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comparison interproscan5/ips5.xml @ 0:fe8e43a26870 draft

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date Thu, 28 Jan 2016 19:34:51 -0500
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1 <tool id="ips5" name="Interproscan functional predictions of ORFs" version="5.0.0mkh">
2 <description>Interproscan functional predictions of ORFs.</description>
3 <requirements>
4 <!--
5 <requirement type="package">signalp</requirement>
6 <requirement type="package">phobius</requirement>
7 <requirement type="package">tmhmm</requirement>
8 -->
9 <requirement type="set_environment">INTERPROSCAN_SCRIPT_PATH</requirement>
10 </requirements>
11
12 <command>
13 #import os
14
15 \$IPS_HOME/interproscan.sh
16 ## disables the precalculated lookup service, all calculation will be run locally
17 -dp
18 --input $infile
19 --seqtype $seqtype
20 -f $output_types
21 --applications $appl
22 --tempdir \$TEMP
23
24 $pathways
25 $goterms
26 $iprlookup
27 $mode
28 --output-file-base __base__
29 2>&#38;1;
30
31 #if 'tsv' in str($output_types):
32 mv __base__.tsv $tsv_file;
33 #end if
34
35 #if 'gff3' in str($output_types):
36 mv __base__.gff3 $gff3_file;
37 #end if
38
39 #if 'xml' in str($output_types):
40 mv __base__.xml $xml_file;
41 #end if
42
43 #if 'html' in str($output_types):
44 mkdir -p $html_file.files_path;
45 #set temp_archive_file = '__base__.html.tar.gz'
46 tar -C $html_file.files_path -xvmzf $temp_archive_file;
47 python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_index.py $html_file $html_file.files_path;
48 rm $temp_archive_file;
49 #end if
50
51 #if 'svg' in str($output_types):
52 mkdir -p $svg_file.files_path;
53 #set temp_archive_file = '__base__.svg.tar.gz'
54 tar -C $svg_file.files_path -xvmzf $temp_archive_file;
55 python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_index.py $svg_file $svg_file.files_path;
56 rm $temp_archive_file;
57 #end if
58
59 echo "End of ipsfaux"
60 </command>
61
62 <inputs>
63 <param name="infile" type="data" format="fasta" label="Sequence Fasta File (ignored -- faux mode)"/>
64
65 <param name="seqtype" type="select" label="Type of the input sequences" help="">
66 <option value="p" selected="true">Protein</option>
67 <option value="n">DNA / RNA</option>
68 </param>
69
70 <param name="mode" type="boolean" label="Run on cluster?" help="Check to submit job to cluster."
71 truevalue="--mode=cluster --clusterrunid=gtdi-ips-analysis"
72 falsevalue=""/>
73
74 <param name="appl" type="select" multiple="True" display="checkboxes" label="Applications to run"
75 help="Select your programm.">
76 <option value="TIGRFAM"
77 selected="true">TIGRFAM: protein families based on Hidden Markov Models or HMMs</option>
78 <option value="PIRSF" selected="true">PIRSF: non-overlapping clustering of UniProtKB sequences into a hierarchical order (evolutionary relationships)</option>
79 <option value="ProDom"
80 selected="true">ProDom: set of protein domain families generated from the UniProtKB</option>
81 <option value="Panther"
82 selected="true">Panther: Protein ANalysis THrough Evolutionary Relationships</option>
83 <option value="SMART" selected="true">SMART: identification and analysis of domain architectures based on Hidden Markov Models or HMMs</option>
84 <option value="PrositeProfiles" selected="true">PROSITE Profiles: protein domains, families and functional sites as well as associated profiles to identify them</option>
85 <option value="PrositePatterns" selected="true">PROSITE Pattern: protein domains, families and functional sites as well as associated patterns to identify them</option>
86 <option value="HAMAP"
87 selected="true">HAMAP: High-quality Automated Annotation of Microbial Proteomes</option>
88 <option value="PfamA" selected="true">PfamA: protein families, each represented by multiple sequence alignments and hidden Markov models</option>
89 <option value="PRINTS" selected="true">PRINTS: group of conserved motifs (fingerprints) used to characterise a protein family</option>
90 <option value="SuperFamily"
91 selected="true">SUPERFAMILY: database of structural and functional annotation</option>
92 <option value="Coils" selected="true">Coils: Prediction of Coiled Coil Regions in Proteins</option>
93 <option value="Gene3d" selected="true">Gene3d: Structural assignment for whole genes and genomes using the CATH domain structure database</option>
94 <option value="SignalP-GRAM_POSITIVE" selected="false">SignalP Gram Positive Bacteria</option>
95 <option value="SignalP-GRAM_NEGATIVE" selected="false">SignalP Gram Negative Bacteria</option>
96 <option value="SignalP-EUK" selected="false">SignalP Eukaryotic Bacteria</option>
97 <option value="Phobius" selected="false">Phobius: combined transmembrane topology and signal peptide predictor</option>
98 <option value="TMHMM" selected="false">TMHMM: Prediction of transmembrane helices in proteins</option>
99 </param>
100
101 <param name="pathways" truevalue="--pathways" falsevalue="" checked="True" type="boolean"
102 label="Include pathway information"
103 help="Option that provides mappings from matches to pathway information, which is based on the matched manually curated InterPro entries. (--pathways)"/>
104 <param name="goterms" truevalue="--goterms" falsevalue="" checked="True" type="boolean"
105 label="Include Gene Ontology (GO) mappings"
106 help="Look up of corresponding Gene Ontology annotation. Implies -iprlookup option. (--goterms)"/>
107
108 <param name="iprlookup" truevalue="--iprlookup" falsevalue="" checked="False" type="boolean"
109 label="Provide additional mappings"
110 help="Provide mappings from matched member database signatures to the InterPro entries that they are integrated into (--iprlookup)"/>
111
112 <param name="output_types" type="select" display="checkboxes" multiple="true" label="Output formats"
113 help="Select the output formats to generate (at least one)">
114 <option value="tsv" selected="true">Raw (TSV)</option>
115 <option value="html" selected="true">HTML (Graphical)</option>
116 <option value="svg" selected="false">SVG (Scalable Vector Graphics)</option>
117 <option value="gff3" selected="true">GFF3</option>
118 <option value="xml" selected="false">XML</option>
119 </param>
120 </inputs>
121
122 <outputs>
123 <data format="tabular" name="tsv_file" label="Interproscan TSV on ${on_string}">
124 <filter>'tsv' in output_types</filter>
125 </data>
126 <data format="html" name="html_file" label="Interproscan HTML on ${on_string}">
127 <filter>'html' in output_types</filter>
128 </data>
129 <data format="html" name="svg_file" label="Interproscan SVG on ${on_string}">
130 <filter>'svg' in output_types</filter>
131 </data>
132 <data format="gff3" name="gff3_file" label="Interproscan GFF3 on ${on_string}">
133 <filter>'gff3' in output_types</filter>
134 </data>
135 <data format="xml" name="xml_file" label="Interproscan XML on ${on_string}">
136 <filter>'xml' in output_types</filter>
137 </data>
138 </outputs>
139
140 <requirements>
141 </requirements>
142
143 <help>
144
145 **What it does**
146
147 Interproscan is a batch tool to query the Interpro database. It provides annotations based on multiple searches of profile and other functional databases.
148
149
150 #####
151 Input
152 #####
153
154 Required is a FASTA file containing protein or nucleotide sequences.
155
156
157 ######
158 Output
159 ######
160
161 In this version of InterProScan_, you can retrieve output in any of the following five formats:
162
163 * TSV: a simple tab-delimited file format
164 * XML: the new "IMPACT" XML format (XSD available here_).
165 * GFF: The `GFF 3.0`_ format
166 * HTML: An HTML representation of the protein matches
167 * SVG: An Scalable Vector Graphics representation of the protein matches
168
169
170 .. _`GFF 3.0`: http://gmod.org/wiki/GFF#GFF3_Format
171 .. _here: http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5
172
173
174
175 Tab-separated values format (TSV)
176 =================================
177
178 Basic tab delimited format.
179
180
181 Example Output
182 --------------
183
184 ::
185
186 P51587 14086411a2cdf1c4cba63020e1622579 3418 Pfam PF09103 BRCA2, oligonucleotide/oligosaccharide-binding, domain 1 2670 2799 7.9E-43 T 15-03-2013
187 P51587 14086411a2cdf1c4cba63020e1622579 3418 ProSiteProfiles PS50138 BRCA2 repeat profile. 1002 1036 0.0 T 18-03-2013 IPR002093 BRCA2 repeat GO:0005515|GO:0006302
188 P51587 14086411a2cdf1c4cba63020e1622579 3418 Gene3D G3DSA:2.40.50.140 2966 3051 3.1E-52 T 15-03-2013
189 ...
190
191
192 The TSV format presents the match data in columns as follows:
193
194 - Protein Accession (e.g. P51587)
195 - Sequence MD5 digest (e.g. 14086411a2cdf1c4cba63020e1622579)
196 - Sequence Length (e.g. 3418)
197 - Analysis (e.g. Pfam / PRINTS / Gene3D)
198 - Signature Accession (e.g. PF09103 / G3DSA:2.40.50.140)
199 - Signature Description (e.g. BRCA2 repeat profile)
200 - Start location
201 - Stop location
202 - Score - is the e-value of the match reported by member database method (e.g. 3.1E-52)
203 - Status - is the status of the match (T: true)
204 - Date - is the date of the run
205 - (InterProScan_ annotations - accession (e.g. IPR002093) - optional column; only displayed if -iprscan option is switched on)
206 - (InterProScan_ annotations - description (e.g. BRCA2 repeat) - optional column; only displayed if -iprscan option is switched on)
207 - (GO annotations (e.g. GO:0005515) - optional column; only displayed if --goterms option is switched on)
208 - (Pathways annotations (e.g. REACT_71) - optional column; only displayed if --pathways option is switched on)
209
210
211 Extensible Markup Language (XML)
212 ================================
213
214 XML representation of the matches - this is the richest form of the data. The XML Schema Definition (XSD) is available [http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5 here].
215
216 Example Output
217 --------------
218
219 .. image:: $PATH_TO_IMAGES/example_xml_output.png
220
221
222
223 Generic Feature Format Version 3 (GFF3)
224 =======================================
225
226 The GFF3 format is a flat tab-delimited file, which is much richer then the TSV output format. It allows you to trace back from matches to predicted proteins and to nucleic acid sequences. It also contains a FASTA format representation of the predicted protein sequences and their matches. You will find a documentation of all the columns and attributes used on [http://www.sequenceontology.org/gff3.shtml].
227
228 Example Output
229 --------------
230
231 ::
232
233 ##gff-version 3
234 ##feature-ontology http://song.cvs.sourceforge.net/viewvc/song/ontology/sofa.obo?revision=1.269
235 ##sequence-region AACH01000027 1 1347
236 ##seqid|source|type|start|end|score|strand|phase|attributes
237 AACH01000027 provided_by_user nucleic_acid 1 1347 . + . Name=AACH01000027;md5=b2a7416cb92565c004becb7510f46840;ID=AACH01000027
238 AACH01000027 getorf ORF 1 1347 . + . Name=AACH01000027.2_21;Target=pep_AACH01000027_1_1347 1 449;md5=b2a7416cb92565c004becb7510f46840;ID=orf_AACH01000027_1_1347
239 AACH01000027 getorf polypeptide 1 449 . + . md5=fd0743a673ac69fb6e5c67a48f264dd5;ID=pep_AACH01000027_1_1347
240 AACH01000027 Pfam protein_match 84 314 1.2E-45 + . Name=PF00696;signature_desc=Amino acid kinase family;Target=null 84 314;status=T;ID=match$8_84_314;Ontology_term="GO:0008652";date=15-04-2013;Dbxref="InterPro:IPR001048","Reactome:REACT_13"
241 ##sequence-region 2
242 ...
243 >pep_AACH01000027_1_1347
244 LVLLAAFDCIDDTKLVKQIIISEIINSLPNIVNDKYGRKVLLYLLSPRDPAHTVREIIEV
245 LQKGDGNAHSKKDTEIRRREMKYKRIVFKVGTSSLTNEDGSLSRSKVKDITQQLAMLHEA
246 GHELILVSSGAIAAGFGALGFKKRPTKIADKQASAAVGQGLLLEEYTTNLLLRQIVSAQI
247 LLTQDDFVDKRRYKNAHQALSVLLNRGAIPIINENDSVVIDELKVGDNDTLSAQVAAMVQ
248 ADLLVFLTDVDGLYTGNPNSDPRAKRLERIETINREIIDMAGGAGSSNGTGGMLTKIKAA
249 TIATESGVPVYICSSLKSDSMIEAAEETEDGSYFVAQEKGLRTQKQWLAFYAQSQGSIWV
250 DKGAAEALSQYGKSLLLSGIVEAEGVFSYGDIVTVFDKESGKSLGKGRVQFGASALEDML
251 RSQKAKGVLIYRDDWISITPEIQLLFTEF
252 ...
253 >match$8_84_314
254 KRIVFKVGTSSLTNEDGSLSRSKVKDITQQLAMLHEAGHELILVSSGAIAAGFGALGFKK
255 RPTKIADKQASAAVGQGLLLEEYTTNLLLRQIVSAQILLTQDDFVDKRRYKNAHQALSVL
256 LNRGAIPIINENDSVVIDELKVGDNDTLSAQVAAMVQADLLVFLTDVDGLYTGNPNSDPR
257 AKRLERIETINREIIDMAGGAGSSNGTGGMLTKIKAATIATESGVPVYICS
258
259
260 Scalable Vector Graphics (SVG) and HyperText Markup Language (HTML)
261 ====================================================================
262
263 InterProScan_ 5 outputs a single HTML/SVG file for each protein sequence analysed.
264
265
266 Example Output
267 --------------
268
269 .. image:: $PATH_TO_IMAGES/P51587.svg.png
270
271 .. _InterProScan: http://www.ebi.ac.uk/interpro
272
273
274 ----------
275 References
276 ----------
277
278
279 If you use this Galaxy tool in work leading to a scientific publication please
280 cite the following papers:
281
282 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
283 Galaxy tools and workflows for sequence analysis with applications
284 in molecular plant pathology. PeerJ 1:e167
285 http://dx.doi.org/10.7717/peerj.167
286
287 Zdobnov EM, Apweiler R (2001)
288 InterProScan an integration platform for the signature-recognition methods in InterPro.
289 Bioinformatics 17, 847-848.
290 http://dx.doi.org/10.1093/bioinformatics/17.9.847
291
292 Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R (2005)
293 InterProScan: protein domains identifier.
294 Nucleic Acids Research 33 (Web Server issue), W116-W120.
295 http://dx.doi.org/10.1093/nar/gki442
296
297 Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJ, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C. (2009)
298 InterPro: the integrative protein signature database.
299 Nucleic Acids Research 37 (Database Issue), D224-228.
300 http://dx.doi.org/10.1093/nar/gkn785
301
302
303 This wrapper is available to install into other Galaxy Instances via the Galaxy Tool Shed at
304 http://toolshed.g2.bx.psu.edu/view/bgruening/interproscan5
305
306
307 **Galaxy Wrapper Author**::
308
309 * Bjoern Gruening, University of Freiburg
310 * Konrad Paszkiewicz, University of Exeter
311
312 </help>
313 </tool>