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comparison interproscan5/ips5.xml @ 0:0da2847fc108 draft default tip

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date Thu, 24 May 2018 14:57:30 -0400
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1 <tool id="ips5" name="Interproscan" version="5.0.2mkh">
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 echo "Start timestamp: \$(date)";
15 \$INTERPROSCAN_SCRIPT_PATH/interproscan.sh
16 ## disables the precalculated lookup service, all calculation will be run locally
17 -dp
18 --input $infile
19 --seqtype $seqtype
20 -f tsv,$output_types
21 --applications $appl
22
23 $pathways
24 $goterms
25 $iprlookup
26 $mode
27 --output-file-base __base__
28 2>&#38;1;
29
30 mv __base__.tsv $tsv_file;
31
32 #if 'gff3' in str($output_types):
33 mv __base__.gff3 $gff3_file;
34 #end if
35
36 #if 'xml' in str($output_types):
37 mv __base__.xml $xml_file;
38 #end if
39
40 #if 'html' in str($output_types):
41 mkdir -p $html_file.files_path;
42 #set temp_archive_file = '__base__.html.tar.gz'
43 tar -C $html_file.files_path -xvmzf $temp_archive_file;
44 #if str($seqtype) == 'p' and not str($getorfed):
45 python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_html_index.py 0 $tsv_file $html_file $html_file.files_path;
46 #else
47 python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_html_index.py 1 $tsv_file $html_file $html_file.files_path;
48 #end if
49 rm $temp_archive_file;
50 #end if
51
52 #if 'svg' in str($output_types):
53 mkdir -p $svg_file.files_path;
54 #set temp_archive_file = '__base__.svg.tar.gz'
55 tar -C $svg_file.files_path -xvmzf $temp_archive_file;
56 #if str($seqtype) == 'p' and not str($getorfed):
57 python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_html_index.py 0 $tsv_file $svg_file $svg_file.files_path;
58 #else
59 python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_html_index.py 1 $tsv_file $svg_file $svg_file.files_path;
60 #end if
61 rm $temp_archive_file;
62 #end if
63
64 echo "End timestamp: \$(date)"
65 </command>
66
67 <inputs>
68 <param name="infile" type="data" format="fasta" label="Sequence Fasta File"/>
69
70 <param name="seqtype" type="select" label="Type of the input sequences" help="">
71 <option value="p" selected="true">Protein</option>
72 <option value="n">DNA / RNA</option>
73 </param>
74
75 <param name="getorfed" type="boolean" label="DNA/RNA was externally processed by getorf?" help="Ignored for DNA inputs."
76 truevalue="getorfed"
77 falsevalue=""/>
78
79 <param name="mode" type="boolean" label="Run on cluster?" help="Check to submit job to cluster."
80 truevalue="--mode=cluster --clusterrunid=gtdi-ips-analysis"
81 falsevalue=""/>
82
83 <param name="appl" type="select" multiple="True" display="checkboxes" label="Applications to run"
84 help="Select your programm.">
85 <option value="TIGRFAM"
86 selected="true">TIGRFAM: protein families based on Hidden Markov Models or HMMs</option>
87 <option value="PIRSF" selected="true">PIRSF: non-overlapping clustering of UniProtKB sequences into a hierarchical order (evolutionary relationships)</option>
88 <option value="ProDom"
89 selected="true">ProDom: set of protein domain families generated from the UniProtKB</option>
90 <option value="Panther"
91 selected="true">Panther: Protein ANalysis THrough Evolutionary Relationships</option>
92 <option value="SMART" selected="true">SMART: identification and analysis of domain architectures based on Hidden Markov Models or HMMs</option>
93 <option value="PrositeProfiles" selected="true">PROSITE Profiles: protein domains, families and functional sites as well as associated profiles to identify them</option>
94 <option value="PrositePatterns" selected="true">PROSITE Pattern: protein domains, families and functional sites as well as associated patterns to identify them</option>
95 <option value="HAMAP"
96 selected="true">HAMAP: High-quality Automated Annotation of Microbial Proteomes</option>
97 <option value="PfamA" selected="true">PfamA: protein families, each represented by multiple sequence alignments and hidden Markov models</option>
98 <option value="PRINTS" selected="true">PRINTS: group of conserved motifs (fingerprints) used to characterise a protein family</option>
99 <option value="SuperFamily"
100 selected="true">SUPERFAMILY: database of structural and functional annotation</option>
101 <option value="Coils" selected="true">Coils: Prediction of Coiled Coil Regions in Proteins</option>
102 <option value="Gene3d" selected="true">Gene3d: Structural assignment for whole genes and genomes using the CATH domain structure database</option>
103 <option value="SignalP-GRAM_POSITIVE" selected="false">SignalP Gram Positive Bacteria</option>
104 <option value="SignalP-GRAM_NEGATIVE" selected="false">SignalP Gram Negative Bacteria</option>
105 <option value="SignalP-EUK" selected="false">SignalP Eukaryotic Bacteria</option>
106 <option value="Phobius" selected="false">Phobius: combined transmembrane topology and signal peptide predictor</option>
107 <option value="TMHMM" selected="false">TMHMM: Prediction of transmembrane helices in proteins</option>
108 </param>
109
110 <param name="pathways" truevalue="--pathways" falsevalue="" checked="True" type="boolean"
111 label="Include pathway information"
112 help="Option that provides mappings from matches to pathway information, which is based on the matched manually curated InterPro entries. (--pathways)"/>
113 <param name="goterms" truevalue="--goterms" falsevalue="" checked="True" type="boolean"
114 label="Include Gene Ontology (GO) mappings"
115 help="Look up of corresponding Gene Ontology annotation. Implies -iprlookup option. (--goterms)"/>
116
117 <param name="iprlookup" truevalue="--iprlookup" falsevalue="" checked="False" type="boolean"
118 label="Provide additional mappings"
119 help="Provide mappings from matched member database signatures to the InterPro entries that they are integrated into (--iprlookup)"/>
120
121 <param name="output_types" type="select" display="checkboxes" multiple="true" label="Output formats (in addition to TSV)"
122 help="Select the output formats to generate (at least one)">
123 <option value="html" selected="true">HTML (Graphical)</option>
124 <option value="svg" selected="false">SVG (Scalable Vector Graphics)</option>
125 <option value="gff3" selected="true">GFF3</option>
126 <option value="xml" selected="false">XML</option>
127 </param>
128 </inputs>
129
130 <outputs>
131 <data format="tabular" name="tsv_file" label="Interproscan TSV on ${on_string}"/>
132 <data format="html" name="html_file" label="Interproscan HTML on ${on_string}">
133 <filter>'html' in output_types</filter>
134 </data>
135 <data format="html" name="svg_file" label="Interproscan SVG on ${on_string}">
136 <filter>'svg' in output_types</filter>
137 </data>
138 <data format="gff3" name="gff3_file" label="Interproscan GFF3 on ${on_string}">
139 <filter>'gff3' in output_types</filter>
140 </data>
141 <data format="xml" name="xml_file" label="Interproscan XML on ${on_string}">
142 <filter>'xml' in output_types</filter>
143 </data>
144 </outputs>
145
146 <requirements>
147 </requirements>
148
149 <help>
150
151 **What it does**
152
153 Interproscan is a batch tool to query the Interpro database. It provides annotations based on multiple searches of profile and other functional databases.
154
155
156 #####
157 Input
158 #####
159
160 Required is a FASTA file containing protein or nucleotide sequences.
161
162
163 ######
164 Output
165 ######
166
167 In this version of InterProScan_, you can retrieve output in any of the following five formats:
168
169 * TSV: a simple tab-delimited file format
170 * XML: the new "IMPACT" XML format (XSD available here_).
171 * GFF: The `GFF 3.0`_ format
172 * HTML: An HTML representation of the protein matches
173 * SVG: An Scalable Vector Graphics representation of the protein matches
174
175
176 .. _`GFF 3.0`: http://gmod.org/wiki/GFF#GFF3_Format
177 .. _here: http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5
178
179
180
181 Tab-separated values format (TSV)
182 =================================
183
184 Basic tab delimited format.
185
186
187 Example Output
188 --------------
189
190 ::
191
192 P51587 14086411a2cdf1c4cba63020e1622579 3418 Pfam PF09103 BRCA2, oligonucleotide/oligosaccharide-binding, domain 1 2670 2799 7.9E-43 T 15-03-2013
193 P51587 14086411a2cdf1c4cba63020e1622579 3418 ProSiteProfiles PS50138 BRCA2 repeat profile. 1002 1036 0.0 T 18-03-2013 IPR002093 BRCA2 repeat GO:0005515|GO:0006302
194 P51587 14086411a2cdf1c4cba63020e1622579 3418 Gene3D G3DSA:2.40.50.140 2966 3051 3.1E-52 T 15-03-2013
195 ...
196
197
198 The TSV format presents the match data in columns as follows:
199
200 - Protein Accession (e.g. P51587)
201 - Sequence MD5 digest (e.g. 14086411a2cdf1c4cba63020e1622579)
202 - Sequence Length (e.g. 3418)
203 - Analysis (e.g. Pfam / PRINTS / Gene3D)
204 - Signature Accession (e.g. PF09103 / G3DSA:2.40.50.140)
205 - Signature Description (e.g. BRCA2 repeat profile)
206 - Start location
207 - Stop location
208 - Score - is the e-value of the match reported by member database method (e.g. 3.1E-52)
209 - Status - is the status of the match (T: true)
210 - Date - is the date of the run
211 - (InterProScan_ annotations - accession (e.g. IPR002093) - optional column; only displayed if -iprscan option is switched on)
212 - (InterProScan_ annotations - description (e.g. BRCA2 repeat) - optional column; only displayed if -iprscan option is switched on)
213 - (GO annotations (e.g. GO:0005515) - optional column; only displayed if --goterms option is switched on)
214 - (Pathways annotations (e.g. REACT_71) - optional column; only displayed if --pathways option is switched on)
215
216
217 Extensible Markup Language (XML)
218 ================================
219
220 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].
221
222 Example Output
223 --------------
224
225 .. image:: $PATH_TO_IMAGES/example_xml_output.png
226
227
228
229 Generic Feature Format Version 3 (GFF3)
230 =======================================
231
232 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].
233
234 Example Output
235 --------------
236
237 ::
238
239 ##gff-version 3
240 ##feature-ontology http://song.cvs.sourceforge.net/viewvc/song/ontology/sofa.obo?revision=1.269
241 ##sequence-region AACH01000027 1 1347
242 ##seqid|source|type|start|end|score|strand|phase|attributes
243 AACH01000027 provided_by_user nucleic_acid 1 1347 . + . Name=AACH01000027;md5=b2a7416cb92565c004becb7510f46840;ID=AACH01000027
244 AACH01000027 getorf ORF 1 1347 . + . Name=AACH01000027.2_21;Target=pep_AACH01000027_1_1347 1 449;md5=b2a7416cb92565c004becb7510f46840;ID=orf_AACH01000027_1_1347
245 AACH01000027 getorf polypeptide 1 449 . + . md5=fd0743a673ac69fb6e5c67a48f264dd5;ID=pep_AACH01000027_1_1347
246 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"
247 ##sequence-region 2
248 ...
249 >pep_AACH01000027_1_1347
250 LVLLAAFDCIDDTKLVKQIIISEIINSLPNIVNDKYGRKVLLYLLSPRDPAHTVREIIEV
251 LQKGDGNAHSKKDTEIRRREMKYKRIVFKVGTSSLTNEDGSLSRSKVKDITQQLAMLHEA
252 GHELILVSSGAIAAGFGALGFKKRPTKIADKQASAAVGQGLLLEEYTTNLLLRQIVSAQI
253 LLTQDDFVDKRRYKNAHQALSVLLNRGAIPIINENDSVVIDELKVGDNDTLSAQVAAMVQ
254 ADLLVFLTDVDGLYTGNPNSDPRAKRLERIETINREIIDMAGGAGSSNGTGGMLTKIKAA
255 TIATESGVPVYICSSLKSDSMIEAAEETEDGSYFVAQEKGLRTQKQWLAFYAQSQGSIWV
256 DKGAAEALSQYGKSLLLSGIVEAEGVFSYGDIVTVFDKESGKSLGKGRVQFGASALEDML
257 RSQKAKGVLIYRDDWISITPEIQLLFTEF
258 ...
259 >match$8_84_314
260 KRIVFKVGTSSLTNEDGSLSRSKVKDITQQLAMLHEAGHELILVSSGAIAAGFGALGFKK
261 RPTKIADKQASAAVGQGLLLEEYTTNLLLRQIVSAQILLTQDDFVDKRRYKNAHQALSVL
262 LNRGAIPIINENDSVVIDELKVGDNDTLSAQVAAMVQADLLVFLTDVDGLYTGNPNSDPR
263 AKRLERIETINREIIDMAGGAGSSNGTGGMLTKIKAATIATESGVPVYICS
264
265
266 Scalable Vector Graphics (SVG) and HyperText Markup Language (HTML)
267 ====================================================================
268
269 InterProScan_ 5 outputs a single HTML/SVG file for each protein sequence analysed.
270
271
272 Example Output
273 --------------
274
275 .. image:: $PATH_TO_IMAGES/P51587.svg.png
276
277 .. _InterProScan: http://www.ebi.ac.uk/interpro
278
279
280 ----------
281 References
282 ----------
283
284
285 If you use this Galaxy tool in work leading to a scientific publication please
286 cite the following papers:
287
288 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
289 Galaxy tools and workflows for sequence analysis with applications
290 in molecular plant pathology. PeerJ 1:e167
291 http://dx.doi.org/10.7717/peerj.167
292
293 Zdobnov EM, Apweiler R (2001)
294 InterProScan an integration platform for the signature-recognition methods in InterPro.
295 Bioinformatics 17, 847-848.
296 http://dx.doi.org/10.1093/bioinformatics/17.9.847
297
298 Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R (2005)
299 InterProScan: protein domains identifier.
300 Nucleic Acids Research 33 (Web Server issue), W116-W120.
301 http://dx.doi.org/10.1093/nar/gki442
302
303 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)
304 InterPro: the integrative protein signature database.
305 Nucleic Acids Research 37 (Database Issue), D224-228.
306 http://dx.doi.org/10.1093/nar/gkn785
307
308
309 This wrapper is available to install into other Galaxy Instances via the Galaxy Tool Shed at
310 http://toolshed.g2.bx.psu.edu/view/bgruening/interproscan5
311
312
313 **Galaxy Wrapper Author**::
314
315 * Bjoern Gruening, University of Freiburg
316 * Konrad Paszkiewicz, University of Exeter
317
318 </help>
319 </tool>