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comparison peptide_shaker.xml @ 30:ad60446b1e93 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit bdb5ee12705a3494eee96d1963f16f68bbe41d5c
author galaxyp
date Fri, 13 Jan 2017 14:15:42 -0500
parents 78fad25eff17
children ff592231f118
comparison
equal deleted inserted replaced
29:78fad25eff17 30:ad60446b1e93
1 <tool id="peptide_shaker" name="Peptide Shaker" version="1.11.0"> 1 <tool id="peptide_shaker" name="Peptide Shaker" version="1.13.6">
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="1.11">peptide_shaker</requirement> 9 <requirement type="package" version="1.13.6">peptide-shaker</requirement>
10 </requirements> 10 </requirements>
11 <expand macro="stdio" /> 11 <expand macro="stdio" />
12 <command> 12 <command>
13 <![CDATA[ 13 <![CDATA[
14 #from datetime import datetime 14 #from datetime import datetime
15 #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")
16 #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")
17 #set $temp_stderr = "peptideshaker_stderr" 17 #set $temp_stderr = "peptideshaker_stderr"
18 #set $bin_dir = "bin"
18 19
19 20
20 mkdir output_reports; 21 mkdir output_reports;
21 cwd=`pwd`; 22 cwd=`pwd`;
22 23
23 cp -r "\${PEPTIDESHAKER_JAR_PATH%/*}" bin;
24 tmp_peptideshaker_jar_path=`echo "\$cwd/bin/\${PEPTIDESHAKER_JAR_PATH\#\#/*/}"`;
25
26 ln -s '$searchgui_input' searchgui_input.zip && 24 ln -s '$searchgui_input' searchgui_input.zip &&
25 jar xvf searchgui_input.zip SEARCHGUI_IdentificationParameters.par &&
27 ###################### 26 ######################
28 ## PeptideShakerCLI ## 27 ## PeptideShakerCLI ##
29 ###################### 28 ######################
30 (java -cp \$tmp_peptideshaker_jar_path eu.isas.peptideshaker.cmd.PeptideShakerCLI 29 (peptide-shaker eu.isas.peptideshaker.cmd.PeptideShakerCLI
30 --exec_dir="\$cwd/${bin_dir}"
31 -temp_folder \$cwd/PeptideShakerCLI 31 -temp_folder \$cwd/PeptideShakerCLI
32 -experiment '$exp_str' 32 -experiment '$exp_str'
33 -sample '$samp_str' 33 -sample '$samp_str'
34 -replicate 1 34 -replicate 1
35 -identification_files \$cwd/searchgui_input.zip 35 -identification_files \$cwd/searchgui_input.zip
36 -id_params \$cwd/SEARCHGUI_IdentificationParameters.par
36 -out \$cwd/peptideshaker_output.cpsx 37 -out \$cwd/peptideshaker_output.cpsx
37 -zip \$cwd/peptideshaker_output.zip 38 -zip \$cwd/peptideshaker_output.zip
38 39
39 -threads "\${GALAXY_SLOTS:-12}" 40 -threads "\${GALAXY_SLOTS:-12}"
40
41 ##Optional gene annotation parameter
42 #if $species_type.species_type_selector != 'no_species_type':
43 -species_type "${species_type.species_type_selector}"
44 -species "${species_type.species}"
45 -species_update 1
46 #end if
47 41
48 ##Optional processing parameters: 42 ##Optional processing parameters:
49 #if $processing_options.processing_options_selector == "yes" 43 #if $processing_options.processing_options_selector == "yes"
50 -protein_fdr "${processing_options.protein_fdr}" 44 -protein_fdr "${processing_options.protein_fdr}"
51 -peptide_fdr "${processing_options.peptide_fdr}" 45 -peptide_fdr "${processing_options.peptide_fdr}"
83 ## PeptideShaker Report options ## 77 ## PeptideShaker Report options ##
84 ################################## 78 ##################################
85 79
86 #if 'mzidentML' in str($outputs).split(','): 80 #if 'mzidentML' in str($outputs).split(','):
87 echo "Generating mzIdentML"; 81 echo "Generating mzIdentML";
88 (java -cp \$tmp_peptideshaker_jar_path eu.isas.peptideshaker.cmd.MzidCLI 82 (peptide-shaker eu.isas.peptideshaker.cmd.MzidCLI
83 --exec_dir="\$cwd/${bin_dir}"
89 -in \$cwd/peptideshaker_output.zip 84 -in \$cwd/peptideshaker_output.zip
90 -output_file output.mzid 85 -output_file output.mzid
91 -contact_first_name "Proteomics" 86 #if $contact_options.contact_options_selector == "yes":
92 -contact_last_name "Galaxy" 87 -contact_first_name "$contact_options.contact_first_name"
93 -contact_email "galaxyp@umn.edu" 88 -contact_last_name "$contact_options.contact_last_name"
94 -contact_address "galaxyp@umn.edu" 89 -contact_email "$contact_options.contact_email"
95 -organization_name "University of Minnesota" 90 -contact_address "$contact_options.contact_address"
96 -organization_email "galaxyp@umn.edu" 91 #if str($contact_options.contact_url).strip() != '':
97 -organization_address "Minneapolis, MN 55455, Vereinigte Staaten" 92 -contact_url = "$contact_options.contact_url"
93 #end if
94 -organization_name "$contact_options.organization_name"
95 -organization_email "$contact_options.organization_email"
96 -organization_address "$contact_options.organization_address"
97 #if str($contact_options.organization_url).strip() != '':
98 -organization_url = "$contact_options.organization_url"
99 #end if
100 #else:
101 -contact_first_name "Proteomics"
102 -contact_last_name "Galaxy"
103 -contact_email "galaxyp@umn.edu"
104 -contact_address "galaxyp@umn.edu"
105 -organization_name "University of Minnesota"
106 -organization_email "galaxyp@umn.edu"
107 -organization_address "Minneapolis, MN 55455, Vereinigte Staaten"
108 #end if
98 2>> $temp_stderr) 109 2>> $temp_stderr)
99 && 110 &&
100 #end if 111 #end if
101 112
102 ## Generate Reports if the user has selected one of the 8 additional reports 113 ## Generate Reports if the user has selected one of the 8 additional reports
103 ## 'cps', 'mzidentML' and 'zip' are not valid options for PeptideShaker 114 ## 'cps', 'mzidentML' and 'zip' are not valid options for PeptideShaker
104 ## and will not be passed to the command line 115 ## and will not be passed to the command line
105 #if set(["0","1","2","3","4","5","6","7"]).intersection( set( str( $outputs ).split(',') ) ): 116 #if set(["0","1","2","3","4","5","6","7"]).intersection( set( str( $outputs ).split(',') ) ):
106 117
107 (java -cp \$tmp_peptideshaker_jar_path eu.isas.peptideshaker.cmd.ReportCLI 118 (peptide-shaker eu.isas.peptideshaker.cmd.ReportCLI
119 --exec_dir="\$cwd/${bin_dir}"
108 -temp_folder \$cwd/ReportCLI 120 -temp_folder \$cwd/ReportCLI
109 -in \$cwd/peptideshaker_output.zip 121 -in \$cwd/peptideshaker_output.zip
110 -out_reports \$cwd/output_reports 122 -out_reports \$cwd/output_reports
111 #set $cleaned_list = str($outputs).split(',') 123 #set $cleaned_list = str($outputs).split(',')
112 #if 'cps' in $cleaned_list: 124 #if 'cps' in $cleaned_list:
123 135
124 2>> $temp_stderr) 136 2>> $temp_stderr)
125 && 137 &&
126 #end if 138 #end if
127 139
140 ## # ls -l \$cwd/output_reports/* ;
128 141
129 #if '0' in str($outputs).split(','): 142 #if '0' in str($outputs).split(','):
130 find \$cwd/output_reports -name '*Certificate_of_Analysis*' -exec bash -c 'mv "$0" "certificate.txt"' {} \; 143 find \$cwd/output_reports -name '*Certificate_of_Analysis*' -exec bash -c 'mv "$0" "certificate.txt"' {} \;
131 ; 144 ;
132 #end if 145 #end if
134 find \$cwd/output_reports -name '*Hierarchical*' -exec bash -c 'mv "$0" "hierarchical.txt"' {} \; 147 find \$cwd/output_reports -name '*Hierarchical*' -exec bash -c 'mv "$0" "hierarchical.txt"' {} \;
135 ; 148 ;
136 #end if 149 #end if
137 #if '2' in str($outputs).split(','): 150 #if '2' in str($outputs).split(','):
138 find \$cwd/output_reports -name '*PSM_Phosphorylation_Report*' -exec bash -c 'mv "$0" "psm_phospho.txt"' {} \; 151 find \$cwd/output_reports -name '*PSM_Phosphorylation_Report*' -exec bash -c 'mv "$0" "psm_phospho.txt"' {} \;
152 ;
153 #end if
154 #if '8' in str($outputs).split(','):
155 find \$cwd/output_reports -name '*Extended_PSM_Report*' -exec bash -c 'mv "$0" "psmx.txt"' {} \;
139 ; 156 ;
140 #end if 157 #end if
141 #if '3' in str($outputs).split(','): 158 #if '3' in str($outputs).split(','):
142 find \$cwd/output_reports -name '*PSM_Report*' -exec bash -c 'mv "$0" "psm.txt"' {} \; 159 find \$cwd/output_reports -name '*PSM_Report*' -exec bash -c 'mv "$0" "psm.txt"' {} \;
143 ; 160 ;
170 help="SearchGUI Results from History"> 187 help="SearchGUI Results from History">
171 <options options_filter_attribute="metadata.searchgui_major_version" > 188 <options options_filter_attribute="metadata.searchgui_major_version" >
172 <filter type="add_value" value="@SEARCHGUI_MAJOR_VERSION@" /> 189 <filter type="add_value" value="@SEARCHGUI_MAJOR_VERSION@" />
173 </options> 190 </options>
174 </param> 191 </param>
175
176 <conditional name="species_type">
177 <param name="species_type_selector" type="select" optional="true" label="The species type to use for the gene annotation"
178 help="(Optional) If your species is supported under one of the groups, selecting it will allow GO annotations and other information to be included in the results">
179 <option value="Fungi">Fungi</option>
180 <option value="Plants">Plants</option>
181 <option value="Metazoa">Metazoa</option>
182 <option value="Vertebrates">Vertebrates</option>
183 <option value="Protists">Protists</option>
184 <option value="no_species_type" selected="true">No species restriction</option>
185 </param>
186 <when value="no_species_type"/>
187 <when value="Protists">
188 <param name="species" type="select" label="The species to use for the gene annotation"
189 help="">
190 <option value="Albugo laibachii">Albugo laibachii</option>
191 <option value="Bigelowiella natans">Bigelowiella natans</option>
192 <option value="Dictyostelium discoideum">Dictyostelium discoideum</option>
193 <option value="Emiliania huxleyi">Emiliania huxleyi</option>
194 <option value="Entamoeba histolytica">Entamoeba histolytica</option>
195 <option value="Giardia lamblia">Giardia lamblia</option>
196 <option value="Guillardia theta CCMP2712">Guillardia theta CCMP2712</option>
197 <option value="Hyaloperonospora arabidopsidis">Hyaloperonospora arabidopsidis</option>
198 <option value="Leishmania major">Leishmania major</option>
199 <option value="Paramecium tetraurelia">Paramecium tetraurelia</option>
200 <option value="Phaeodactylum tricornutum">Phaeodactylum tricornutum</option>
201 <option value="Phytophthora infestans">Phytophthora infestans</option>
202 <option value="Phytophthora kernoviae">Phytophthora kernoviae</option>
203 <option value="Phytophthora lateralis">Phytophthora lateralis</option>
204 <option value="Phytophthora parasitica">Phytophthora parasitica</option>
205 <option value="Phytophthora ramorum">Phytophthora ramorum</option>
206 <option value="Phytophthora sojae">Phytophthora sojae</option>
207 <option value="Plasmodium berghei">Plasmodium berghei</option>
208 <option value="Plasmodium chabaudi">Plasmodium chabaudi</option>
209 <option value="Plasmodium falciparum">Plasmodium falciparum</option>
210 <option value="Plasmodium knowlesi">Plasmodium knowlesi</option>
211 <option value="Plasmodium vivax">Plasmodium vivax</option>
212 <option value="Pythium aphanidermatum">Pythium aphanidermatum</option>
213 <option value="Pythium arrhenomanes">Pythium arrhenomanes</option>
214 <option value="Pythium irregulare">Pythium irregulare</option>
215 <option value="Pythium iwayamai">Pythium iwayamai</option>
216 <option value="Pythium ultimum">Pythium ultimum</option>
217 <option value="Pythium vexans">Pythium vexans</option>
218 <option value="Tetrahymena thermophila">Tetrahymena thermophila</option>
219 <option value="Thalassiosira pseudonana">Thalassiosira pseudonana</option>
220 <option value="Toxoplasma gondii">Toxoplasma gondii</option>
221 <option value="Trypanosoma brucei">Trypanosoma brucei</option>
222 </param>
223 </when>
224 <when value="Plants">
225 <param name="species" type="select" label="The species to use for the gene annotation"
226 help="">
227 <option value="Amborella (Amborella trichopoda)">Amborella (Amborella trichopoda)</option>
228 <option value="Arabidopsis lyrata (Lyrate rockcress)">Arabidopsis lyrata (Lyrate rockcress)</option>
229 <option value="Arabidopsis thaliana (Thale-cress)">Arabidopsis thaliana (Thale-cress)</option>
230 <option value="Brachypodium distachyon (False brome)">Brachypodium distachyon (False brome)</option>
231 <option value="Brassica oleracea">Brassica oleracea</option>
232 <option value="Brassica rapa genes (Field mustard)">Brassica rapa genes (Field mustard)</option>
233 <option value="Chlamydomonas reinhardtii (Green algae)">Chlamydomonas reinhardtii (Green algae)</option>
234 <option value="Cyanidioschyzon merolae (Red algae)">Cyanidioschyzon merolae (Red algae)</option>
235 <option value="Glycine max (Soybean)">Glycine max (Soybean)</option>
236 <option value="Hordeum vulgare (Barley)">Hordeum vulgare (Barley)</option>
237 <option value="Leersia perrieri (Leersia)">Leersia perrieri (Leersia)</option>
238 <option value="Medicago truncatula (Barrel medic)">Medicago truncatula (Barrel medic)</option>
239 <option value="Musa acuminata (Banana)">Musa acuminata (Banana)</option>
240 <option value="Oryza brachyantha">Oryza brachyantha</option>
241 <option value="Oryza glumaepatula">Oryza glumaepatula</option>
242 <option value="Oryza meridionalis">Oryza meridionalis</option>
243 <option value="Oryza nivara">Oryza nivara</option>
244 <option value="Oryza punctata">Oryza punctata</option>
245 <option value="Oryza rufipogon (Common wild rice)">Oryza rufipogon (Common wild rice)</option>
246 <option value="Oryza sativa (Indica rice)">Oryza sativa (Indica rice)</option>
247 <option value="Oryza sativa Indica Group">Oryza sativa Indica Group</option>
248 <option value="Oryza sativa Japonica (Japonica rice)">Oryza sativa Japonica (Japonica rice)</option>
249 <option value="Ostreococcus lucimarinus (Green algae)">Ostreococcus lucimarinus (Green algae)</option>
250 <option value="Physcomitrella patens">Physcomitrella patens</option>
251 <option value="Physcomitrella patens (Moss)">Physcomitrella patens (Moss)</option>
252 <option value="Populus trichocarpa">Populus trichocarpa</option>
253 <option value="Populus trichocarpa (Western balsam poplar)">Populus trichocarpa (Western balsam poplar)</option>
254 <option value="Prunus persica (Peach)">Prunus persica (Peach)</option>
255 <option value="Selaginella moellendorffii (Spike moss)">Selaginella moellendorffii (Spike moss)</option>
256 <option value="Setaria italica (Foxtail millet)">Setaria italica (Foxtail millet)</option>
257 <option value="Solanum lycopersicum (Tomato)">Solanum lycopersicum (Tomato)</option>
258 <option value="Solanum tuberosum (Potato)">Solanum tuberosum (Potato)</option>
259 <option value="Sorghum bicolor (Sorghum)">Sorghum bicolor (Sorghum)</option>
260 <option value="Theobroma cacao (Cocoa)">Theobroma cacao (Cocoa)</option>
261 <option value="Triticum aestivum (Bread wheat)">Triticum aestivum (Bread wheat)</option>
262 <option value="Triticum urartu (Einkorn)">Triticum urartu (Einkorn)</option>
263 <option value="Vitis vinifera (Wine grape)">Vitis vinifera (Wine grape)</option>
264 <option value="Zea mays (Maize)">Zea mays (Maize)</option>
265 </param>
266 </when>
267 <when value="Metazoa">
268 <param name="species" type="select" label="The species to use for the gene annotation"
269 help="">
270 <option value="Acyrthosiphon pisum">Acyrthosiphon pisum</option>
271 <option value="Aedes aegypti (Yellow fever mosquito)">Aedes aegypti (Yellow fever mosquito)</option>
272 <option value="Amphimedon queenslandica">Amphimedon queenslandica</option>
273 <option value="Anopheles darlingi">Anopheles darlingi</option>
274 <option value="Anopheles gambiae (African malaria mosquito) ">Anopheles gambiae (African malaria mosquito) </option>
275 <option value="Apis mellifera ">Apis mellifera </option>
276 <option value="Atta cephalotes ">Atta cephalotes </option>
277 <option value="Bombyx mori ">Bombyx mori </option>
278 <option value="Brugia malayi ">Brugia malayi </option>
279 <option value="Caenorhabditis brenneri ">Caenorhabditis brenneri </option>
280 <option value="Caenorhabditis briggsae ">Caenorhabditis briggsae </option>
281 <option value="Caenorhabditis elegans ">Caenorhabditis elegans </option>
282 <option value="Caenorhabditis japonica ">Caenorhabditis japonica </option>
283 <option value="Caenorhabditis remanei ">Caenorhabditis remanei </option>
284 <option value="Culex quinquefasciatus (Southern house mosquito) ">Culex quinquefasciatus (Southern house mosquito) </option>
285 <option value="Danaus plexippus ">Danaus plexippus </option>
286 <option value="Daphnia pulex ">Daphnia pulex </option>
287 <option value="Dendroctonus ponderosae">Dendroctonus ponderosae</option>
288 <option value="Drosophila ananassae ">Drosophila ananassae </option>
289 <option value="Drosophila erecta ">Drosophila erecta </option>
290 <option value="Drosophila grimshawi ">Drosophila grimshawi </option>
291 <option value="Drosophila melanogaster (Fruit fly) ">Drosophila melanogaster (Fruit fly) </option>
292 <option value="Drosophila mojavensis ">Drosophila mojavensis </option>
293 <option value="Drosophila persimilis ">Drosophila persimilis </option>
294 <option value="Drosophila pseudoobscura ">Drosophila pseudoobscura </option>
295 <option value="Drosophila sechellia ">Drosophila sechellia </option>
296 <option value="Drosophila simulans ">Drosophila simulans </option>
297 <option value="Drosophila virilis ">Drosophila virilis </option>
298 <option value="Drosophila willistoni ">Drosophila willistoni </option>
299 <option value="Drosophila yakuba ">Drosophila yakuba </option>
300 <option value="Heliconius melpomene ">Heliconius melpomene </option>
301 <option value="Helobdella robusta">Helobdella robusta</option>
302 <option value="Ixodes scapularis (Black-legged tick) ">Ixodes scapularis (Black-legged tick) </option>
303 <option value="Loa loa ">Loa loa </option>
304 <option value="Lottia gigantea">Lottia gigantea</option>
305 <option value="Megaselia scalaris ">Megaselia scalaris </option>
306 <option value="Melitaea cinxia">Melitaea cinxia</option>
307 <option value="Mnemiopsis leidyi">Mnemiopsis leidyi</option>
308 <option value="Nasonia vitripennis ">Nasonia vitripennis </option>
309 <option value="Nematostella vectensis ">Nematostella vectensis </option>
310 <option value="Onchocerca volvulus">Onchocerca volvulus</option>
311 <option value="Pediculus humanus (Human louse) ">Pediculus humanus (Human louse) </option>
312 <option value="Pristionchus pacificus ">Pristionchus pacificus </option>
313 <option value="Rhodnius prolixus">Rhodnius prolixus</option>
314 <option value="Schistosoma mansoni ">Schistosoma mansoni </option>
315 <option value="Solenopsis invicta (Red fire ant)">Solenopsis invicta (Red fire ant)</option>
316 <option value="Strigamia maritima ">Strigamia maritima </option>
317 <option value="Strongylocentrotus purpuratus ">Strongylocentrotus purpuratus </option>
318 <option value="Tetranychus urticae">Tetranychus urticae</option>
319 <option value="Tribolium castaneum (red flour beetle) ">Tribolium castaneum (red flour beetle) </option>
320 <option value="Trichinella spiralis ">Trichinella spiralis </option>
321 <option value="Trichoplax adhaerens ">Trichoplax adhaerens </option>
322 <option value="Zootermopsis nevadensis">Zootermopsis nevadensis</option>
323 </param>
324 </when>
325 <when value="Fungi">
326 <param name="species" type="select" label="The species to use for the gene annotation"
327 help="">
328 <option value="Ashbya gossypii">Ashbya gossypii</option>
329 <option value="Aspergillus clavatus">Aspergillus clavatus</option>
330 <option value="Aspergillus flavus">Aspergillus flavus</option>
331 <option value="Aspergillus fumigatus">Aspergillus fumigatus</option>
332 <option value="Aspergillus fumigatusa1163">Aspergillus fumigatusa1163</option>
333 <option value="Aspergillus nidulans">Aspergillus nidulans</option>
334 <option value="Aspergillus niger">Aspergillus niger</option>
335 <option value="Aspergillus oryzae">Aspergillus oryzae</option>
336 <option value="Aspergillus terreus">Aspergillus terreus</option>
337 <option value="Blumeria graminis">Blumeria graminis</option>
338 <option value="Botrytis cinerea">Botrytis cinerea</option>
339 <option value="Colletotrichum gloeosporioides">Colletotrichum gloeosporioides</option>
340 <option value="Colletotrichum higginsianum">Colletotrichum higginsianum</option>
341 <option value="Colletotrichum orbiculare">Colletotrichum orbiculare</option>
342 <option value="Cryptococcus neoformans">Cryptococcus neoformans</option>
343 <option value="Dothistroma septosporum">Dothistroma septosporum</option>
344 <option value="Fusarium fujikuroi">Fusarium fujikuroi</option>
345 <option value="Fusarium graminearum">Fusarium graminearum</option>
346 <option value="Fusarium oxysporum">Fusarium oxysporum</option>
347 <option value="Fusarium pseudograminearum">Fusarium pseudograminearum</option>
348 <option value="Fusarium solani">Fusarium solani</option>
349 <option value="Fusarium verticillioides">Fusarium verticillioides</option>
350 <option value="Gaeumannomyces graminis">Gaeumannomyces graminis</option>
351 <option value="Colletotrichum graminicola">Colletotrichum graminicola</option>
352 <option value="Komagataella pastoris">Komagataella pastoris</option>
353 <option value="Leptosphaeria maculans">Leptosphaeria maculans</option>
354 <option value="Magnaporthe oryzae">Magnaporthe oryzae</option>
355 <option value="Magnaporthe poae">Magnaporthe poae</option>
356 <option value="Melampsora larici-populina">Melampsora larici-populina</option>
357 <option value="Neosartorya fischeri">Neosartorya fischeri</option>
358 <option value="Neurospora crassa">Neurospora crassa</option>
359 <option value="Phaeosphaeria nodorum">Phaeosphaeria nodorum</option>
360 <option value="Puccinia graminis">Puccinia graminis</option>
361 <option value="Puccinia graminis Ug99">Puccinia graminis Ug99</option>
362 <option value="Puccinia triticina">Puccinia triticina</option>
363 <option value="Pyrenophora teres">Pyrenophora teres</option>
364 <option value="Pyrenophora tritici-repentis">Pyrenophora tritici-repentis</option>
365 <option value="Saccharomyces cerevisiae">Saccharomyces cerevisiae</option>
366 <option value="Schizosaccharomyces cryophilus">Schizosaccharomyces cryophilus</option>
367 <option value="Schizosaccharomyces japonicus">Schizosaccharomyces japonicus</option>
368 <option value="Schizosaccharomyces octosporus">Schizosaccharomyces octosporus</option>
369 <option value="Schizosaccharomyces pombe">Schizosaccharomyces pombe</option>
370 <option value="Sclerotinia sclerotiorum">Sclerotinia sclerotiorum</option>
371 <option value="Sporisorium reilianum">Sporisorium reilianum</option>
372 <option value="Trichoderma reesei">Trichoderma reesei</option>
373 <option value="Trichoderma virens">Trichoderma virens</option>
374 <option value="Tuber melanosporum">Tuber melanosporum</option>
375 <option value="Ustilago maydis">Ustilago maydis</option>
376 <option value="Verticillium dahliae JR2">Verticillium dahliae JR2</option>
377 <option value="Verticillium dahliae">Verticillium dahliae</option>
378 <option value="Yarrowia lipolytica">Yarrowia lipolytica</option>
379 <option value="Zymoseptoria tritici">Zymoseptoria tritici</option>
380 </param>
381 </when>
382 <when value="Vertebrates">
383 <param name="species" type="select" label="The species to use for the gene annotation"
384 help="">
385 <option value="Alpaca (Vicugna pacos)">Alpaca (Vicugna pacos)</option>
386 <option value="Amazon molly (Poecilia formosa)">Amazon molly (Poecilia formosa)</option>
387 <option value="Anole lizard (Anolis carolinensis)">Anole lizard (Anolis carolinensis)</option>
388 <option value="Armadillo (Dasypus novemcinctus)">Armadillo (Dasypus novemcinctus)</option>
389 <option value="Bushbaby (Otolemur garnettii)">Bushbaby (Otolemur garnettii)</option>
390 <option value="C. elegans (Caenorhabditis elegans)">C. elegans (Caenorhabditis elegans)</option>
391 <option value="C.intestinalis (Ciona intestinalis)">C.intestinalis (Ciona intestinalis)</option>
392 <option value="C.savignyi (Ciona savignyi)">C.savignyi (Ciona savignyi)</option>
393 <option value="Cat (Felis catus)">Cat (Felis catus)</option>
394 <option value="Cave fish (Astyanax mexicanus)">Cave fish (Astyanax mexicanus)</option>
395 <option value="Chicken (Gallus gallus)">Chicken (Gallus gallus)</option>
396 <option value="Chimpanzee (Pan troglodytes)">Chimpanzee (Pan troglodytes)</option>
397 <option value="Chinese softshell turtle (Pelodiscus sinensis)">Chinese softshell turtle (Pelodiscus sinensis)</option>
398 <option value="Cod (Gadus morhua)">Cod (Gadus morhua)</option>
399 <option value="Coelacanth (Latimeria chalumnae)">Coelacanth (Latimeria chalumnae)</option>
400 <option value="Cow (Bos taurus)">Cow (Bos taurus)</option>
401 <option value="Dog (Canis lupus familiaris)">Dog (Canis lupus familiaris)</option>
402 <option value="Dolphin (Tursiops truncatus)">Dolphin (Tursiops truncatus)</option>
403 <option value="Duck (Anas platyrhynchos)">Duck (Anas platyrhynchos)</option>
404 <option value="Elephant (Loxodonta africana)">Elephant (Loxodonta africana)</option>
405 <option value="Ferret (Mustela putorius furo)">Ferret (Mustela putorius furo)</option>
406 <option value="Flycatcher (Ficedula albicollis)">Flycatcher (Ficedula albicollis)</option>
407 <option value="Fruitfly (Drosophila melanogaster)">Fruitfly (Drosophila melanogaster)</option>
408 <option value="Fugu (Takifugu rubripes)">Fugu (Takifugu rubripes)</option>
409 <option value="Gibbon (Nomascus leucogenys)">Gibbon (Nomascus leucogenys)</option>
410 <option value="Gorilla (Gorilla gorilla gorilla)">Gorilla (Gorilla gorilla gorilla)</option>
411 <option value="Guinea Pig (Cavia porcellus)">Guinea Pig (Cavia porcellus)</option>
412 <option value="Hedgehog (Erinaceus europaeus)">Hedgehog (Erinaceus europaeus)</option>
413 <option value="Horse (Equus caballus)">Horse (Equus caballus)</option>
414 <option value="Human (Homo sapiens)">Human (Homo sapiens)</option>
415 <option value="Hyrax (Procavia capensis)">Hyrax (Procavia capensis)</option>
416 <option value="Kangaroo rat (Dipodomys ordii)">Kangaroo rat (Dipodomys ordii)</option>
417 <option value="Lamprey (Petromyzon marinus)">Lamprey (Petromyzon marinus)</option>
418 <option value="Lesser hedgehog tenrec (Echinops telfairi)">Lesser hedgehog tenrec (Echinops telfairi)</option>
419 <option value="Macaque (Macaca mulatta)">Macaque (Macaca mulatta)</option>
420 <option value="Marmoset (Callithrix jacchus)">Marmoset (Callithrix jacchus)</option>
421 <option value="Medaka (Oryzias latipes)">Medaka (Oryzias latipes)</option>
422 <option value="Megabat (Pteropus vampyrus)">Megabat (Pteropus vampyrus)</option>
423 <option value="Microbat (Myotis lucifugus)">Microbat (Myotis lucifugus)</option>
424 <option value="Mouse (Mus musculus)">Mouse (Mus musculus)</option>
425 <option value="Mouse Lemur (Microcebus murinus)">Mouse Lemur (Microcebus murinus)</option>
426 <option value="Opossum (Monodelphis domestica)">Opossum (Monodelphis domestica)</option>
427 <option value="Orangutan (Pongo abelii)">Orangutan (Pongo abelii)</option>
428 <option value="Panda (Ailuropoda melanoleuca)">Panda (Ailuropoda melanoleuca)</option>
429 <option value="Pig (Sus scrofa)">Pig (Sus scrofa)</option>
430 <option value="Pika (Ochotona princeps)">Pika (Ochotona princeps)</option>
431 <option value="Platyfish (Xiphophorus maculatus)">Platyfish (Xiphophorus maculatus)</option>
432 <option value="Platypus (Ornithorhynchus anatinus)">Platypus (Ornithorhynchus anatinus)</option>
433 <option value="Rabbit (Oryctolagus cuniculus)">Rabbit (Oryctolagus cuniculus)</option>
434 <option value="Rat (Rattus norvegicus)">Rat (Rattus norvegicus)</option>
435 <option value="S. cerevisiae (Saccharomyces cerevisiae)">S. cerevisiae (Saccharomyces cerevisiae)</option>
436 <option value="Sheep (Ovis aries)">Sheep (Ovis aries)</option>
437 <option value="Shrew (Sorex araneus)">Shrew (Sorex araneus)</option>
438 <option value="Sloth (Choloepus hoffmanni)">Sloth (Choloepus hoffmanni)</option>
439 <option value="Spotted gar (Lepisosteus oculatus)">Spotted gar (Lepisosteus oculatus)</option>
440 <option value="Squirrel (Ictidomys tridecemlineatus)">Squirrel (Ictidomys tridecemlineatus)</option>
441 <option value="Stickleback (Gasterosteus aculeatus)">Stickleback (Gasterosteus aculeatus)</option>
442 <option value="Tarsier (Tarsius syrichta)">Tarsier (Tarsius syrichta)</option>
443 <option value="Tasmanian devil (Sarcophilus harrisii)">Tasmanian devil (Sarcophilus harrisii)</option>
444 <option value="Tetraodon (Tetraodon nigroviridis)">Tetraodon (Tetraodon nigroviridis)</option>
445 <option value="Tilapia (Oreochromis niloticus)">Tilapia (Oreochromis niloticus)</option>
446 <option value="Tree Shrew (Tupaia belangeri)">Tree Shrew (Tupaia belangeri)</option>
447 <option value="Turkey (Meleagris gallopavo)">Turkey (Meleagris gallopavo)</option>
448 <option value="Vervet-AGM (Chlorocebus sabaeus)">Vervet-AGM (Chlorocebus sabaeus)</option>
449 <option value="Wallaby (Macropus eugenii)">Wallaby (Macropus eugenii)</option>
450 <option value="Xenopus (Xenopus tropicalis)">Xenopus (Xenopus tropicalis)</option>
451 <option value="Zebra Finch (Taeniopygia guttata)">Zebra Finch (Taeniopygia guttata)</option>
452 <option value="Zebrafish (Danio rerio)">Zebrafish (Danio rerio)</option>
453 </param>
454 </when>
455 </conditional>
456 <conditional name="processing_options"> 192 <conditional name="processing_options">
457 <param name="processing_options_selector" type="select" label="Specify Advanced PeptideShaker Processing Options"> 193 <param name="processing_options_selector" type="select" label="Specify Advanced PeptideShaker Processing Options">
458 <option value="no" selected="True">Default Processing Options</option> 194 <option value="no" selected="True">Default Processing Options</option>
459 <option value="yes">Advanced Processing Options</option> 195 <option value="yes">Advanced Processing Options</option>
460 </param> 196 </param>
501 <!--param name="max_omssa_e" label="Maximum OMSSA e-value" value="100" type="float" help="" /--> 237 <!--param name="max_omssa_e" label="Maximum OMSSA e-value" value="100" type="float" help="" /-->
502 <!--param name="max_mascot_e" label="Maximum Mascot e-value filter" value="100" type="float" help="" /--> 238 <!--param name="max_mascot_e" label="Maximum Mascot e-value filter" value="100" type="float" help="" /-->
503 <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" type="boolean" truevalue="1" falsevalue="0" checked="true" /> 239 <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" type="boolean" truevalue="1" falsevalue="0" checked="true" />
504 </when> 240 </when>
505 </conditional> 241 </conditional>
242 <conditional name="contact_options">
243 <param name="contact_options_selector" type="select" label="Specify Contact Information for mzIdendML"
244 help="Create a Galaxy workflow to save these values">
245 <option value="no" selected="True">GalaxyP Project contact (Not suitable for PRIDE submission)</option>
246 <option value="yes">Specify Contact Information</option>
247 </param>
248 <when value="no" />
249 <when value="yes">
250 <param name="contact_first_name" type="text" value="" label="Contact first name.">
251 <validator type="regex" message="">\S+.*</validator>
252 </param>
253 <param name="contact_last_name" type="text" value="" label="Contact last name.">
254 <validator type="regex" message="">\S+.*</validator>
255 </param>
256 <param name="contact_email" type="text" value="" label="Contact e-mail.">
257 <validator type="regex" message="">\S+@\S+</validator>
258 </param>
259 <param name="contact_address" type="text" value="" label="Contact address.">
260 <validator type="regex" message="">\S+.*</validator>
261 </param>
262 <param name="contact_url" type="text" value="" optional="true" label="Contact URL.">
263 </param>
264 <param name="organization_name" type="text" value="" label="Organization name.">
265 <validator type="regex" message="">\S+.*</validator>
266 </param>
267 <param name="organization_email" type="text" value="" label="Organization e-mail.">
268 <validator type="regex" message="">\S+@\S+</validator>
269 </param>
270 <param name="organization_address" type="text" value="" label="Organization address.">
271 <validator type="regex" message="">\S+.*</validator>
272 </param>
273 <param name="organization_url" type="text" value="" optional="true" label="Organization URL.">
274 </param>
275 </when>
276 </conditional>
277
278 <param name="include_sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Include the protein sequences in mzIdentML" />
506 <param name="outputs" type="select" display="checkboxes" multiple="True" label="Output options"> 279 <param name="outputs" type="select" display="checkboxes" multiple="True" label="Output options">
507 <option value="zip">Zip File for import to Desktop App</option> 280 <option value="zip">Zip File for import to Desktop App</option>
508 <option value="mzidentML" selected="True">mzidentML File</option> 281 <option value="mzidentML" selected="True">mzidentML File</option>
509 <option value="3" >PSM Report</option> 282 <option value="3">PSM Report</option>
510 <option value="4" >Peptide Phosphorylation Report</option> 283 <option value="8">Extended PSM Report</option>
511 <option value="5" >Peptide Report</option>
512 <option value="6" >Protein Phosphorylation Report</option>
513 <option value="7" >Protein Report</option>
514 <option value="2">PSM Phosphorylation Report</option> 284 <option value="2">PSM Phosphorylation Report</option>
285 <option value="5">Peptide Report</option>
286 <option value="4">Peptide Phosphorylation Report</option>
287 <option value="7">Protein Report</option>
288 <option value="6">Protein Phosphorylation Report</option>
515 <option value="0">Certificate of Analysis</option> 289 <option value="0">Certificate of Analysis</option>
516 <option value="1">Hierarchical Report</option> 290 <option value="1">Hierarchical Report</option>
517 <option value="cps">CPS file</option> 291 <option value="cps">CPS file</option>
518 <validator type="no_options" message="Please select at least one output file" /> 292 <validator type="no_options" message="Please select at least one output file" />
519 </param> 293 </param>
539 <filter>'2' in outputs</filter> 313 <filter>'2' in outputs</filter>
540 </data> 314 </data>
541 <data format="tabular" name="output_psm" from_work_dir="psm.txt" label="${tool.name} on ${on_string}: PSM Report"> 315 <data format="tabular" name="output_psm" from_work_dir="psm.txt" label="${tool.name} on ${on_string}: PSM Report">
542 <filter>'3' in outputs</filter> 316 <filter>'3' in outputs</filter>
543 </data> 317 </data>
318 <data format="tabular" name="output_extended_psm" from_work_dir="psmx.txt" label="${tool.name} on ${on_string}: Extended PSM Report">
319 <filter>'8' in outputs</filter>
320 </data>
544 <data format="tabular" name="output_peptides_phosphorylation" from_work_dir="peptides_phospho.txt" label="${tool.name} on ${on_string}: Peptide Phosphorylation Report"> 321 <data format="tabular" name="output_peptides_phosphorylation" from_work_dir="peptides_phospho.txt" label="${tool.name} on ${on_string}: Peptide Phosphorylation Report">
545 <filter>'4' in outputs</filter> 322 <filter>'4' in outputs</filter>
546 </data> 323 </data>
547 <data format="tabular" name="output_peptides" from_work_dir="peptides.txt" label="${tool.name} on ${on_string}: Peptide Report"> 324 <data format="tabular" name="output_peptides" from_work_dir="peptides.txt" label="${tool.name} on ${on_string}: Peptide Report">
548 <filter>'5' in outputs</filter> 325 <filter>'5' in outputs</filter>
555 </data> 332 </data>
556 </outputs> 333 </outputs>
557 <tests> 334 <tests>
558 <test> 335 <test>
559 <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/> 336 <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/>
560 <param name="species_type_selector" value="no_species_type"/>
561 <param name="processing_options_selector" value="no"/> 337 <param name="processing_options_selector" value="no"/>
562 <param name="filtering_options_selector" value="no"/> 338 <param name="filtering_options_selector" value="no"/>
563 <param name="outputs" value="zip,cps,3"/> 339 <param name="outputs" value="zip,3"/>
564 <output name="output_zip" file="peptide_shaker_result1.zip" ftype="zip" compare="sim_size" delta="600" /> 340 <output name="output_zip" file="peptide_shaker_result1.zip" ftype="zip" compare="sim_size" delta="600" />
565 <output name="output_cps" file="peptide_shaker_result1.cps" ftype="peptideshaker_archive" compare="sim_size" delta="600" />
566 <output name="output_psm" file="peptide_shaker_psm_result1.tabular" ftype="tabular" /> 341 <output name="output_psm" file="peptide_shaker_psm_result1.tabular" ftype="tabular" />
567 </test> 342 </test>
568 <test> 343 <test>
569 <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/> 344 <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/>
570 <param name="species_type_selector" value="no_species_type"/>
571 <param name="processing_options_selector" value="no"/> 345 <param name="processing_options_selector" value="no"/>
572 <param name="filtering_options_selector" value="yes"/> 346 <param name="filtering_options_selector" value="yes"/>
573 <param name="min_peptide_length" value="1"/> 347 <param name="min_peptide_length" value="1"/>
574 <param name="outputs" value="0,1,2,3,4,5,6,7"/> 348 <param name="outputs" value="0,1,2,3,4,5,6,7"/>
575 <output name="output_certificate" file="peptide_shaker_certificate_result2.txt" ftype="txt" lines_diff="6"/> 349 <output name="output_certificate" file="peptide_shaker_certificate_result2.txt" ftype="txt" lines_diff="6"/>
579 <output name="output_peptides" file="peptide_shaker_peptides_result2.tabular" ftype="tabular" /> 353 <output name="output_peptides" file="peptide_shaker_peptides_result2.tabular" ftype="tabular" />
580 <output name="output_peptides_phosphorylation" file="peptide_shaker_peptides_phoshorylation_result2.tabular" ftype="tabular" /> 354 <output name="output_peptides_phosphorylation" file="peptide_shaker_peptides_phoshorylation_result2.tabular" ftype="tabular" />
581 <output name="output_proteins" file="peptide_shaker_proteins_result2.tabular" ftype="tabular" /> 355 <output name="output_proteins" file="peptide_shaker_proteins_result2.tabular" ftype="tabular" />
582 <output name="output_proteins_phosphorylation" file="peptide_shaker_proteins_phoshorylation_result2.tabular" ftype="tabular" /> 356 <output name="output_proteins_phosphorylation" file="peptide_shaker_proteins_phoshorylation_result2.tabular" ftype="tabular" />
583 </test> 357 </test>
584 <test>
585 <param name="searchgui_input" value="tiny_searchgui_result1.zip" ftype="searchgui_archive"/>
586 <param name="species_type_selector" value="Vertebrates"/>
587 <param name="species" value="Human (Homo sapiens)"/>
588 <param name="processing_options_selector" value="no"/>
589 <param name="filtering_options_selector" value="yes"/>
590 <param name="min_peptide_length" value="1"/>
591 <param name="outputs" value="5"/>
592 <output name="output_peptides" file="peptide_shaker_peptides_result3.tabular" ftype="tabular" />
593 </test>
594 </tests> 358 </tests>
595 <help> 359 <help>
596 **What it does** 360 **What it does**
597 361
598 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. 362 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.
599 363
600 https://code.google.com/p/peptide-shaker/ 364 http://compomics.github.io/projects/peptide-shaker.html
601 365 http://compomics.github.io/projects/searchgui.html
602 https://code.google.com/p/searchgui/
603 366
604 ---- 367 ----
605 368
606 Reports 369 Reports
607 ======= 370 =======
744 507
745 ------ 508 ------
746 509
747 **Citation** 510 **Citation**
748 511
749 To cite the underlying tools (PeptideShaker and SearchGUI) please refer to the list of papers at http://peptide-shaker.googlecode.com 512 To cite the underlying tools (PeptideShaker and SearchGUI) please refer to the list of papers at http://compomics.github.io
750 513
751 If you use this tool in Galaxy, please cite Chilton J, Ira Cooke, Bjoern Gruening et al. https://bitbucket.org/galaxyp/peptideshaker 514 If you use this tool in Galaxy, please cite Chilton J, Ira Cooke, Bjoern Gruening et al.
752 </help> 515 </help>
753 <expand macro="citations" /> 516 <expand macro="citations" />
754 </tool> 517 </tool>