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comparison peptide_shaker.xml @ 3:7939608a991c draft

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author bgruening
date Fri, 02 May 2014 15:34:25 -0400
parents e873824c4198
children 020836ac3b8e
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2:e873824c4198 3:7939608a991c
1 <tool id="peptide_shaker" name="Peptide Shaker" version="0.1.0"> 1 <tool id="peptide_shaker" name="Peptide Shaker" version="0.1.0">
2 <!-- TODO: Set defaults for weights correctly --> 2 <description>
3 Peform protein identification combining X! Tandem and OMSSA (using SearchGUI) and PeptideShaker pipeline.
4 </description>
3 <requirements> 5 <requirements>
4 <requirement type="package" version="0.28.0">peptide_shaker</requirement> 6 <requirement type="package" version="0.28.0">peptide_shaker</requirement>
5 <requirement type="package" version="1.18.0">searchgui</requirement> 7 <requirement type="package" version="1.18.0">searchgui</requirement>
6 <!--<requirement type="package" version="2.2.29">blast+</requirement>--> 8 <requirement type="package" version="2.2.29">blast+</requirement>
7 </requirements> 9 </requirements>
8 <description> 10 <stdio>
9 Peform protein identification combining X! Tandem and OMSSA (using SearchGUI) and PeptideShaker pipeline. 11 <exit_code range="1:" level="fatal" description="Job Failed" />
10 </description> 12 </stdio>
11 <command> 13 <command>
12 #from datetime import datetime 14 #from datetime import datetime
13 #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s") 15 #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
14 #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s") 16 #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
15 mkdir spectra;
16 mkdir output; 17 mkdir output;
17 mkdir output_reports; 18 mkdir output_reports;
18 cwd=`pwd`; 19 cwd=`pwd`;
19 #for $mgf in $peak_lists: 20 #for $mgf in $peak_lists:
20 #set $input_name = $mgf.display_name.replace(".mgf", "") + ".mgf" 21 #set $input_name = $mgf.display_name.replace(".mgf", "") + ".mgf"
21 ln -s '${mgf}' 'spectra/${input_name}'; 22 ln -s '${mgf}' '${input_name}';
22 #end for 23 #end for
23 ln -s ${input_database} input_database.fasta; 24 #ln -s "${input_database}" input_database.fasta;
25 cp "${input_database}" input_database.fasta;
24 26
25 ########################################### 27 ###########################################
26 #### Creating decoy database #### 28 #### Creating decoy database ####
27 ########################################### 29 ###########################################
28 #if $create_decoy: 30 #if $create_decoy:
29 echo "Creating decoy database."; 31 echo "Creating decoy database.";
30 java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.FastaCLI -in input_database.fasta -decoy; 32 java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.FastaCLI -in input_database.fasta -decoy;
31 ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta; 33 rm input_database.fasta;
34 cp input_database_concatenated_target_decoy.fasta input_database.fasta;
35 #ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta;
32 #end if 36 #end if
33 37
34 ##################################################### 38 #####################################################
35 ## generate IdentificationParameters for SearchGUI ## 39 ## generate IdentificationParameters for SearchGUI ##
36 ##################################################### 40 #####################################################
39 -out SEARCHGUI_IdentificationParameters.parameters 43 -out SEARCHGUI_IdentificationParameters.parameters
40 -prec_ppm "${precursor_ion_tol_units}" 44 -prec_ppm "${precursor_ion_tol_units}"
41 -prec_tol "${precursor_ion_tol}" 45 -prec_tol "${precursor_ion_tol}"
42 -frag_tol "${fragment_tol}" 46 -frag_tol "${fragment_tol}"
43 -enzyme "${enzyme}" 47 -enzyme "${enzyme}"
44 #set $fixed_mods_str = ${fixed_modifications} or '' 48 #set $fixed_mods_str = $fixed_modifications or ''
45 #set $variable_mods_str = ${variable_modifications} or '' 49 #set $variable_mods_str = $variable_modifications or ''
46 #if $fixed_mods_str 50 #if $fixed_mods_str
47 -fixed_mods "${fixed_mods_str}" 51 -fixed_mods "${fixed_mods_str}"
48 #end if 52 #end if
49 #if $variable_mods_str 53 #if $variable_mods_str
50 -variable_mods "${variable_mods_str}" 54 -variable_mods "${variable_mods_str}"
80 ################ 84 ################
81 ## Search CLI ## 85 ## Search CLI ##
82 ################ 86 ################
83 java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.SearchCLI 87 java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.SearchCLI
84 -temp_folder `pwd` 88 -temp_folder `pwd`
85 -spectrum_files \$cwd/spectra 89 -spectrum_files \$cwd
86 -output_folder \$cwd/output 90 -output_folder \$cwd/output
87 -id_params SEARCHGUI_IdentificationParameters.parameters 91 -id_params SEARCHGUI_IdentificationParameters.parameters
88 92
89 -threads "\${GALAXY_SLOTS:-12}" 93 -threads "\${GALAXY_SLOTS:-12}"
90 -correct_titles $correct_titles 94 -correct_titles "${correct_titles}"
91 -mgf_splitting "${mgf_splitting}" 95 -mgf_splitting "${mgf_splitting}"
92 -mgf_spectrum_count "${mgf_spectrum_count}" 96 -mgf_spectrum_count "${mgf_spectrum_count}"
93 97
94 #if $advanced.advanced_type_selector == "advanced": 98 #if $advanced.advanced_type_selector == "advanced":
95 99
99 -xtandem 0 103 -xtandem 0
100 #end if 104 #end if
101 105
102 #if $advanced.omssa.omssa_selector == "yes" 106 #if $advanced.omssa.omssa_selector == "yes"
103 -omssa 1 107 -omssa 1
108 -makeblastdb_folder \$BLAST_ROOT_DIR
104 #else 109 #else
105 -omssa 0 110 -omssa 0
106 #end if 111 #end if
107 112
108 #if $advanced.msgf.msgf_selector == "yes" 113 #if $advanced.msgf.msgf_selector == "yes"
123 ######################################################### 128 #########################################################
124 ## generate IdentificationParameters for PeptideShaker ## 129 ## generate IdentificationParameters for PeptideShaker ##
125 ######################################################### 130 #########################################################
126 java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.IdentificationParametersCLI 131 java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.IdentificationParametersCLI
127 -out PEPTIDESHAKER_IdentificationParameters.parameters 132 -out PEPTIDESHAKER_IdentificationParameters.parameters
128 -prec_ppm $precursor_ion_tol_units 133 -prec_ppm "${precursor_ion_tol_units}"
129 -prec_tol $precursor_ion_tol 134 -prec_tol "${precursor_ion_tol}"
130 -frag_tol $fragment_tol 135 -frag_tol "${fragment_tol}"
131 -enzyme '$enzyme' 136 -enzyme "${enzyme}"
132 #set $fixed_mods_str = $fixed_modifications or '' 137 #set $fixed_mods_str = $fixed_modifications or ''
133 #set $variable_mods_str = $variable_modifications or '' 138 #set $variable_mods_str = $variable_modifications or ''
134 #if $fixed_mods_str 139 #if $fixed_mods_str
135 -fixed_mods "$fixed_mods_str" 140 -fixed_mods "$fixed_mods_str"
136 #end if 141 #end if
151 java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.PeptideShakerCLI 156 java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.PeptideShakerCLI
152 -temp_folder `pwd` 157 -temp_folder `pwd`
153 -experiment '${exp_str}' 158 -experiment '${exp_str}'
154 -sample '${samp_str}' 159 -sample '${samp_str}'
155 -replicate 1 160 -replicate 1
156 -spectrum_files \$cwd/spectra 161 -spectrum_files \$cwd
157 -identification_files \$cwd/output 162 -identification_files \$cwd/output
158 -out \$cwd/peptide_shaker_output.cps 163 -out \$cwd/peptide_shaker_output.cps
159 -id_params PEPTIDESHAKER_IdentificationParameters.parameters 164 -id_params PEPTIDESHAKER_IdentificationParameters.parameters
160 165
161 ##Optional gene annotation parameter 166 ##Optional gene annotation parameter
162 #if "${species_type.species_type_selector}" != 'no_species_type': 167 #if $species_type.species_type_selector != 'no_species_type':
163 -species_type "${species_type.species_type_selector}" 168 -species_type "${species_type.species_type_selector}"
164 -species "{$species_type.species}" 169 -species "${species_type.species}"
165 #end if 170 #end if
166 171
167 ##Optional processing parameters: 172 ##Optional processing parameters:
168 #if $processing_options.processing_options_selector == "yes" 173 #if $processing_options.processing_options_selector == "yes"
169 -protein_FDR "${processing_options.protein_fdr}" 174 -protein_FDR "${processing_options.protein_fdr}"
177 #end if 182 #end if
178 #end if 183 #end if
179 -protein_fraction_mw_confidence "${processing_options.protein_fraction_mw_confidence}" 184 -protein_fraction_mw_confidence "${processing_options.protein_fraction_mw_confidence}"
180 #end if 185 #end if
181 186
182
183 ##Optional filtering parameters: 187 ##Optional filtering parameters:
184 #if $filtering_options.filtering_options_selector == "yes": 188 #if $filtering_options.filtering_options_selector == "yes":
185 -min_peptide_length "${filtering_options.min_peptide_length}" 189 -min_peptide_length "${filtering_options.min_peptide_length}"
186 -max_peptide_length "${filtering_options.max_peptide_length}" 190 -max_peptide_length "${filtering_options.max_peptide_length}"
187 -max_precursor_error "${filtering_options.max_precursor_error}" 191 -max_precursor_error "${filtering_options.max_precursor_error}"
189 -max_xtandem_e "${filtering_options.max_xtandem_e}" 193 -max_xtandem_e "${filtering_options.max_xtandem_e}"
190 -max_omssa_e "${filtering_options.max_omssa_e}" 194 -max_omssa_e "${filtering_options.max_omssa_e}"
191 -max_mascot_e "${filtering_options.max_mascot_e}" 195 -max_mascot_e "${filtering_options.max_mascot_e}"
192 -exclude_unknown_ptms "${filtering_options.exclude_unknown_ptms}" 196 -exclude_unknown_ptms "${filtering_options.exclude_unknown_ptms}"
193 #end if 197 #end if
194
195 ; 198 ;
196 199
197 ################################## 200 ##################################
198 ## PeptideShaker Report options ## 201 ## PeptideShaker Report options ##
199 ################################## 202 ##################################
200 java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.ReportCLI 203 java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.ReportCLI
201 -temp_folder `pwd` 204 -temp_folder `pwd`
202 -in \$cwd/peptide_shaker_output.cps 205 -in \$cwd/peptide_shaker_output.cps
203 -out_reports \$cwd/output_reports 206 -out_reports \$cwd/output_reports
204 207 -reports str($outputs).split(',').remove('cps')
205 ; 208 ;
206 209
207 ##mv output_reports/*peptides.txt peptides.txt ; 210 #if '0' in str($outputs).split(','):
208 ##mv output_reports/*psms.txt psms.txt ; 211 find . -name '\$cwd/output_reports/*Certificate*' -exec bash -c 'mv "$0" "certificate.txt"' {} \;
209 ##mv output_reports/*proteins.txt proteins.txt 212 #end if
213 #if '1' in str($outputs).split(','):
214 find . -name '\$cwd/output_reports/*PSM*' -exec bash -c 'mv "$0" "psm.txt"' {} \;
215 #end if
216 #if '2' in str($outputs).split(','):
217 find . -name '\$cwd/output_reports/*Peptide*' -exec bash -c 'mv "$0" "peptides.txt"' {} \;
218 #end if
219 #if '3' in str($outputs).split(','):
220 find . -name '\$cwd/output_reports/*Protein*' -exec bash -c 'mv "$0" "proteins.txt"' {} \;
221 #end if
222 #if '4' in str($outputs).split(','):
223 find . -name '\$cwd/output_reports/*Top*' -exec bash -c 'mv "$0" ".txt"' {} \;
224 #end if
210 </command> 225 </command>
211 <stdio>
212 <exit_code range="1:" level="fatal" description="Job Failed" />
213 </stdio>
214 <inputs> 226 <inputs>
215 <param format="fasta" name="input_database" type="data" label="Protein Database" 227 <param format="fasta" name="input_database" type="data" label="Protein Database"
216 help="Select FASTA database from history. Typically, a target-decoy database is incorporated into the Scaffold engine for FDR analysis"/> 228 help="Select FASTA database from history. Typically, a target-decoy database is incorporated into the Scaffold engine for FDR analysis"/>
217 229
218 <param name="create_decoy" label="Create a concatenated target/decoy database before running PeptideShaker." type="boolean" truevalue="True" falsevalue="False" checked="true" /> 230 <param name="create_decoy" label="Create a concatenated target/decoy database before running PeptideShaker." type="boolean" truevalue="True" falsevalue="False" checked="true" />
620 <param name="max_omssa_e" label="Maximum OMSSA e-value" value="100" type="float" help="" /> 632 <param name="max_omssa_e" label="Maximum OMSSA e-value" value="100" type="float" help="" />
621 <param name="max_mascot_e" label="Maximum Mascot e-value filter" value="100" type="float" help="(-max_mascot_e)" /> 633 <param name="max_mascot_e" label="Maximum Mascot e-value filter" value="100" type="float" help="(-max_mascot_e)" />
622 <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" type="boolean" truevalue="1" falsevalue="0" checked="true" /> 634 <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" type="boolean" truevalue="1" falsevalue="0" checked="true" />
623 </when> 635 </when>
624 </conditional> 636 </conditional>
637
638 <param name="outputs" type="select" display="checkboxes" multiple="True" label="Output options">
639 <option value="2" selected="True">Peptide Report</option>
640 <option value="3" selected="True">Protein Report</option>
641 <option value="1">PSM Report</option>
642 <option value="0">Certificate of Analysis</option>
643 <option value="4">Top Down Report</option>
644 <option value="cps">CPS file</option>
645 <validator type="no_options" message="Please select at least one output file." />
646 </param>
625 </inputs> 647 </inputs>
626 <outputs> 648 <outputs>
627 <data format="cps" name="output" from_work_dir="peptide_shaker_output.cps" label="PeptideShaker CPS results for ${on_string}" /> 649 <data format="cps" name="output" from_work_dir="peptide_shaker_output.cps" label="${tool.name} on ${on_string}: CPS file">
628 <data format="tabular" name="output_peptides" from_work_dir="peptides.txt" label="PeptideShaker Peptide Report for ${on_string}" /> 650 <filter>'cps' in outputs</filter>
629 <data format="tabular" name="output_proteins" from_work_dir="proteins.txt" label="PeptideShaker Protein Report for ${on_string}" /> 651 </data>
630 <data format="tabular" name="output_psms" from_work_dir="psms.txt" label="PeptideShaker PSM Report for ${on_string}" /> 652 <data format="text" name="output_certificate" from_work_dir="certificate.txt" label="${tool.name} on ${on_string}: Parameters">
653 <filter>'0' in outputs</filter>
654 </data>
655 <data format="text" name="output_psm" from_work_dir="psm.txt" label="${tool.name} on ${on_string}: PSM Report">
656 <filter>'1' in outputs</filter>
657 </data>
658 <data format="tabular" name="output_peptides" from_work_dir="peptides.txt" label="${tool.name} on ${on_string}: Peptide Report">
659 <filter>'2' in outputs</filter>
660 </data>
661 <data format="tabular" name="output_proteins" from_work_dir="proteins.txt" label="${tool.name} on ${on_string}: Protein Report">
662 <filter>'3' in outputs</filter>
663 </data>
664 <data format="tabular" name="output_top_down" from_work_dir="top_down.txt" label="${tool.name} on ${on_string}: Top Down Report">
665 <filter>'4' in outputs</filter>
666 </data>
631 </outputs> 667 </outputs>
632 <help> 668 <help>
633 **What it does** 669 **What it does**
634 670
635 Runs multiple search engines (X! Tandem and OMSSA) on any number of MGF peak lists using the SearchGUI application and combines the results. 671 Runs multiple search engines (X! Tandem and OMSSA) on any number of MGF peak lists using the SearchGUI application and combines the results.