94 #else
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
95 -myrimatch 0
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
96 #end if
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
97
21
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
98 #if 'MSGF' in $engines_list:
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
99 -msgf 1
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
100 #else
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
101 -msgf 0
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
102 #end if
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
103
21
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
104 #if 'OMSSA' in $engines_list:
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
105 -omssa 1
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
106 #else
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
107 -omssa 0
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
108 #end if
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
109
21
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
110 #if 'Comet' in $engines_list:
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
111 -comet 1
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
112 #else
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
113 -comet 0
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
114 #end if
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
115
21
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
116 #if 'Tide' in $engines_list:
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
117 -tide 1
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
118 #else
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
119 -tide 0
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
120 #end if
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
121
21
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
122 #if 'MS_Amanda' in $engines_list:
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
123 -ms_amanda 1
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
124 #else
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
125 -ms_amanda 0
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
126 #end if
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
127
24
815f93bb3e1b Uploaded
galaxyp
parents: 23
diff changeset
128 #if 'Andromeda' in $engines_list:
815f93bb3e1b Uploaded
galaxyp
parents: 23
diff changeset
129 -andromeda 1
815f93bb3e1b Uploaded
galaxyp
parents: 23
diff changeset
130 #else
815f93bb3e1b Uploaded
galaxyp
parents: 23
diff changeset
131 -andromeda 0
815f93bb3e1b Uploaded
galaxyp
parents: 23
diff changeset
132 #end if
815f93bb3e1b Uploaded
galaxyp
parents: 23
diff changeset
133
55
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents: 52
diff changeset
134 #if 'MetaMorpheus' in $engines_list:
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents: 52
diff changeset
135 -meta_morpheus 1
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents: 52
diff changeset
136 #else
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents: 52
diff changeset
137 -meta_morpheus 0
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents: 52
diff changeset
138 #end if
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents: 52
diff changeset
139
30
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 28
diff changeset
140 #if 'Novor' in $engines_list:
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 28
diff changeset
141 -novor 1
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 28
diff changeset
142 #else
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 28
diff changeset
143 -novor 0
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 28
diff changeset
144 #end if
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 28
diff changeset
145
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 28
diff changeset
146 #if 'DirecTag' in $engines_list:
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 28
diff changeset
147 -directag 1
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 28
diff changeset
148 #else
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 28
diff changeset
149 -directag 0
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 28
diff changeset
150 #end if
ad60446b1e93 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
galaxyp
parents: 28
diff changeset
151
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
152 ## single zip file
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
153 -output_option 0
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
154
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
155 ## mgf and database in output
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
156 -output_data 1
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
157
57
da885ca16cb2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1"
galaxyp
parents: 56
diff changeset
158 &&
da885ca16cb2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1"
galaxyp
parents: 56
diff changeset
159
da885ca16cb2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1"
galaxyp
parents: 56
diff changeset
160 echo '>log_folder:' &&
da885ca16cb2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1"
galaxyp
parents: 56
diff changeset
161
da885ca16cb2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1"
galaxyp
parents: 56
diff changeset
162 ls -l \$cwd/log_folder &&
da885ca16cb2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1"
galaxyp
parents: 56
diff changeset
163
da885ca16cb2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1"
galaxyp
parents: 56
diff changeset
164 mv output/searchgui_out.zip searchgui_out.zip
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
165
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
166 &&
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
167
57
da885ca16cb2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1"
galaxyp
parents: 56
diff changeset
168 zip -u searchgui_out.zip searchgui.properties
20
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
169 ]]>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
170 </command>
2cafc729b2ae planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
iracooke
parents:
diff changeset
171 <inputs>
55
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents: 52
diff changeset
172 <param format="json" name="input_parameters_file" type="data" label="Identification Parameters file"/>
21
dfaea053e32f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
iracooke
parents: 20
diff changeset
173
58
07ff622ec007 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0f6ab8b5647a33b2b051d7aa808ef42546436b23"
galaxyp
parents: 57
diff changeset
174 <param format="fasta" name="input_fasta_file" type="data" label="Fasta file" help="For postprocessing with PeptideShaker the sequences must have UniProt style headers and contain decoy sequences (see help)."/>
55
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents: 52
diff changeset
175
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents: 52
diff changeset
176 <param name="peak_lists_files" format="mgf,mzml" type="data" multiple="true" label="Input Peak Lists"
59
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177 help="Select appropriate MGF/MZML dataset(s) from history.
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178 Remember to choose only .mzML files when using MetaMorpheus." />
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179
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180 <!-- Search Engine Selection -->
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181 <section name="search_engines_options" expanded="true" title="Search Engine Options">
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182 <param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines">
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183 <help>Comet and Tide shouldn't both be selected since they use a similar algoritm. OMSSA might not work into isolated environments like containers. Ms Amanda may not work either when executed into isolated environments based on MacOS X (use SG 4.0.22 to solve any problem running MsAmanda).
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184 MetaMorpheus only produce results when using mzML format.</help>
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185 <option value="X!Tandem" selected="True">X!Tandem</option>
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186 <option value="MSGF" selected="True">MS-GF+</option>
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187 <option value="OMSSA">OMSSA</option>
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188 <option value="Comet">Comet</option>
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189 <option value="Tide">Tide</option>
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190 <option value="MyriMatch">MyriMatch</option>
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191 <option value="MS_Amanda">MS_Amanda</option>
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192 <option value="MetaMorpheus">MetaMorpheus</option>
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193 <!-- Windows only
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194 <option value="Andromeda">Andromeda</option>
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195 -->
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196 <!-- New with version 3.0
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197 -->
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198 <!--working in tests
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199 -->
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200 <option value="DirecTag">DirecTag</option>
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201 <option value="Novor">Novor (Select for non-commercial use only)</option>
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202 <validator type="no_options" message="Please select at least one output file" />
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203 </param>
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204 </section>
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205
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206 <conditional name="searchgui_advanced">
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207 <param name="searchgui_advanced_selector" type="select" label="SearchGUI Options">
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208 <option value="basic" selected="True">Default</option>
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209 <option value="advanced">Advanced</option>
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210 </param>
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211 <when value="basic" />
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212 <when value="advanced">
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213 <param name="correct_titles" type="select" label="How should PeptideShaker deal with duplicate spectra?"
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214 help="Unless you suspect some input files to be genuine duplicates then rename spectra is the safest option">
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215 <option value="0">no correction</option>
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216 <option value="1" selected="True">rename spectra</option>
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217 <option value="2">delete spectra</option>
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218 </param>
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219 <param name="missing_titles" type="boolean" checked="false" truevalue="-missing_titles 1" falsevalue="-missing_titles 0"
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220 label="Add missing spectrum titles" help="(-missing_titles)"/>
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221 <param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf"
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222 help="Choose a smaller value if you are running on a machine with limited memory"/>
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223 <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting"
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224 help="Choose a smaller value if you are running on a machine with limited memory"/>
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225 <param name="output_gzip" type="boolean" checked="true" truevalue="1" falsevalue="0"
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226 label="Gzip result files"/>
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227 </when>
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228 </conditional>
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229
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230 </inputs>
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231 <outputs>
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232 <data name="searchgui_results" format="searchgui_archive" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" />
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233 </outputs>
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234 <tests>
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235
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236 <!-- Test that specifying non-default search engines with default parameters works -->
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237 <test>
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238 <param name="peak_lists_files" value="searchgui_tinyspectra1.mgf"/>
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239 <param name="input_parameters_file" value="Identification_Parameters_default.par"/>
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240 <param name="input_fasta_file" value="fastacli_searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta" />
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241 <param name="engines" value="X!Tandem,MSGF,MyriMatch,Comet"/>
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242 <output name="searchgui_results" file="searchgui_tiny_result_default_4engines.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" />
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243 </test>
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244
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245
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246 <!-- Test that search works with MetaMorpheus with default parameters works-->
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247 <!-- Test data has been taken from metamorpheus galaxy tool -->
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248 <test>
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249 <param name="peak_lists_files" value="searchgui_smallCalibratible_Yeast.mzML"/>
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250 <param name="input_parameters_file" value="Identification_Parameters_default.par"/>
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251 <param name="input_fasta_file" value="searchgui_smallYeast.fasta" ftype="fasta" />
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252 <param name="engines" value="MetaMorpheus"/>
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253 <output name="searchgui_results" ftype="searchgui_archive">
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254 <assert_contents>
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255 <has_size value="798597" delta="10000"/>
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256 </assert_contents>
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257 </output>
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258 </test>
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259
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260 <!-- Test that search works with MSAmanda with default parameters works-->
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261 <test>
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262 <param name="peak_lists_files" value="searchgui_smallspectra.mgf"/>
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263 <param name="input_parameters_file" value="Identification_Parameters_default.par"/>
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264 <param name="input_fasta_file" value="fastacli_searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta" />
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265 <param name="engines" value="MS_Amanda"/>
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266 <output name="searchgui_results" ftype="searchgui_archive">
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267 <assert_contents>
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268 <has_size value="635138" delta="5000"/>
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269 </assert_contents>
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270 </output>
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271 </test>
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272
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273 <!-- Test that specifying non-default search engines with non-default parameters works -->
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274 <test>
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275 <param name="peak_lists_files" value="searchgui_tinyspectra1.mgf"/>
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276 <param name="input_parameters_file" value="Identification_Parameters_specific.par"/>
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277 <param name="input_fasta_file" value="fastacli_searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta" />
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278 <param name="engines" value="X!Tandem,MSGF,MyriMatch,Comet"/>
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279 <output name="searchgui_results" ftype="searchgui_archive">
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280 <assert_contents>
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281 <has_size value="159330" delta="20000"/>
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282 </assert_contents>
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283 </output>
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284 </test>
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285
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286 <!--
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287 NOTE: Identification_Parameters_specific.par is equivalent to the default .par plus these parameters:
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288 <param name="precursor_ion_tol" value="100"/>
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289 <param name="min_charge" value="1"/>
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290 <param name="max_charge" value="3"/>
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291 <param name="xtandem|xtandem_advanced" value="yes"/>
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292 <param name="xtandem|xtandem_advanced|xtandem_refine_selector" value="yes"/>
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293 -->
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294
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295 <!-- Test that specifying MsAmanda as search engine with non-default parameters works -->
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296 <test>
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297 <param name="peak_lists_files" value="searchgui_smallspectra.mgf"/>
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298 <param name="input_parameters_file" value="Identification_Parameters_specific.par"/>
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299 <param name="input_fasta_file" value="fastacli_searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta" />
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300 <param name="engines" value="MS_Amanda"/>
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301 <output name="searchgui_results" ftype="searchgui_archive">
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302 <assert_contents>
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303 <has_size value="635158" delta="5000"/>
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304 </assert_contents>
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305 </output>
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306 </test>
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307
55
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308 <!-- Test that specifying non-default search engines with default parameters works using modifications -->
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309 <test>
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310 <param name="peak_lists_files" value="searchgui_tinyspectra1.mgf"/>
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311 <param name="input_parameters_file" value="Identification_Parameters_default_modifications.par"/>
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312 <param name="input_fasta_file" value="fastacli_searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta" />
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313 <param name="engines" value="X!Tandem,MSGF,MyriMatch,Comet"/>
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314 <output name="searchgui_results" file="searchgui_tiny_result_default_4engines_modifications.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" />
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315 </test>
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316
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317 <!--
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318 NOTE: Identification_Parameters_default_modifications.par adds:
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319 - "Carbamidomethylation of C" as fixed modification
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320 - "Oxidation of M" as variable modification
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321 -->
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322
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323 <!-- Test that search works with MSAmanda with default default parameters - with modifications -->
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324 <test>
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325 <param name="peak_lists_files" value="searchgui_tinyspectra1.mgf"/>
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326 <param name="input_parameters_file" value="Identification_Parameters_default_modifications.par"/>
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327 <param name="input_fasta_file" value="fastacli_searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta" />
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328 <param name="engines" value="MS_Amanda"/>
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329 <output name="searchgui_results" ftype="searchgui_archive">
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330 <assert_contents>
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331 <has_size value="118136" delta="30000"/>
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332 </assert_contents>
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333 </output>
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334 </test>
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335
20
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336 </tests>
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337 <help>
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338 **What it does**
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339
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340 Runs multiple search engines on any number of MGF peak lists using SearchGUI.
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341
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342 Default: X! Tandem and MS-GF+ are executed.
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343
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344 Optional: MyriMatch, MS-Amanda, MetaMorpheus, OMSSA (it may not work into isolated environments like containers), Comet, Tide, DirecTag and Novor can be executed.
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345
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346 **Input FASTA**
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347
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348 In order to allow for postprocessing with PeptideShaker the sequences must contain decoy sequences (see _here: https://github.com/compomics/searchgui/wiki/DatabaseHelp#decoy-sequences)
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349 and the FASTA header must either contain no "|" characters (then the whole header will be used as ID) or have the following format:
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350
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351 >generic[your tag]|[protein accession]|[protein description]
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352
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353 or
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354
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355 >generic[your tag]|[protein accession]
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356
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357 See _here: https://github.com/compomics/searchgui/wiki/DatabaseHelp#non-standard-fasta.
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358
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359
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360
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361 </help>
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362 <expand macro="citations" />
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363 </tool>