Mercurial > repos > galaxyp > peptideshaker

comparison peptide_shaker.xml @ 49:58a3e6cb2598 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6e846f7195a9e939047ac975c6523e8cf99da6b4
author galaxyp
date Fri, 12 Oct 2018 08:56:06 -0400
parents baeced706dbc
children 5814883aa217
comparison
equal deleted inserted replaced
48:64e3a8cc8ffb 49:58a3e6cb2598
1 <tool id="peptide_shaker" name="Peptide Shaker" version="1.16.26"> 1 <tool id="peptide_shaker" name="Peptide Shaker" version="@PEPTIDESHAKER_VERSION@">
2 <description> 2 <description>
3 Perform protein identification using various search engines based on results from SearchGUI 3 Perform protein identification using various search engines based on results from SearchGUI
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 </macros> 7 </macros>
8 <requirements> 8 <requirements>
9 <requirement type="package" version="1.16.26">peptide-shaker</requirement> 9 <requirement type="package" version="@PEPTIDESHAKER_VERSION@">peptide-shaker</requirement>
10 </requirements> 10 </requirements>
11 <expand macro="stdio" /> 11 <expand macro="stdio" />
12 <command> 12
13 <![CDATA[ 13 <command><![CDATA[
14 ## When supporting more advanced Galaxy versions: command use_shared_home="false"
14 #from datetime import datetime 15 #from datetime import datetime
15 #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s") 16 #set $exp_str = "Galaxy_Experiment_%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") 17 #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
17 #set $temp_stderr = "peptideshaker_stderr" 18 #set $temp_stderr = "peptideshaker_stderr"
18 #set $bin_dir = "bin" 19 #set $bin_dir = "bin"
19 20
20 21
21 mkdir output_reports; 22 mkdir output_reports &&
22 cwd=`pwd`; 23 cwd=`pwd` &&
24 export HOME=\$cwd &&
25
26 echo "" > $temp_stderr &&
23 27
24 ln -s '$searchgui_input' searchgui_input.zip && 28 ln -s '$searchgui_input' searchgui_input.zip &&
25 jar xvf searchgui_input.zip SEARCHGUI_IdentificationParameters.par && 29 jar xvf searchgui_input.zip SEARCHGUI_IdentificationParameters.par &&
30
31
32 peptide-shaker eu.isas.peptideshaker.cmd.PathSettingsCLI
33 --exec_dir="\$cwd/${bin_dir}"
34 -temp_folder \$cwd/PathSettingsCLI
35 -log \$cwd/peptideshaker.log &&
36
37 #if str($exporting_options.output_reports) != "None"
38 #set $output_reports_list = set(str($exporting_options.output_reports).split(','))
39 #else
40 #set $output_reports_list = set()
41 #end if
42
26 ###################### 43 ######################
27 ## PeptideShakerCLI ## 44 ## PeptideShakerCLI ##
28 ###################### 45 ######################
29 (peptide-shaker eu.isas.peptideshaker.cmd.PeptideShakerCLI 46 (peptide-shaker -Djava.awt.headless=true eu.isas.peptideshaker.cmd.PeptideShakerCLI
30 --exec_dir="\$cwd/${bin_dir}" 47 --exec_dir="\$cwd/${bin_dir}"
48 -gui 0
31 -temp_folder \$cwd/PeptideShakerCLI 49 -temp_folder \$cwd/PeptideShakerCLI
32 -experiment '$exp_str' 50 -experiment '$exp_str'
33 -sample '$samp_str' 51 -sample '$samp_str'
34 -replicate 1 52 -replicate 1
35 -identification_files \$cwd/searchgui_input.zip 53 -identification_files \$cwd/searchgui_input.zip
36 -id_params \$cwd/SEARCHGUI_IdentificationParameters.par 54 -id_params \$cwd/SEARCHGUI_IdentificationParameters.par
37 -out \$cwd/peptideshaker_output.cpsx 55 -out \$cwd/peptideshaker_output.cpsx
56 #if $exporting_options.zip_conditional.zip_output_boolean == 'zip':
38 -zip \$cwd/peptideshaker_output.zip 57 -zip \$cwd/peptideshaker_output.zip
39 #set $cleaned_list = str($outputs).split(',') 58 #end if
40 #if 'cps' in $cleaned_list:
41 #silent $cleaned_list.remove('cps')
42 #end if
43 #if 'mzidentML' in $cleaned_list:
44 #silent $cleaned_list.remove('mzidentML')
45 #end if
46 #if 'zip' in $cleaned_list:
47 #silent $cleaned_list.remove('zip')
48 #end if
49 #if len($cleaned_list) > 0
50 ## Only numbers are left over. These corresponds to different reports.
51 -reports #echo ','.join($cleaned_list)#
52 #end if
53
54 -threads "\${GALAXY_SLOTS:-12}" 59 -threads "\${GALAXY_SLOTS:-12}"
55 60
56 ##Optional processing parameters: 61 ##Optional processing parameters:
57 #if $processing_options.processing_options_selector == "yes" 62 #if $processing_options.processing_options_selector == "yes"
58 -protein_fdr "${processing_options.protein_fdr}" 63 -protein_fdr "${processing_options.protein_fdr}"
59 -peptide_fdr "${processing_options.peptide_fdr}" 64 -peptide_fdr "${processing_options.peptide_fdr}"
60 -psm_fdr "${processing_options.psm_fdr}" 65 -psm_fdr "${processing_options.psm_fdr}"
61 -ptm_score "${processing_options.ptm_score.ptm_score_selector}" 66 -ptm_score "${processing_options.ptm_score.ptm_score_selector}"
62 #if $processing_options.ptm_score.ptm_score_selector == 1 67 #if $processing_options.ptm_score.ptm_score_selector == 1
63 -score_neutral_losses "${processing_options.ptm_score.neutral_losses}" 68 -score_neutral_losses "${processing_options.ptm_score.neutral_losses}"
64 #if str($processing_options.ptm_score.ptm_threshold) != '' 69 #if str($processing_options.ptm_score.ptm_threshold) != ''
65 -ptm_threshold "${processing_options.ptm_score.ptm_threshold}" 70 -ptm_threshold "${processing_options.ptm_score.ptm_threshold}"
66 #end if
67 #end if 71 #end if
68 -ptm_alignment "${processing_options.ptm_alignment}" 72 #end if
69 -ptm_sequence_matching_type "${processing_options.ptm_sequence_matching_type}" 73 -ptm_alignment "${processing_options.ptm_alignment}"
70 -protein_fraction_mw_confidence "${processing_options.protein_fraction_mw_confidence}" 74 -ptm_sequence_matching_type "${processing_options.ptm_sequence_matching_type}"
71 #end if 75 -protein_fraction_mw_confidence "${processing_options.protein_fraction_mw_confidence}"
72 76 #end if
73 ##Optional filtering parameters: 77
74 #if $filtering_options.filtering_options_selector == "yes": 78 ##Optional filtering parameters:
75 -import_peptide_length_min "${filtering_options.min_peptide_length}" 79 #if $filtering_options.filtering_options_selector == "yes":
76 -import_peptide_length_max "${filtering_options.max_peptide_length}" 80 -import_peptide_length_min "${filtering_options.min_peptide_length}"
77 -import_precurosor_mz "${filtering_options.max_precursor_error}" 81 -import_peptide_length_max "${filtering_options.max_peptide_length}"
78 -import_precurosor_mz_ppm "${filtering_options.max_precursor_error_type}" 82 -import_precurosor_mz "${filtering_options.max_precursor_error}"
79 ##-max_xtandem_e "${filtering_options.max_xtandem_e}" 83 -import_precurosor_mz_ppm "${filtering_options.max_precursor_error_type}"
80 ##-max_omssa_e "${filtering_options.max_omssa_e}" 84 ##-max_xtandem_e "${filtering_options.max_xtandem_e}"
81 ##-max_mascot_e "${filtering_options.max_mascot_e}" 85 ##-max_omssa_e "${filtering_options.max_omssa_e}"
82 -exclude_unknown_ptms "${filtering_options.exclude_unknown_ptms}" 86 ##-max_mascot_e "${filtering_options.max_mascot_e}"
83 #end if 87 -exclude_unknown_ptms "${filtering_options.exclude_unknown_ptms}"
84 88 #end if
85 2>> $temp_stderr) 89
86 90 ##################################
87 && 91 ## mzidCLI options ##
88 92 ##################################
89 echo "Running Reports"; 93
94 #if $exporting_options.mzidentml_conditional.mzidentml_creation == 1:
95 -output_file \$cwd/output.mzid
96 -include_sequences ${exporting_options.mzidentml_conditional.include_sequences}
97 #if $contact_options.contact_options_selector == "yes":
98 -contact_first_name "$contact_options.contact_first_name"
99 -contact_last_name "$contact_options.contact_last_name"
100 -contact_email "$contact_options.contact_email"
101 -contact_address "$contact_options.contact_address"
102 #if str($contact_options.contact_url).strip() != '':
103 -contact_url = "$contact_options.contact_url"
104 #end if
105 -organization_name "$contact_options.organization_name"
106 -organization_email "$contact_options.organization_email"
107 -organization_address "$contact_options.organization_address"
108 #if str($contact_options.organization_url).strip() != '':
109 -organization_url = "$contact_options.organization_url"
110 #end if
111 #else:
112 -contact_first_name "Proteomics"
113 -contact_last_name "Galaxy"
114 -contact_email "galaxyp@umn.edu"
115 -contact_address "galaxyp@umn.edu"
116 -organization_name "University of Minnesota"
117 -organization_email "galaxyp@umn.edu"
118 -organization_address "Minneapolis, MN 55455, Vereinigte Staaten"
119 #end if
120 #end if
90 121
91 ################################## 122 ##################################
92 ## PeptideShaker Report options ## 123 ## PeptideShaker Report options ##
93 ################################## 124 ##################################
94 125 ## Generate Reports if the user has selected one of the 11 additional reports
95 #if 'mzidentML' in str($outputs).split(','): 126 #if len($output_reports_list) > 0
96 echo "Generating mzIdentML"; 127 -out_reports \$cwd/output_reports
97 (peptide-shaker eu.isas.peptideshaker.cmd.MzidCLI 128 -reports #echo ','.join($output_reports_list)#
98 --exec_dir="\$cwd/${bin_dir}"
99 -in \$cwd/peptideshaker_output.zip
100 -output_file \$cwd/output.mzid
101 #if $contact_options.contact_options_selector == "yes":
102 -contact_first_name "$contact_options.contact_first_name"
103 -contact_last_name "$contact_options.contact_last_name"
104 -contact_email "$contact_options.contact_email"
105 -contact_address "$contact_options.contact_address"
106 #if str($contact_options.contact_url).strip() != '':
107 -contact_url = "$contact_options.contact_url"
108 #end if
109 -organization_name "$contact_options.organization_name"
110 -organization_email "$contact_options.organization_email"
111 -organization_address "$contact_options.organization_address"
112 #if str($contact_options.organization_url).strip() != '':
113 -organization_url = "$contact_options.organization_url"
114 #end if
115 #else:
116 -contact_first_name "Proteomics"
117 -contact_last_name "Galaxy"
118 -contact_email "galaxyp@umn.edu"
119 -contact_address "galaxyp@umn.edu"
120 -organization_name "University of Minnesota"
121 -organization_email "galaxyp@umn.edu"
122 -organization_address "Minneapolis, MN 55455, Vereinigte Staaten"
123 #end if
124 2>> $temp_stderr)
125 &&
126 #end if 129 #end if
127 130
128 ## Generate Reports if the user has selected one of the 8 additional reports 131 2>> $temp_stderr)
129 ## 'cps', 'mzidentML' and 'zip' are not valid options for PeptideShaker 132
130 ## and will not be passed to the command line 133 #if len(output_reports_list)>0:
131 #if set(["0","1","2","3","4","5","6","7"]).intersection( set( str( $outputs ).split(',') ) ): 134 #if '0' in $output_reports_list:
132 135 && find \$cwd/output_reports -name '*Certificate_of_Analysis.txt' -exec bash -c 'mv "$0" "certificate.txt"' {} \;
133 (peptide-shaker eu.isas.peptideshaker.cmd.ReportCLI 136 #end if
134 --exec_dir="\$cwd/${bin_dir}" 137 #if '1' in $output_reports_list:
135 -temp_folder \$cwd/ReportCLI 138 && find \$cwd/output_reports -name '*Default_Hierarchical_Report.txt' -exec bash -c 'mv "$0" "hierarchical.txt"' {} \;
136 -in \$cwd/peptideshaker_output.zip 139 #end if
137 -out_reports \$cwd/output_reports 140 #if '2' in $output_reports_list:
138 #set $cleaned_list = str($outputs).split(',') 141 && find \$cwd/output_reports -name '*Default_PSM_Phosphorylation_Report.txt' -exec bash -c 'mv "$0" "psm_phospho.txt"' {} \;
139 #if 'cps' in $cleaned_list: 142 #end if`
140 #silent $cleaned_list.remove('cps') 143 #if '3' in $output_reports_list:
141 #end if 144 && find \$cwd/output_reports -name '*Default_PSM_Report.txt' -exec bash -c 'mv "$0" "psm.txt"' {} \;
142 #if 'mzidentML' in $cleaned_list: 145 #end if
143 #silent $cleaned_list.remove('mzidentML') 146 #if '4' in $output_reports_list:
144 #end if 147 && find \$cwd/output_reports -name '*Default_PSM_Report_with_non-validated_matches.txt' -exec bash -c 'mv "$0" "psm_nonvalidated.txt"' {} \;
145 #if 'zip' in $cleaned_list: 148 #end if
146 #silent $cleaned_list.remove('zip') 149 #if '5' in $output_reports_list:
147 #end if 150 && find \$cwd/output_reports -name '*Default_Peptide_Phosphorylation_Report.txt' -exec bash -c 'mv "$0" "peptides_phospho.txt"' {} \;
148 ## Only numbers are left over. These corresponds to different reports. 151 #end if
149 -reports #echo ','.join($cleaned_list)# 152 #if '6' in $output_reports_list:
150 153 && find \$cwd/output_reports -name '*Default_Peptide_Report.txt' -exec bash -c 'mv "$0" "peptides.txt"' {} \;
151 2>> $temp_stderr) 154 #end if
152 && 155 #if '7' in $output_reports_list:
156 && find \$cwd/output_reports -name '*Default_Peptide_Report_with_non-validated_matches.txt' -exec bash -c 'mv "$0" "peptides_nonvalidated.txt"' {} \;
157 #end if
158 #if '8' in $output_reports_list:
159 && find \$cwd/output_reports -name '*Default_Protein_Phosphorylation_Report.txt' -exec bash -c 'mv "$0" "proteins_phospho.txt"' {} \;
160 #end if
161 #if '9' in $output_reports_list:
162 && find \$cwd/output_reports -name '*Default_Protein_Report.txt' -exec bash -c 'mv "$0" "proteins.txt"' {} \;
163 #end if
164 #if '10' in $output_reports_list:
165 && find \$cwd/output_reports -name '*Default_Protein_Report_with_non-validated_matches.txt' -exec bash -c 'mv "$0" "proteins_nonvalidated.txt"' {} \;
166 #end if
167 #if '11' in $output_reports_list:
168 && find \$cwd/output_reports -name '*Extended_PSM_Report.txt' -exec bash -c 'mv "$0" "psmx.txt"' {} \;
169 #end if
153 #end if 170 #end if
154 171
155 ## # ls -l \$cwd/output_reports/* ; 172 && cat $temp_stderr 2>&1;
156
157 #if '0' in str($outputs).split(','):
158 find \$cwd/output_reports -name '*Certificate_of_Analysis*' -exec bash -c 'mv "$0" "certificate.txt"' {} \;
159 ;
160 #end if
161 #if '1' in str($outputs).split(','):
162 find \$cwd/output_reports -name '*Hierarchical*' -exec bash -c 'mv "$0" "hierarchical.txt"' {} \;
163 ;
164 #end if
165 #if '2' in str($outputs).split(','):
166 find \$cwd/output_reports -name '*PSM_Phosphorylation_Report*' -exec bash -c 'mv "$0" "psm_phospho.txt"' {} \;
167 ;
168 #end if
169 #if '8' in str($outputs).split(','):
170 find \$cwd/output_reports -name '*Extended_PSM_Report*' -exec bash -c 'mv "$0" "psmx.txt"' {} \;
171 ;
172 #end if
173 #if '3' in str($outputs).split(','):
174 find \$cwd/output_reports -name '*PSM_Report*' -exec bash -c 'mv "$0" "psm.txt"' {} \;
175 ;
176 #end if
177 #if '4' in str($outputs).split(','):
178 find \$cwd/output_reports -name '*Peptide_Phosphorylation_Report*' -exec bash -c 'mv "$0" "peptides_phospho.txt"' {} \;
179 ;
180 #end if
181 #if '5' in str($outputs).split(','):
182 find \$cwd/output_reports -name '*Peptide_Report*' -exec bash -c 'mv "$0" "peptides.txt"' {} \;
183 ;
184 #end if
185 #if '6' in str($outputs).split(','):
186 find \$cwd/output_reports -name '*Protein_Phosphorylation_Report*' -exec bash -c 'mv "$0" "proteins_phospho.txt"' {} \;
187 ;
188 #end if
189 #if '7' in str($outputs).split(','):
190 find \$cwd/output_reports -name '*Protein_Report*' -exec bash -c 'mv "$0" "proteins.txt"' {} \;
191 ;
192 #end if
193
194 exit_code_for_galaxy=\$?;
195 cat $temp_stderr 2>&1;
196 (exit \$exit_code_for_galaxy)
197
198 ]]> 173 ]]>
199 </command> 174 </command>
200 <inputs> 175 <inputs>
201 <param name="searchgui_input" format="searchgui_archive" type="data" label="Compressed SearchGUI results" 176 <param name="searchgui_input" format="searchgui_archive" type="data" label="Compressed SearchGUI results"
202 help="SearchGUI Results from History"> 177 help="SearchGUI Results from History">
295 <param name="organization_url" type="text" value="" optional="true" label="Organization URL."> 270 <param name="organization_url" type="text" value="" optional="true" label="Organization URL.">
296 </param> 271 </param>
297 </when> 272 </when>
298 </conditional> 273 </conditional>
299 274
300 <param name="include_sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Include the protein sequences in mzIdentML" /> 275 <section name="exporting_options" expanded="true" title="Exporting options">
301 <param name="outputs" type="select" display="checkboxes" multiple="True" label="Output options"> 276
302 <option value="zip">Zip File for import to Desktop App</option> 277 <conditional name="mzidentml_conditional">
303 <option value="mzidentML" selected="True">mzidentML File</option> 278 <param name="mzidentml_creation" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Creates a mzIdentML file" />
304 <option value="3">PSM Report</option> 279 <when value="1">
305 <option value="8">Extended PSM Report</option> 280 <param name="include_sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Include the protein sequences in the mzIdentML file" />
306 <option value="2">PSM Phosphorylation Report</option> 281 </when>
307 <option value="5">Peptide Report</option> 282 <when value="0" />
308 <option value="4">Peptide Phosphorylation Report</option> 283 </conditional>
309 <option value="7">Protein Report</option> 284
310 <option value="6">Protein Phosphorylation Report</option> 285 <conditional name="zip_conditional">
311 <option value="0">Certificate of Analysis</option> 286 <param name="zip_output_boolean" type="boolean" truevalue="zip" falsevalue="separate" checked="false" label="Compress results into a single zip file" />
312 <option value="1">Hierarchical Report</option> 287 <when value="separate">
313 <option value="cps">CPS file</option> 288 <param name="export_cps" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Exports the CPS file" />
314 <validator type="no_options" message="Please select at least one output file" /> 289 </when>
315 </param> 290 <when value="zip" />
291 </conditional>
292
293 <param name="output_reports" type="select" display="checkboxes" multiple="True" optional="true" label="Reports to be generated">
294 <option value="3">PSM Report</option>
295 <option value="4">PSM Report with non-validated matches</option>
296 <option value="2">PSM Phosphorylation Report</option>
297 <option value="11">Extended PSM Report</option>
298 <option value="6">Peptide Report</option>
299 <option value="7">Peptide Report with non-validated matches</option>
300 <option value="5">Peptide Phosphorylation Report</option>
301 <option value="9">Protein Report</option>
302 <option value="10">Protein Report with non-validated matches</option>
303 <option value="8">Protein Phosphorylation Report</option>
304 <option value="0">Certificate of Analysis</option>
305 <option value="1">Hierarchical Report</option>
306 </param>
307
308 </section>
316 309
317 </inputs> 310 </inputs>
318 <outputs> 311 <outputs>
319 <data format="mzid" name="mzidentML" from_work_dir="output.mzid" label="${tool.name} on ${on_string}: mzidentML file"> 312 <data format="mzid" name="mzidentML" from_work_dir="output.mzid" label="${tool.name} on ${on_string}: mzidentML file">
320 <filter>'mzidentML' in outputs</filter> 313 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and mzidentml_conditional['mzidentml_creation'] is True</filter>
321 </data> 314 </data>
322 <data format="peptideshaker_archive" name="output_cps" from_work_dir="peptideshaker_output.cpsx" label="${tool.name} on ${on_string}: CPS file"> 315 <data format="peptideshaker_archive" name="output_cps" from_work_dir="peptideshaker_output.cpsx" label="${tool.name} on ${on_string}: CPS file">
323 <filter>'cps' in outputs</filter> 316 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and exporting_options['zip_conditional']['export_cps'] is True</filter>
324 </data> 317 </data>
325 <data format="zip" name="output_zip" from_work_dir="peptideshaker_output.zip" label="${tool.name} on ${on_string}: Archive"> 318 <data format="zip" name="output_zip" from_work_dir="peptideshaker_output.zip" label="${tool.name} on ${on_string}: Archive">
326 <filter>'zip' in outputs</filter> 319 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is True</filter>
327 </data> 320 </data>
328 <data format="txt" name="output_certificate" from_work_dir="certificate.txt" label="${tool.name} on ${on_string}: Parameters"> 321 <!--
329 <filter>'0' in outputs</filter> 322 <data format="tabular" name="reports">
323 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tabular" directory="output_reports" visible="true" assign_primary_output="true" />
324 </data>
325 -->
326 <data format="txt" name="output_certificate" from_work_dir="certificate.txt" label="${tool.name} on ${on_string}: Parameters">
327 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '0' in exporting_options['output_reports']</filter>
330 </data> 328 </data>
331 <data format="tabular" name="output_hierarchical" from_work_dir="hierarchical.txt" label="${tool.name} on ${on_string}: Hierarchical Report"> 329 <data format="tabular" name="output_hierarchical" from_work_dir="hierarchical.txt" label="${tool.name} on ${on_string}: Hierarchical Report">
332 <filter>'1' in outputs</filter> 330 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '1' in exporting_options['output_reports']</filter>
333 </data> 331 </data>
334 <data format="tabular" name="output_psm_phosphorylation" from_work_dir="psm_phospho.txt" label="${tool.name} on ${on_string}: PSM Phosphorylation Report"> 332 <data format="tabular" name="output_psm_phosphorylation" from_work_dir="psm_phospho.txt" label="${tool.name} on ${on_string}: PSM Phosphorylation Report">
335 <filter>'2' in outputs</filter> 333 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '2' in exporting_options['output_reports']</filter>
336 </data> 334 </data>
337 <data format="tabular" name="output_psm" from_work_dir="psm.txt" label="${tool.name} on ${on_string}: PSM Report"> 335 <data format="tabular" name="output_psm" from_work_dir="psm.txt" label="${tool.name} on ${on_string}: PSM Report">
338 <filter>'3' in outputs</filter> 336 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '3' in exporting_options['output_reports']</filter>
337 </data>
338 <data format="tabular" name="output_psm_nonvalidated" from_work_dir="psm_nonvalidated.txt" label="${tool.name} on ${on_string}: PSM Report with non-validated matches">
339 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '4' in exporting_options['output_reports']</filter>
339 </data> 340 </data>
340 <data format="tabular" name="output_extended_psm" from_work_dir="psmx.txt" label="${tool.name} on ${on_string}: Extended PSM Report"> 341 <data format="tabular" name="output_extended_psm" from_work_dir="psmx.txt" label="${tool.name} on ${on_string}: Extended PSM Report">
341 <filter>'8' in outputs</filter> 342 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '11' in exporting_options['output_reports']</filter>
342 </data> 343 </data>
343 <data format="tabular" name="output_peptides_phosphorylation" from_work_dir="peptides_phospho.txt" label="${tool.name} on ${on_string}: Peptide Phosphorylation Report"> 344 <data format="tabular" name="output_peptides_phosphorylation" from_work_dir="peptides_phospho.txt" label="${tool.name} on ${on_string}: Peptide Phosphorylation Report">
344 <filter>'4' in outputs</filter> 345 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '5' in exporting_options['output_reports']</filter>
345 </data> 346 </data>
346 <data format="tabular" name="output_peptides" from_work_dir="peptides.txt" label="${tool.name} on ${on_string}: Peptide Report"> 347 <data format="tabular" name="output_peptides" from_work_dir="peptides.txt" label="${tool.name} on ${on_string}: Peptide Report">
347 <filter>'5' in outputs</filter> 348 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '6' in exporting_options['output_reports']</filter>
349 </data>
350 <data format="tabular" name="output_peptides_nonvalidated" from_work_dir="peptides_nonvalidated.txt" label="${tool.name} on ${on_string}: Peptide Report with non-validated matches">
351 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '7' in exporting_options['output_reports']</filter>
348 </data> 352 </data>
349 <data format="tabular" name="output_proteins_phosphorylation" from_work_dir="proteins_phospho.txt" label="${tool.name} on ${on_string}: Protein Phosphorylation Report"> 353 <data format="tabular" name="output_proteins_phosphorylation" from_work_dir="proteins_phospho.txt" label="${tool.name} on ${on_string}: Protein Phosphorylation Report">
350 <filter>'6' in outputs</filter> 354 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '8' in exporting_options['output_reports']</filter>
351 </data> 355 </data>
352 <data format="tabular" name="output_proteins" from_work_dir="proteins.txt" label="${tool.name} on ${on_string}: Protein Report"> 356 <data format="tabular" name="output_proteins" from_work_dir="proteins.txt" label="${tool.name} on ${on_string}: Protein Report">
353 <filter>'7' in outputs</filter> 357 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '9' in exporting_options['output_reports']</filter>
358 </data>
359 <data format="tabular" name="output_proteins_nonvalidated" from_work_dir="proteins_nonvalidated.txt" label="${tool.name} on ${on_string}: Protein Repor with non-validated matches">
360 <filter>exporting_options['zip_conditional']['zip_output_boolean'] is False and str(exporting_options['output_reports']) != 'None' and '10' in exporting_options['output_reports']</filter>
354 </data> 361 </data>
355 </outputs> 362 </outputs>
356 <tests> 363 <tests>
357 <test> 364 <test>
358 <param name="searchgui_input" value="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive"/> 365 <param name="searchgui_input" value="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive"/>
359 <param name="processing_options_selector" value="no"/> 366 <param name="processing_options_selector" value="no"/>
360 <param name="filtering_options_selector" value="no"/> 367 <param name="filtering_options_selector" value="no"/>
361 <param name="outputs" value="zip,3"/> 368 <param name="mzidentml_creation" value="0"/>
369 <param name="zip_output_boolean" value="zip"/>
370 <param name="export_cps" value="1"/>
362 <output name="output_zip" file="peptide_shaker_modifications_result1.zip" ftype="zip" compare="sim_size" delta="3000" /> 371 <output name="output_zip" file="peptide_shaker_modifications_result1.zip" ftype="zip" compare="sim_size" delta="3000" />
363 <output name="output_psm">
364 <assert_contents>
365 <has_text text="cds.comp41779_c0_seq1" />
366 </assert_contents>
367 </output>
368 </test> 372 </test>
369 <test> 373 <test>
370 <param name="searchgui_input" value="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive"/> 374 <param name="searchgui_input" value="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive"/>
371 <param name="processing_options_selector" value="no"/> 375 <param name="processing_options_selector" value="no"/>
372 <param name="filtering_options_selector" value="yes"/> 376 <param name="filtering_options_selector" value="yes"/>
373 <param name="min_peptide_length" value="1"/> 377 <param name="min_peptide_length" value="1"/>
374 <param name="outputs" value="0,1,2,3,4,5,6,7"/> 378 <param name="mzidentml_creation" value="0"/>
375 <output name="output_certificate"> 379 <param name="zip_output_boolean" value="separate"/>
376 <assert_contents> 380 <param name="output_reports" value="0,1,2,3,4,5,6,7,8,9,10,11"/>
377 <has_text text="Tolerance: 100" /> 381 <output name="output_certificate" file="peptide_shaker_modifications_result1.output_certificate" ftype="txt" lines_diff="6"/>
378 <has_text text="Carbamidomethylation of C" /> 382 <output name="output_hierarchical" file="peptide_shaker_modifications_result1.output_hierarchical" ftype="tabular"/>
379 </assert_contents> 383 <output name="output_extended_psm" file="peptide_shaker_modifications_result1.output_extended_psm" ftype="tabular"/>
380 </output> 384 <output name="output_psm" file="peptide_shaker_modifications_result1.output_psm" ftype="tabular"/>
381 <output name="output_hierarchical"> 385 <output name="output_psm_phosphorylation" file="peptide_shaker_modifications_result1.output_psm_phosphorylation" ftype="tabular"/>
382 <assert_contents> 386 <output name="output_psm_nonvalidated" file="peptide_shaker_modifications_result1.output_psm_nonvalidated" ftype="tabular"/>
383 <has_text_matching expression="1.1\tcds.comp" /> 387 <output name="output_peptides" file="peptide_shaker_modifications_result1.output_peptides" ftype="tabular"/>
384 </assert_contents> 388 <output name="output_peptides_phosphorylation" file="peptide_shaker_modifications_result1.output_peptides_phosphorylation" ftype="tabular"/>
385 </output> 389 <output name="output_peptides_nonvalidated" file="peptide_shaker_modifications_result1.output_peptides_nonvalidated" ftype="tabular"/>
386 <output name="output_psm"> 390 <output name="output_proteins" file="peptide_shaker_modifications_result1.output_proteins" ftype="tabular"/>
387 <assert_contents> 391 <output name="output_proteins_phosphorylation" file="peptide_shaker_modifications_result1.output_proteins_phosphorylation" ftype="tabular"/>
388 <not_has_text text="Phosphosite" /> 392 <output name="output_proteins_nonvalidated" file="peptide_shaker_modifications_result1.output_proteins_nonvalidated" ftype="tabular"/>
389 <has_text text="cds.comp41779_c0_seq1" />
390 </assert_contents>
391 </output>
392 <output name="output_psm_phosphorylation">
393 <assert_contents>
394 <has_text text="Phosphosite" />
395 <has_text text="cds.comp41779_c0_seq1" />
396 </assert_contents>
397 </output>
398 <output name="output_peptides">
399 <assert_contents>
400 <has_text text="Modification" />
401 <has_text text="cds.comp41779_c0_seq1" />
402 </assert_contents>
403 </output>
404 <output name="output_peptides_phosphorylation">
405 <assert_contents>
406 <has_text text="Phosphosite" />
407 <has_text text="cds.comp41779_c0_seq1" />
408 </assert_contents>
409 </output>
410 <output name="output_proteins">
411 <assert_contents>
412 <has_text text="Modification" />
413 <has_text text="cds.comp41779_c0_seq1" />
414 </assert_contents>
415 </output>
416 <output name="output_proteins_phosphorylation">
417 <assert_contents>
418 <has_text text="Phosphosite" />
419 <has_text text="cds.comp41779_c0_seq1" />
420 </assert_contents>
421 </output>
422 </test> 393 </test>
423 <test> 394 <test>
424 <param name="searchgui_input" value="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive"/> 395 <param name="searchgui_input" value="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive"/>
425 <param name="processing_options_selector" value="no"/> 396 <param name="processing_options_selector" value="no"/>
426 <param name="filtering_options_selector" value="no"/> 397 <param name="filtering_options_selector" value="no"/>
427 <param name="outputs" value="3,cps"/> 398 <param name="mzidentml_creation" value="0"/>
399 <param name="zip_output_boolean" value="separate"/>
400 <param name="export_cps" value="1"/>
401 <param name="output_reports" value="3"/>
428 <output name="output_cps" file="peptide_shaker_modifications_result1.cpsx" ftype="peptideshaker_archive" compare="sim_size" delta="3000"/> 402 <output name="output_cps" file="peptide_shaker_modifications_result1.cpsx" ftype="peptideshaker_archive" compare="sim_size" delta="3000"/>
429 <output name="output_psm"> 403 <output name="output_psm" file="peptide_shaker_modifications_result1.output_psm" ftype="tabular"/>
430 <assert_contents>
431 <has_text text="cds.comp41779_c0_seq1" />
432 </assert_contents>
433 </output>
434 </test> 404 </test>
435 </tests> 405 </tests>
436 <help> 406 <help>
437 **What it does** 407 **What it does**
438 408
439 Runs multiple search engines (X! Tandem, OMSSA and MS-GF+) on any number of MGF peak lists using the SearchGUI application and combines the results. 409 PeptideShaker is a search engine for interpretation of proteomics identification results from multiple search engines, currently supporting X!Tandem, MS-GF+, MS Amanda, OMSSA, MyriMatch, Comet, Tide, Mascot, Andromeda and mzIdentML.
440 410
441 http://compomics.github.io/projects/peptide-shaker.html 411 http://compomics.github.io/projects/peptide-shaker.html
442 http://compomics.github.io/projects/searchgui.html
443 412
444 ---- 413 ----
445 414
446 Reports 415 Reports
447 ======= 416 =======