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comparison interproscan.xml @ 0:82547f0d3a29 draft

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Initial interproscan5 wrapper.
author bgruening
date Tue, 08 Oct 2013 09:18:17 -0400
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-1:000000000000 0:82547f0d3a29
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
11 #import os
12 interproscan.sh
13 ## disables the precalculated lookup service, all calculation will be run locally
14 -dp
15 --input $infile
16 --seqtype $seqtype
17 -f $oformat
18 --applications $appl
19 --tempdir \$TEMP
20
21 $pathways
22 $goterms
23 $iprlookup
24
25 #if str($oformat) in ['SVG', 'HTML']:
26 --output-file-base $outfile
27 2>&#38;1;
28 mkdir -p $outfile.files_path;
29 #set temp_archive_file = str($outfile) + '.' + str($oformat).lower() + '.tar.gz'
30 tar -C $outfile.files_path -xvmzf $temp_archive_file;
31 python \$INTERPROSCAN_SCRIPT_PATH/create_index.py $outfile $outfile.files_path;
32 rm $temp_archive_file
33 #else:
34 -o $outfile
35 2>&#38;1
36 #end if
37
38 </command>
39 <inputs>
40 <param name="infile" type="data" format="fasta" label="Protein Fasta File"/>
41
42 <param name="seqtype" type="select" label="Type of the input sequences" help="">
43 <option value="p" selected="true">Protein</option>
44 <option value="n">DNA / RNA</option>
45 </param>
46
47 <param name="appl" type="select" multiple="True" display="checkboxes" label="Applications to run" help="Select your programm.">
48 <option value="TIGRFAM" selected="true">TIGRFAM: protein families based on Hidden Markov Models or HMMs</option>
49 <option value="PIRSF" selected="true">PIRSF: non-overlapping clustering of UniProtKB sequences into a hierarchical order (evolutionary relationships)</option>
50 <option value="ProDom" selected="true">ProDom: set of protein domain families generated from the UniProtKB</option>
51 <option value="Panther" selected="true">Panther: Protein ANalysis THrough Evolutionary Relationships</option>
52 <option value="SMART" selected="true">SMART: identification and analysis of domain architectures based on Hidden Markov Models or HMMs</option>
53 <option value="PrositeProfiles" selected="true">PROSITE Profiles: protein domains, families and functional sites as well as associated profiles to identify them</option>
54 <option value="PrositePatterns" selected="true">PROSITE Pattern: protein domains, families and functional sites as well as associated patterns to identify them</option>
55 <option value="HAMAP" selected="true">HAMAP: High-quality Automated Annotation of Microbial Proteomes</option>
56 <option value="PfamA" selected="true">PfamA: protein families, each represented by multiple sequence alignments and hidden Markov models</option>
57 <option value="PRINTS" selected="true">PRINTS: group of conserved motifs (fingerprints) used to characterise a protein family</option>
58 <option value="SuperFamily" selected="true">SUPERFAMILY: database of structural and functional annotation</option>
59 <option value="Coils" selected="true">Coils: Prediction of Coiled Coil Regions in Proteins</option>
60 <option value="Gene3d" selected="true">Gene3d: Structural assignment for whole genes and genomes using the CATH domain structure database</option>
61 <option value="SignalP-GRAM_POSITIVE" selected="false">SignalP Gram Positive Bacteria</option>
62 <option value="SignalP-GRAM_NEGATIVE" selected="false">SignalP Gram Negative Bacteria</option>
63 <option value="SignalP-EUK" selected="true">SignalP Eukaryotic Bacteria</option>
64 <option value="Phobius" selected="true">Phobius: combined transmembrane topology and signal peptide predictor</option>
65 <option value="TMHMM" selected="true">TMHMM: Prediction of transmembrane helices in proteins</option>
66 </param>
67
68 <param name="pathways" truevalue="--pathways" falsevalue="" checked="True" type="boolean" label="Include pathway information"
69 help="Option that provides mappings from matches to pathway information, which is based on the matched manually curated InterPro entries. (--pathways)"/>
70 <param name="goterms" truevalue="--goterms" falsevalue="" checked="True" type="boolean" label="Include Gene Ontology (GO) mappings"
71 help="Look up of corresponding Gene Ontology annotation. Implies -iprlookup option. (--goterms)"/>
72 <param name="iprlookup" truevalue="--iprlookup" falsevalue="" checked="False" type="boolean"
73 label="Provide additional mappings" help="Provide mappings from matched member database signatures to the InterPro entries that they are integrated into (--iprlookup)"/>
74
75 <param name="oformat" type="select" label="Output format" help="Please select a output format.">
76 <option value="TSV" selected="true">Tab-separated values format (TSV)</option>
77 <option value="GFF3">GFF3</option>
78 <option value="SVG">SVG</option>
79 <option value="HTML">HTML</option>
80 <option value="XML">XML</option>
81 </param>
82
83 </inputs>
84 <outputs>
85
86 <data format="tabular" name="outfile" label="Interproscan calculation on ${on_string}">
87 <change_format>
88 <when input="oformat" value="HTML" format="html"/>
89 <when input="oformat" value="XML" format="xml"/>
90 <when input="oformat" value="SVG" format="html"/>
91 <when input="oformat" value="GFF3" format="gff"/>
92 </change_format>
93 </data>
94
95 </outputs>
96 <requirements>
97 </requirements>
98 <help>
99
100 **What it does**
101
102 Interproscan is a batch tool to query the Interpro database. It provides annotations based on multiple searches of profile and other functional databases.
103
104
105 #####
106 Input
107 #####
108
109 Required is a FASTA file containing protein or nucleotide sequences.
110
111
112 ######
113 Output
114 ######
115
116 In this version of InterProScan_, you can retrieve output in any of the following five formats:
117
118 * TSV: a simple tab-delimited file format
119 * XML: the new "IMPACT" XML format (XSD available here_).
120 * GFF: The `GFF 3.0`_ format
121 * HTML: An HTML representation of the protein matches
122 * SVG: An Scalable Vector Graphics representation of the protein matches
123
124
125 .. _`GFF 3.0`: http://gmod.org/wiki/GFF#GFF3_Format
126 .. _here: http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5
127
128
129
130 Tab-separated values format (TSV)
131 =================================
132
133 Basic tab delimited format.
134
135
136 Example Output
137 --------------
138
139 ::
140
141 P51587 14086411a2cdf1c4cba63020e1622579 3418 Pfam PF09103 BRCA2, oligonucleotide/oligosaccharide-binding, domain 1 2670 2799 7.9E-43 T 15-03-2013
142 P51587 14086411a2cdf1c4cba63020e1622579 3418 ProSiteProfiles PS50138 BRCA2 repeat profile. 1002 1036 0.0 T 18-03-2013 IPR002093 BRCA2 repeat GO:0005515|GO:0006302
143 P51587 14086411a2cdf1c4cba63020e1622579 3418 Gene3D G3DSA:2.40.50.140 2966 3051 3.1E-52 T 15-03-2013
144 ...
145
146
147 The TSV format presents the match data in columns as follows:
148
149 - Protein Accession (e.g. P51587)
150 - Sequence MD5 digest (e.g. 14086411a2cdf1c4cba63020e1622579)
151 - Sequence Length (e.g. 3418)
152 - Analysis (e.g. Pfam / PRINTS / Gene3D)
153 - Signature Accession (e.g. PF09103 / G3DSA:2.40.50.140)
154 - Signature Description (e.g. BRCA2 repeat profile)
155 - Start location
156 - Stop location
157 - Score - is the e-value of the match reported by member database method (e.g. 3.1E-52)
158 - Status - is the status of the match (T: true)
159 - Date - is the date of the run
160 - (InterProScan_ annotations - accession (e.g. IPR002093) - optional column; only displayed if -iprscan option is switched on)
161 - (InterProScan_ annotations - description (e.g. BRCA2 repeat) - optional column; only displayed if -iprscan option is switched on)
162 - (GO annotations (e.g. GO:0005515) - optional column; only displayed if --goterms option is switched on)
163 - (Pathways annotations (e.g. REACT_71) - optional column; only displayed if --pathways option is switched on)
164
165
166 Extensible Markup Language (XML)
167 ================================
168
169 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].
170
171 Example Output
172 --------------
173
174 .. image:: $PATH_TO_IMAGES/example_xml_output.png
175
176
177
178 Generic Feature Format Version 3 (GFF3)
179 =======================================
180
181 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].
182
183 Example Output
184 --------------
185
186 ::
187
188 ##gff-version 3
189 ##feature-ontology http://song.cvs.sourceforge.net/viewvc/song/ontology/sofa.obo?revision=1.269
190 ##sequence-region AACH01000027 1 1347
191 ##seqid|source|type|start|end|score|strand|phase|attributes
192 AACH01000027 provided_by_user nucleic_acid 1 1347 . + . Name=AACH01000027;md5=b2a7416cb92565c004becb7510f46840;ID=AACH01000027
193 AACH01000027 getorf ORF 1 1347 . + . Name=AACH01000027.2_21;Target=pep_AACH01000027_1_1347 1 449;md5=b2a7416cb92565c004becb7510f46840;ID=orf_AACH01000027_1_1347
194 AACH01000027 getorf polypeptide 1 449 . + . md5=fd0743a673ac69fb6e5c67a48f264dd5;ID=pep_AACH01000027_1_1347
195 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"
196 ##sequence-region 2
197 ...
198 >pep_AACH01000027_1_1347
199 LVLLAAFDCIDDTKLVKQIIISEIINSLPNIVNDKYGRKVLLYLLSPRDPAHTVREIIEV
200 LQKGDGNAHSKKDTEIRRREMKYKRIVFKVGTSSLTNEDGSLSRSKVKDITQQLAMLHEA
201 GHELILVSSGAIAAGFGALGFKKRPTKIADKQASAAVGQGLLLEEYTTNLLLRQIVSAQI
202 LLTQDDFVDKRRYKNAHQALSVLLNRGAIPIINENDSVVIDELKVGDNDTLSAQVAAMVQ
203 ADLLVFLTDVDGLYTGNPNSDPRAKRLERIETINREIIDMAGGAGSSNGTGGMLTKIKAA
204 TIATESGVPVYICSSLKSDSMIEAAEETEDGSYFVAQEKGLRTQKQWLAFYAQSQGSIWV
205 DKGAAEALSQYGKSLLLSGIVEAEGVFSYGDIVTVFDKESGKSLGKGRVQFGASALEDML
206 RSQKAKGVLIYRDDWISITPEIQLLFTEF
207 ...
208 >match$8_84_314
209 KRIVFKVGTSSLTNEDGSLSRSKVKDITQQLAMLHEAGHELILVSSGAIAAGFGALGFKK
210 RPTKIADKQASAAVGQGLLLEEYTTNLLLRQIVSAQILLTQDDFVDKRRYKNAHQALSVL
211 LNRGAIPIINENDSVVIDELKVGDNDTLSAQVAAMVQADLLVFLTDVDGLYTGNPNSDPR
212 AKRLERIETINREIIDMAGGAGSSNGTGGMLTKIKAATIATESGVPVYICS
213
214
215 Scalable Vector Graphics (SVG) and HyperText Markup Language (HTML)
216 ====================================================================
217
218 InterProScan_ 5 outputs a single HTML/SVG file for each protein sequence analysed.
219
220
221 Example Output
222 --------------
223
224 .. image:: $PATH_TO_IMAGES/P51587.svg.png
225
226 .. _InterProScan: http://www.ebi.ac.uk/interpro
227
228
229 ----------
230 References
231 ----------
232
233
234 If you use this Galaxy tool in work leading to a scientific publication please
235 cite the following papers:
236
237 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
238 Galaxy tools and workflows for sequence analysis with applications
239 in molecular plant pathology. PeerJ 1:e167
240 http://dx.doi.org/10.7717/peerj.167
241
242 Zdobnov EM, Apweiler R (2001)
243 InterProScan an integration platform for the signature-recognition methods in InterPro.
244 Bioinformatics 17, 847-848.
245 http://dx.doi.org/10.1093/bioinformatics/17.9.847
246
247 Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R (2005)
248 InterProScan: protein domains identifier.
249 Nucleic Acids Research 33 (Web Server issue), W116-W120.
250 http://dx.doi.org/10.1093/nar/gki442
251
252 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)
253 InterPro: the integrative protein signature database.
254 Nucleic Acids Research 37 (Database Issue), D224-228.
255 http://dx.doi.org/10.1093/nar/gkn785
256
257
258 This wrapper is available to install into other Galaxy Instances via the Galaxy Tool Shed at
259 http://toolshed.g2.bx.psu.edu/view/bgruening/interproscan5
260
261
262 **Galaxy Wrapper Author**::
263
264 * Bjoern Gruening, University of Freiburg
265 * Konrad Paszkiewicz, University of Exeter
266
267 </help>
268 </tool>