Mercurial > repos > galaxyp > peptideshaker

annotate searchgui.xml @ 48:b72821cab1d7 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
author galaxyp
date Fri, 15 Jan 2021 14:05:46 +0000
parents a13e9d712194
children 560a08e0de13
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48
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
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1 <tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@+galaxy@SEARCHGUI_VERSION_SUFFIX@">
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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
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4 </description>
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iracooke
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5 <macros>
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6 <import>macros_basic.xml</import>
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7 </macros>
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8 <requirements>
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9 <requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement>
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10 <requirement type="package" version="3.0">zip</requirement>
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11 </requirements>
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12 <expand macro="stdio" />
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13 <command use_shared_home="false">
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14 <![CDATA[
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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15 #from datetime import datetime
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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"
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21 #set $bin_dir = "bin"
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23 mkdir output;
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24 mkdir output_reports;
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25 cwd=`pwd`;
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26 export HOME=\$cwd;
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28 echo "" > $temp_stderr &&
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30 ## echo the search engines to run (single quotes important because X!Tandem)
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31 echo '$search_engines_options.engines';
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32 echo 'DB: ${input_fasta_file.element_identifier} sequences: ${input_fasta_file.metadata.sequences}';
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34 ##Create a searchgui.properties file for the version, which will be added to the searchgui_results if not already present
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35 echo 'searchgui.version=@SEARCHGUI_VERSION@' >> searchgui.properties;
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3ccfbb673089 Update to PS 1.1 and SG 2.1.1
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37 #for $peak_list_file in $peak_lists_files:
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38 #set $input_name = ""
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39 #if $peak_list_file.is_of_type("mgf"):
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40 #set $input_name = $peak_list_file.element_identifier.split('/')[-1].replace(".mgf", "") + ".mgf"
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41 #else if $peak_list_file.is_of_type("mzml"):
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42 #set $input_name = $peak_list_file.element_identifier.split('/')[-1].replace(".mzml", "") + ".mzml"
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43 #end if
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44 ln -s -f '${peak_list_file}' '${input_name}';
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45 #set $encoded_id = $__app__.security.encode_id($peak_list_file.id)
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46 echo 'Spectrums:${peak_list_file.element_identifier}(API:${encoded_id})';
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47 #end for
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49 ## copy the input .par file to the working folder
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50 cp '${input_parameters_file}' './SEARCHGUI_IdentificationParameters.par';
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52 ## copy the input .fasta file to the working folder
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53 cp '${input_fasta_file}' './input_fasta_file.fasta';
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54
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56 ################
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57 ## Search CLI ##
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58 ################
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59 echo 'running search gui' &&
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60 (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI
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61 --exec_dir="\$cwd/${bin_dir}"
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62 -spectrum_files \$cwd
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63 -fasta_file "\$cwd/input_fasta_file.fasta"
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64 -output_folder \$cwd/output
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65 -id_params ./SEARCHGUI_IdentificationParameters.par
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67 -threads "\${GALAXY_SLOTS:-12}"
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69 #if $searchgui_advanced.searchgui_advanced_selector == 'advanced'
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70 -correct_titles "${searchgui_advanced.correct_titles}"
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71 $searchgui_advanced.missing_titles
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72 -mgf_splitting "${searchgui_advanced.mgf_splitting}"
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73 -mgf_spectrum_count "${searchgui_advanced.mgf_spectrum_count}"
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74 -output_gzip "${searchgui_advanced.output_gzip}"
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75 #end if
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76
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77 #set $engines_list = str($search_engines_options.engines).split(',')
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78 #if 'X!Tandem' in $engines_list:
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79 -xtandem 1
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80 #else
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81 -xtandem 0
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82 #end if
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83
6
53bdfaed924d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5943ced37a55ac06f722af5d4ccd568c300c0ea3
iracooke
parents: 4
diff changeset
84 #if 'MyriMatch' in $engines_list:
1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
85 -myrimatch 1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
86 #else
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
87 -myrimatch 0
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
88 #end if
0
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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89
6
53bdfaed924d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5943ced37a55ac06f722af5d4ccd568c300c0ea3
iracooke
parents: 4
diff changeset
90 #if 'MSGF' in $engines_list:
1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
91 -msgf 1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
92 #else
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
93 -msgf 0
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
94 #end if
0
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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95
6
53bdfaed924d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5943ced37a55ac06f722af5d4ccd568c300c0ea3
iracooke
parents: 4
diff changeset
96 #if 'OMSSA' in $engines_list:
1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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97 -omssa 1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
98 #else
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
99 -omssa 0
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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100 #end if
0
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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101
6
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iracooke
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102 #if 'Comet' in $engines_list:
1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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103 -comet 1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
104 #else
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
105 -comet 0
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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106 #end if
0
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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107
6
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iracooke
parents: 4
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108 #if 'Tide' in $engines_list:
1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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109 -tide 1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
110 #else
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
111 -tide 0
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
112 #end if
0
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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113
1
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iracooke
parents: 0
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114 #if 'MS_Amanda' in $engines_list:
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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115 -ms_amanda 1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
diff changeset
116 #else
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iracooke
parents: 0
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117 -ms_amanda 0
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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118 #end if
0
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galaxyp
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119
15
3fa49ed11f3d Uploaded
galaxyp
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diff changeset
120 #if 'Andromeda' in $engines_list:
3fa49ed11f3d Uploaded
galaxyp
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121 -andromeda 1
3fa49ed11f3d Uploaded
galaxyp
parents: 14
diff changeset
122 #else
3fa49ed11f3d Uploaded
galaxyp
parents: 14
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123 -andromeda 0
3fa49ed11f3d Uploaded
galaxyp
parents: 14
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124 #end if
3fa49ed11f3d Uploaded
galaxyp
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125
48
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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126 #if 'MetaMorpheus' in $engines_list:
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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127 -meta_morpheus 1
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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128 #else
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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129 -meta_morpheus 0
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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130 #end if
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
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131
18
ffed32e397cb Uploaded
galaxyp
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diff changeset
132 #if 'Novor' in $engines_list:
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galaxyp
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133 -novor 1
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galaxyp
parents: 17
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134 #else
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galaxyp
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135 -novor 0
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galaxyp
parents: 17
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136 #end if
ffed32e397cb Uploaded
galaxyp
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137
ffed32e397cb Uploaded
galaxyp
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diff changeset
138 #if 'DirecTag' in $engines_list:
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galaxyp
parents: 17
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139 -directag 1
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galaxyp
parents: 17
diff changeset
140 #else
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galaxyp
parents: 17
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141 -directag 0
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galaxyp
parents: 17
diff changeset
142 #end if
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galaxyp
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143
0
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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144 ## single zip file
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galaxyp
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145 -output_option 0
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galaxyp
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146
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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147 ## mgf and database in output
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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148 -output_data 1
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galaxyp
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149
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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150 2>> $temp_stderr)
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151
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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152 &&
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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153
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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154 (mv output/searchgui_out.zip searchgui_out.zip 2>> $temp_stderr)
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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155
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galaxyp
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156 &&
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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157
17
2f8e9d0351a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 4256c7c6fde06722b66f433f5913c2e707bc930f-dirty
galaxyp
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diff changeset
158 (zip -u searchgui_out.zip searchgui.properties 2>> $temp_stderr);
13
3ccfbb673089 Update to PS 1.1 and SG 2.1.1
iracooke
parents: 12
diff changeset
159
0
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galaxyp
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160 cat $temp_stderr 2>&1;
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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161 ]]>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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162 </command>
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
galaxyp
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163 <inputs>
48
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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164 <param format="json" name="input_parameters_file" type="data" label="Identification Parameters file"/>
1
cb1666df2fb3 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 8352ff0127dc95846e12f2b0ff8398525a00d626
iracooke
parents: 0
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165
48
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galaxyp
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166 <param format="fasta" name="input_fasta_file" type="data" label="Fasta file"/>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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167
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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168 <param name="peak_lists_files" format="mgf,mzml" type="data" multiple="true" label="Input Peak Lists"
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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diff changeset
169 help="Select appropriate MGF/MZML dataset(s) from history" />
0
a9e90cdcb97a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
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170
6
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iracooke
parents: 4
diff changeset
171 <!-- Search Engine Selection -->
37
7b72e889dafd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb
galaxyp
parents: 36
diff changeset
172 <section name="search_engines_options" expanded="true" title="Search Engine Options">
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
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173 <param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines">
48
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents: 45
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174 <help>Comet and Tide shouldn't both be selected since they use a similar algoritm. OMSSA may not work into isolated environments like containers.</help>
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
175 <option value="X!Tandem" selected="True">X!Tandem</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
diff changeset
176 <option value="MSGF" selected="True">MS-GF+</option>
48
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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177 <option value="OMSSA">OMSSA</option>
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
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diff changeset
178 <option value="Comet">Comet</option>
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
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179 <option value="Tide">Tide</option>
36
24bcbed3da6a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6afe42e2f4b9d780c4cee76a4dcd9cac1e1ea0ad
galaxyp
parents: 35
diff changeset
180 <option value="MyriMatch">MyriMatch</option>
23
aa3728c18bd9 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit cb53f8e01ae0cc4dc7621f03ba209d040ef30312
galaxyp
parents: 22
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181 <option value="MS_Amanda">MS_Amanda</option>
48
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182 <!-- TODO: MetaMorpheus Waiting for support for dotnet in bioconda package -->
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183 <!-- <option value="MetaMorpheus">MetaMorpheus</option> -->
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184 <!-- Windows only
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185 <option value="Andromeda">Andromeda</option>
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186 -->
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187 <!-- New with version 3.0
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188 -->
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189 <!--working in tests
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190 -->
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191 <option value="DirecTag">DirecTag</option>
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192 <option value="Novor">Novor (Select for non-commercial use only)</option>
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193 <validator type="no_options" message="Please select at least one output file" />
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194 </param>
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195 </section>
0
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196
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197 <conditional name="searchgui_advanced">
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198 <param name="searchgui_advanced_selector" type="select" label="SearchGUI Options">
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199 <option value="basic" selected="True">Default</option>
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200 <option value="advanced">Advanced</option>
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201 </param>
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202 <when value="basic" />
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203 <when value="advanced">
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204 <param name="correct_titles" type="select" label="How should PeptideShaker deal with duplicate spectra?"
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205 help="Unless you suspect some input files to be genuine duplicates then rename spectra is the safest option">
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206 <option value="0">no correction</option>
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207 <option value="1" selected="True">rename spectra</option>
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208 <option value="2">delete spectra</option>
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209 </param>
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210 <param name="missing_titles" type="boolean" checked="false" truevalue="-missing_titles 1" falsevalue="-missing_titles 0"
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211 label="Add missing spectrum titles" help="(-missing_titles)"/>
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212 <param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf"
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213 help="Choose a smaller value if you are running on a machine with limited memory"/>
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214 <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting"
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215 help="Choose a smaller value if you are running on a machine with limited memory"/>
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216 <param name="output_gzip" type="boolean" checked="true" truevalue="1" falsevalue="0"
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217 label="Gzip result files"/>
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218 </when>
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219 </conditional>
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220
0
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221 </inputs>
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222 <outputs>
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223 <data name="searchgui_results" format="searchgui_archive" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" />
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224 </outputs>
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225 <tests>
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226
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227 <!-- Test that specifying non-default search engines with default parameters works -->
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228 <test>
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229 <param name="peak_lists_files" value="searchgui_tinyspectra1.mgf"/>
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230 <param name="input_parameters_file" value="Identification_Parameters_default.par"/>
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231 <param name="input_fasta_file" value="fastacli_searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta" />
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232 <param name="engines" value="X!Tandem,MSGF,MyriMatch,Comet"/>
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233 <output name="searchgui_results" file="searchgui_tiny_result_default_4engines.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" />
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234 </test>
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235
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236 <!-- Test that search works with MSAmanda with default parameters works-->
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237 <test>
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238 <param name="peak_lists_files" value="searchgui_smallspectra.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="MS_Amanda"/>
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242 <output name="searchgui_results" ftype="searchgui_archive">
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243 <assert_contents>
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244 <has_size value="635138" delta="5000"/>
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245 </assert_contents>
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246 </output>
0
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247 </test>
48
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248
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249 <!-- Test that specifying non-default search engines with non-default parameters works -->
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250 <test>
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251 <param name="peak_lists_files" value="searchgui_tinyspectra1.mgf"/>
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252 <param name="input_parameters_file" value="Identification_Parameters_specific.par"/>
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253 <param name="input_fasta_file" value="fastacli_searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta" />
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254 <param name="engines" value="X!Tandem,MSGF,MyriMatch,Comet"/>
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255 <output name="searchgui_results" ftype="searchgui_archive">
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256 <assert_contents>
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257 <has_size value="159330" delta="20000"/>
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258 </assert_contents>
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259 </output>
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260 </test>
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261
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262 <!--
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263 NOTE: Identification_Parameters_specific.par is equivalent to the default .par plus these parameters:
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264 <param name="precursor_ion_tol" value="100"/>
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265 <param name="min_charge" value="1"/>
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266 <param name="max_charge" value="3"/>
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267 <param name="xtandem|xtandem_advanced" value="yes"/>
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268 <param name="xtandem|xtandem_advanced|xtandem_refine_selector" value="yes"/>
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269 -->
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270
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271 <!-- Test that specifying MsAmanda as search engine with non-default parameters works -->
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272 <test>
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273 <param name="peak_lists_files" value="searchgui_smallspectra.mgf"/>
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274 <param name="input_parameters_file" value="Identification_Parameters_specific.par"/>
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275 <param name="input_fasta_file" value="fastacli_searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta" />
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276 <param name="engines" value="MS_Amanda"/>
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277 <output name="searchgui_results" ftype="searchgui_archive">
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278 <assert_contents>
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279 <has_size value="635158" delta="5000"/>
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280 </assert_contents>
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281 </output>
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282 </test>
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283
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284 <!-- Test that specifying non-default search engines with default parameters works using modifications -->
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285 <test>
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286 <param name="peak_lists_files" value="searchgui_tinyspectra1.mgf"/>
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287 <param name="input_parameters_file" value="Identification_Parameters_default_modifications.par"/>
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288 <param name="input_fasta_file" value="fastacli_searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta" />
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289 <param name="engines" value="X!Tandem,MSGF,MyriMatch,Comet"/>
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290 <output name="searchgui_results" file="searchgui_tiny_result_default_4engines_modifications.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" />
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291 </test>
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292
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293 <!--
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294 NOTE: Identification_Parameters_default_modifications.par adds:
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295 - "Carbamidomethylation of C" as fixed modification
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296 - "Oxidation of M" as variable modification
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297 -->
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298
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299 <!-- Test that search works with MSAmanda with default default parameters - with modifications -->
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300 <test>
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301 <param name="peak_lists_files" value="searchgui_tinyspectra1.mgf"/>
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302 <param name="input_parameters_file" value="Identification_Parameters_default_modifications.par"/>
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303 <param name="input_fasta_file" value="fastacli_searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta" />
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304 <param name="engines" value="MS_Amanda"/>
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305 <output name="searchgui_results" ftype="searchgui_archive">
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306 <assert_contents>
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307 <has_size value="118136" delta="30000"/>
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308 </assert_contents>
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309 </output>
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310 </test>
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311
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312 </tests>
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313 <help>
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314 **What it does**
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315
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316 Runs multiple search engines on any number of MGF peak lists using SearchGUI.
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317
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318 Default: X! Tandem and MS-GF+ are executed.
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319
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320 Optional: MyriMatch, MS-Amanda, OMSSA (it may not work into isolated environments like containers), Comet, Tide, DirecTag and Novor can be executed.
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321
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322 </help>
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323 <expand macro="citations" />
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324 </tool>