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1 <tool id="interproscan" name="Interproscan functional predictions of ORFs" version="5.0.0">
2 <description>Interproscan functional predictions of ORFs</description>
3 <requirements>
4 <requirement type="package">signalp</requirement>
5 <requirement type="package">phobius</requirement>
6 <requirement type="package">tmhmm</requirement>
7 <requirement type="set_environment">INTERPROSCAN_SCRIPT_PATH</requirement>
8 </requirements>
9 <command>
10 #import os
11 interproscan.sh -dp --fasta $infile --seqtype $seqtype -f $oformat --applications $appl --tempdir \$TEMP
12
13 $pathways
14 $goterms
15 $iprlookup
16
17 #if str($oformat) in ['SVG', 'HTML']:
18 --output-file-base $outfile
19 2>&#38;1;
20 mkdir -p $outfile.files_path;
21 #set temp_archive_file = str($outfile) + '.' + str($oformat).lower() + '.tar.gz'
22 tar -C $outfile.files_path -xvmzf $temp_archive_file;
23 python \$INTERPROSCAN_SCRIPT_PATH/create_index.py $outfile $outfile.files_path;
24 rm $temp_archive_file
25 #else:
26 -o $outfile
27 2>&#38;1
28 #end if
29
30 </command>
31 <inputs>
32 <param name="infile" type="data" format="fasta" label="Protein Fasta File"/>
33
34 <param name="seqtype" type="select" label="Type of the input sequences" help="">
35 <option value="p" selected="true">Protein</option>
36 <option value="n">DNA / RNA</option>
37 </param>
38
39 <param name="appl" type="select" multiple="True" display="checkboxes" label="Applications to run" help="Select your programm.">
40 <option value="TIGRFAM" selected="true">TIGRFAM: protein families based on Hidden Markov Models or HMMs</option>
41 <option value="PIRSF" selected="true">PIRSF: non-overlapping clustering of UniProtKB sequences into a hierarchical order (evolutionary relationships)</option>
42 <option value="ProDom" selected="true">ProDom: set of protein domain families generated from the UniProtKB</option>
43 <option value="Panther" selected="true">Panther: Protein ANalysis THrough Evolutionary Relationships</option>
44 <option value="SMART" selected="true">SMART: identification and analysis of domain architectures based on Hidden Markov Models or HMMs</option>
45 <option value="PrositeProfiles" selected="true">PROSITE Profiles: protein domains, families and functional sites as well as associated profiles to identify them</option>
46 <option value="PrositePatterns" selected="true">PROSITE Pattern: protein domains, families and functional sites as well as associated patterns to identify them</option>
47 <option value="HAMAP" selected="true">HAMAP: High-quality Automated Annotation of Microbial Proteomes</option>
48 <option value="PfamA" selected="true">PfamA: protein families, each represented by multiple sequence alignments and hidden Markov models</option>
49 <option value="PRINTS" selected="true">PRINTS: group of conserved motifs (fingerprints) used to characterise a protein family</option>
50 <option value="SuperFamily" selected="true">SUPERFAMILY: database of structural and functional annotation</option>
51 <option value="Coils" selected="true">Coils: Prediction of Coiled Coil Regions in Proteins</option>
52 <option value="Gene3d" selected="true">Gene3d: Structural assignment for whole genes and genomes using the CATH domain structure database</option>
53 <option value="SignalP-GRAM_POSITIVE" selected="false">SignalP Gram Positive Bacteria</option>
54 <option value="SignalP-GRAM_NEGATIVE" selected="false">SignalP Gram Negative Bacteria</option>
55 <option value="SignalP-EUK" selected="true">SignalP Eukaryotic Bacteria</option>
56 <option value="Phobius" selected="true">Phobius: combined transmembrane topology and signal peptide predictor</option>
57 <option value="TMHMM" selected="true">TMHMM: Prediction of transmembrane helices in proteins</option>
58 </param>
59
60 <param name="pathways" truevalue="--pathways" falsevalue="" checked="True" type="boolean" label="Include pathway information" help="Option that provides mappings from matches to pathway information, which is based on the matched manually curated InterPro entries."/>
61 <param name="goterms" truevalue="--goterms" falsevalue="" checked="True" type="boolean" label="Include Gene Ontology (GO) mappings" />
62 <param name="iprlookup" truevalue="--iprlookup" falsevalue="" checked="False" type="boolean" label="Provide mappings from matched member database signatures to the InterPro entries that they are integrated into" />
63
64 <param name="oformat" type="select" label="Output format" help="Please select a output format.">
65 <option value="TSV" selected="true">Tab-separated values format (TSV)</option>
66 <option value="GFF3">GFF3</option>
67 <option value="SVG">SVG</option>
68 <option value="HTML">HTML</option>
69 <option value="XML">XML</option>
70 </param>
71
72 </inputs>
73 <outputs>
74
75 <data format="tabular" name="outfile" label="Interproscan calculation on ${on_string}">
76 <change_format>
77 <when input="oformat" value="HTML" format="html"/>
78 <when input="oformat" value="XML" format="xml"/>
79 <when input="oformat" value="SVG" format="html"/>
80 <when input="oformat" value="GFF3" format="gff"/>
81 </change_format>
82 </data>
83
84 </outputs>
85 <requirements>
86 </requirements>
87 <help>
88
89 **What it does**
90
91 Interproscan is a batch tool to query the Interpro database. It provides annotations based on multiple searches of profile and other functional databases.
92
93
94 #####
95 Input
96 #####
97
98 Required is a FASTA file containing protein or nucleotide sequences.
99
100
101 ######
102 Output
103 ######
104
105 In this version of InterProScan_, you can retrieve output in any of the following five formats:
106
107 * TSV: a simple tab-delimited file format
108 * XML: the new "IMPACT" XML format (XSD available here_).
109 * GFF: The `GFF 3.0`_ format
110 * HTML: An HTML representation of the protein matches
111 * SVG: An Scalable Vector Graphics representation of the protein matches
112
113
114 .. _`GFF3 3.0`: http://gmod.org/wiki/GFF#GFF3_Format
115 .. _here: http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5
116
117
118 Previous versions of InterProScan_ 5 (I5RC1 - I5RC6) could only output data for nucleotide sequences in XML and GFF3. This has now changed and InterProScan_ 5 can output results for nucleotide sequences in all formats. *Please note* you can only trace protein match positions to the original nucleotide sequence with GFF3 and XML.
119
120 You can override the default output formats using the *-f* option, e.g.::
121
122 ./interproscan.sh -f XML -f HTML -i /path/to/sequences.fasta -b /path/to/output_file
123
124 or
125
126 ::
127
128 ./interproscan.sh -f XML, HTML -i /path/to/sequences.fasta -b /path/to/output_file
129
130
131 These two equivalent commands will output the results in XML and HTML format.
132
133 Tab-separated values format (TSV)
134 =================================
135
136 Basic tab delimited format.
137
138
139 Example Output
140 --------------
141
142 ::
143
144 P51587 14086411a2cdf1c4cba63020e1622579 3418 Pfam PF09103 BRCA2, oligonucleotide/oligosaccharide-binding, domain 1 2670 2799 7.9E-43 T 15-03-2013
145 P51587 14086411a2cdf1c4cba63020e1622579 3418 ProSiteProfiles PS50138 BRCA2 repeat profile. 1002 1036 0.0 T 18-03-2013 IPR002093 BRCA2 repeat GO:0005515|GO:0006302
146 P51587 14086411a2cdf1c4cba63020e1622579 3418 Gene3D G3DSA:2.40.50.140 2966 3051 3.1E-52 T 15-03-2013
147 ...
148
149
150 The TSV format presents the match data in columns as follows:
151
152 - Protein Accession (e.g. P51587)
153 - Sequence MD5 digest (e.g. 14086411a2cdf1c4cba63020e1622579)
154 - Sequence Length (e.g. 3418)
155 - Analysis (e.g. Pfam / PRINTS / Gene3D)
156 - Signature Accession (e.g. PF09103 / G3DSA:2.40.50.140)
157 - Signature Description (e.g. BRCA2 repeat profile)
158 - Start location
159 - Stop location
160 - Score - is the e-value of the match reported by member database method (e.g. 3.1E-52)
161 - Status - is the status of the match (T: true)
162 - Date - is the date of the run
163 - (InterProScan_ annotations - accession (e.g. IPR002093) - optional column; only displayed if -iprscan option is switched on)
164 - (InterProScan_ annotations - description (e.g. BRCA2 repeat) - optional column; only displayed if -iprscan option is switched on)
165 - (GO annotations (e.g. GO:0005515) - optional column; only displayed if --goterms option is switched on)
166 - (Pathways annotations (e.g. REACT_71) - optional column; only displayed if --pathways option is switched on)
167
168
169 Extensible Markup Language (XML)
170 ================================
171
172 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].
173
174 Example Output
175 --------------
176
177 ::
178
179 .. image:: $PATH_TO_IMAGES/example_xml_output.png
180
181
182
183 Generic Feature Format Version 3 (GFF3)
184 =======================================
185
186 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].
187
188 Example Output
189 --------------
190
191 ::
192
193 ##gff-version 3
194 ##feature-ontology http://song.cvs.sourceforge.net/viewvc/song/ontology/sofa.obo?revision=1.269
195 ##sequence-region AACH01000027 1 1347
196 ##seqid|source|type|start|end|score|strand|phase|attributes
197 AACH01000027 provided_by_user nucleic_acid 1 1347 . + . Name=AACH01000027;md5=b2a7416cb92565c004becb7510f46840;ID=AACH01000027
198 AACH01000027 getorf ORF 1 1347 . + . Name=AACH01000027.2_21;Target=pep_AACH01000027_1_1347 1 449;md5=b2a7416cb92565c004becb7510f46840;ID=orf_AACH01000027_1_1347
199 AACH01000027 getorf polypeptide 1 449 . + . md5=fd0743a673ac69fb6e5c67a48f264dd5;ID=pep_AACH01000027_1_1347
200 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"
201 ##sequence-region 2
202 ...
203 >pep_AACH01000027_1_1347
204 LVLLAAFDCIDDTKLVKQIIISEIINSLPNIVNDKYGRKVLLYLLSPRDPAHTVREIIEV
205 LQKGDGNAHSKKDTEIRRREMKYKRIVFKVGTSSLTNEDGSLSRSKVKDITQQLAMLHEA
206 GHELILVSSGAIAAGFGALGFKKRPTKIADKQASAAVGQGLLLEEYTTNLLLRQIVSAQI
207 LLTQDDFVDKRRYKNAHQALSVLLNRGAIPIINENDSVVIDELKVGDNDTLSAQVAAMVQ
208 ADLLVFLTDVDGLYTGNPNSDPRAKRLERIETINREIIDMAGGAGSSNGTGGMLTKIKAA
209 TIATESGVPVYICSSLKSDSMIEAAEETEDGSYFVAQEKGLRTQKQWLAFYAQSQGSIWV
210 DKGAAEALSQYGKSLLLSGIVEAEGVFSYGDIVTVFDKESGKSLGKGRVQFGASALEDML
211 RSQKAKGVLIYRDDWISITPEIQLLFTEF
212 ...
213 >match$8_84_314
214 KRIVFKVGTSSLTNEDGSLSRSKVKDITQQLAMLHEAGHELILVSSGAIAAGFGALGFKK
215 RPTKIADKQASAAVGQGLLLEEYTTNLLLRQIVSAQILLTQDDFVDKRRYKNAHQALSVL
216 LNRGAIPIINENDSVVIDELKVGDNDTLSAQVAAMVQADLLVFLTDVDGLYTGNPNSDPR
217 AKRLERIETINREIIDMAGGAGSSNGTGGMLTKIKAATIATESGVPVYICS
218
219
220 Scalable Vector Graphics (SVG) and HyperText Markup Language (HTML)
221 ====================================================================
222
223 InterProScan_ 5 outputs a single HTML/SVG file for each protein sequence analysed. The HTML/SVG file(s) are compressed into a single gzipped tar archive (or "tarball") that includes the resources (images, Javascript, style etc) to render the pages/images in a browser or image viewer. (Note that from version 5RC4, the SVG format has no external dependencies.)
224
225 The tarball will be named something similar to::
226
227 base_output_file_name.html.tar.gz OR base_output_file_name.svg.tar.gz
228
229
230 To access the HTML pages/SVG images, unzip the tarball using a command like:
231
232 tar -xvzf base_output_file_name.html(svg).tar.gz
233
234 You can then open the unzipped HTML/SVG files in any browser or image viewer (for SVG).
235
236 Example Output
237 --------------
238
239 .. image:: $PATH_TO_IMAGES/P51587.svg.png
240
241 .. _InterProScan: http://www.ebi.ac.uk/interpro
242
243
244 ----------
245 References
246 ----------
247
248 Zdobnov EM, Apweiler R (2001)
249 InterProScan an integration platform for the signature-recognition methods in InterPro.
250 Bioinformatics 17, 847-848.
251 http://dx.doi.org/10.1093/bioinformatics/17.9.847
252
253 Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R (2005)
254 InterProScan: protein domains identifier.
255 Nucleic Acids Research 33 (Web Server issue), W116-W120.
256 http://dx.doi.org/10.1093/nar/gki442
257
258 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)
259 InterPro: the integrative protein signature database.
260 Nucleic Acids Research 37 (Database Issue), D224-228.
261 http://dx.doi.org/10.1093/nar/gkn785
262
263
264 This wrapper is available to install into other Galaxy Instances via the Galaxy Tool Shed at
265 http://toolshed.g2.bx.psu.edu/view/bgruening/interproscan
266
267
268 **Galaxy Wrapper Author**::
269
270 * Bjoern Gruening, Pharmaceutical Bioinformatics, University of Freiburg
271 * Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter
272
273 </help>
274 </tool>