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comparison interproscan5/ipsfaux.xml @ 0:fe8e43a26870 draft

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date Thu, 28 Jan 2016 19:34:51 -0500
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1 <tool id="ipsfaux" name="Interproscan functional predictions of ORFs (faux)" version="1.0.0a">
2 <description>Interproscan functional predictions of ORFs (faux). Input file and computation options are
3 ignored (other than the types of outputs). The same precomputed results are produced every time.</description>
4 <requirements>
5 <!--
6 <requirement type="package">signalp</requirement>
7 <requirement type="package">phobius</requirement>
8 <requirement type="package">tmhmm</requirement>
9 -->
10 <requirement type="set_environment">INTERPROSCAN_SCRIPT_PATH</requirement>
11 </requirements>
12
13 <command>
14 #import os
15 echo "output_types=$output_types";
16
17 python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/fake_ips.py
18 ## disables the precalculated lookup service, all calculation will be run locally
19 -dp
20 --input $infile
21 --seqtype $seqtype
22 -f $output_types
23 --applications $appl
24 --tempdir \$TEMP
25
26 $pathways
27 $goterms
28 $iprlookup
29 $mode
30 --output-file-base __base__
31 2>&#38;1;
32
33 #if 'tsv' in str($output_types):
34 mv __base__.tsv $tsv_file;
35 #end if
36
37 #if 'gff3' in str($output_types):
38 mv __base__.gff3 $gff3_file;
39 #end if
40
41 #if 'xml' in str($output_types):
42 mv __base__.xml $xml_file;
43 #end if
44
45 #if 'html' in str($output_types):
46 mkdir -p $html_file.files_path;
47 #set temp_archive_file = '__base__.html.tar.gz'
48 tar -C $html_file.files_path -xvmzf $temp_archive_file;
49 python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_index.py $html_file $html_file.files_path;
50 rm $temp_archive_file;
51 #end if
52
53 #if 'svg' in str($output_types):
54 mkdir -p $svg_file.files_path;
55 #set temp_archive_file = '__base__.svg.tar.gz'
56 tar -C $svg_file.files_path -xvmzf $temp_archive_file;
57 python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_index.py $svg_file $svg_file.files_path;
58 rm $temp_archive_file;
59 #end if
60
61 echo "End of ipsfaux"
62 </command>
63
64 <inputs>
65 <param name="infile" type="data" format="fasta" label="Sequence Fasta File (ignored -- faux mode)"/>
66
67 <param name="seqtype" type="select" label="Type of the input sequences" help="">
68 <option value="p" selected="true">Protein</option>
69 <option value="n">DNA / RNA</option>
70 </param>
71
72 <param name="mode" type="boolean" label="Run on cluster?" help="Check to submit job to cluster."
73 truevalue="--mode=cluster --clusterrunid=gtdi-ips-analysis"
74 falsevalue=""/>
75
76 <param name="appl" type="select" multiple="True" display="checkboxes" label="Applications to run"
77 help="Select your programm.">
78 <option value="TIGRFAM"
79 selected="true">TIGRFAM: protein families based on Hidden Markov Models or HMMs</option>
80 <option value="PIRSF" selected="true">PIRSF: non-overlapping clustering of UniProtKB sequences into a hierarchical order (evolutionary relationships)</option>
81 <option value="ProDom"
82 selected="true">ProDom: set of protein domain families generated from the UniProtKB</option>
83 <option value="Panther"
84 selected="true">Panther: Protein ANalysis THrough Evolutionary Relationships</option>
85 <option value="SMART" selected="true">SMART: identification and analysis of domain architectures based on Hidden Markov Models or HMMs</option>
86 <option value="PrositeProfiles" selected="true">PROSITE Profiles: protein domains, families and functional sites as well as associated profiles to identify them</option>
87 <option value="PrositePatterns" selected="true">PROSITE Pattern: protein domains, families and functional sites as well as associated patterns to identify them</option>
88 <option value="HAMAP"
89 selected="true">HAMAP: High-quality Automated Annotation of Microbial Proteomes</option>
90 <option value="PfamA" selected="true">PfamA: protein families, each represented by multiple sequence alignments and hidden Markov models</option>
91 <option value="PRINTS" selected="true">PRINTS: group of conserved motifs (fingerprints) used to characterise a protein family</option>
92 <option value="SuperFamily"
93 selected="true">SUPERFAMILY: database of structural and functional annotation</option>
94 <option value="Coils" selected="true">Coils: Prediction of Coiled Coil Regions in Proteins</option>
95 <option value="Gene3d" selected="true">Gene3d: Structural assignment for whole genes and genomes using the CATH domain structure database</option>
96 <option value="SignalP-GRAM_POSITIVE" selected="false">SignalP Gram Positive Bacteria</option>
97 <option value="SignalP-GRAM_NEGATIVE" selected="false">SignalP Gram Negative Bacteria</option>
98 <option value="SignalP-EUK" selected="false">SignalP Eukaryotic Bacteria</option>
99 <option value="Phobius" selected="false">Phobius: combined transmembrane topology and signal peptide predictor</option>
100 <option value="TMHMM" selected="false">TMHMM: Prediction of transmembrane helices in proteins</option>
101 </param>
102
103 <param name="pathways" truevalue="--pathways" falsevalue="" checked="True" type="boolean"
104 label="Include pathway information"
105 help="Option that provides mappings from matches to pathway information, which is based on the matched manually curated InterPro entries. (--pathways)"/>
106 <param name="goterms" truevalue="--goterms" falsevalue="" checked="True" type="boolean"
107 label="Include Gene Ontology (GO) mappings"
108 help="Look up of corresponding Gene Ontology annotation. Implies -iprlookup option. (--goterms)"/>
109
110 <param name="iprlookup" truevalue="--iprlookup" falsevalue="" checked="False" type="boolean"
111 label="Provide additional mappings"
112 help="Provide mappings from matched member database signatures to the InterPro entries that they are integrated into (--iprlookup)"/>
113
114 <param name="output_types" type="select" display="checkboxes" multiple="true" label="Output formats"
115 help="Select the output formats to generate (at least one)">
116 <option value="tsv" selected="true">Raw (TSV)</option>
117 <option value="html" selected="true">HTML (Graphical)</option>
118 <option value="svg" selected="false">SVG (Scalable Vector Graphics)</option>
119 <option value="gff3" selected="true">GFF3</option>
120 <option value="xml" selected="false">XML</option>
121 </param>
122 </inputs>
123
124 <outputs>
125 <data format="tabular" name="tsv_file" label="Interproscan TSV on ${on_string}">
126 <filter>'tsv' in output_types</filter>
127 </data>
128 <data format="html" name="html_file" label="Interproscan HTML on ${on_string}">
129 <filter>'html' in output_types</filter>
130 </data>
131 <data format="html" name="svg_file" label="Interproscan SVG on ${on_string}">
132 <filter>'svg' in output_types</filter>
133 </data>
134 <data format="gff3" name="gff3_file" label="Interproscan GFF3 on ${on_string}">
135 <filter>'gff3' in output_types</filter>
136 </data>
137 <data format="xml" name="xml_file" label="Interproscan XML on ${on_string}">
138 <filter>'xml' in output_types</filter>
139 </data>
140 </outputs>
141
142 <requirements>
143 </requirements>
144
145 <help>
146
147 **What it does**
148
149 Interproscan is a batch tool to query the Interpro database. It provides annotations based on multiple searches of profile and other functional databases.
150
151
152 #####
153 Input
154 #####
155
156 Required is a FASTA file containing protein or nucleotide sequences.
157
158
159 ######
160 Output
161 ######
162
163 In this version of InterProScan_, you can retrieve output in any of the following five formats:
164
165 * TSV: a simple tab-delimited file format
166 * XML: the new "IMPACT" XML format (XSD available here_).
167 * GFF: The `GFF 3.0`_ format
168 * HTML: An HTML representation of the protein matches
169 * SVG: An Scalable Vector Graphics representation of the protein matches
170
171
172 .. _`GFF 3.0`: http://gmod.org/wiki/GFF#GFF3_Format
173 .. _here: http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5
174
175
176
177 Tab-separated values format (TSV)
178 =================================
179
180 Basic tab delimited format.
181
182
183 Example Output
184 --------------
185
186 ::
187
188 P51587 14086411a2cdf1c4cba63020e1622579 3418 Pfam PF09103 BRCA2, oligonucleotide/oligosaccharide-binding, domain 1 2670 2799 7.9E-43 T 15-03-2013
189 P51587 14086411a2cdf1c4cba63020e1622579 3418 ProSiteProfiles PS50138 BRCA2 repeat profile. 1002 1036 0.0 T 18-03-2013 IPR002093 BRCA2 repeat GO:0005515|GO:0006302
190 P51587 14086411a2cdf1c4cba63020e1622579 3418 Gene3D G3DSA:2.40.50.140 2966 3051 3.1E-52 T 15-03-2013
191 ...
192
193
194 The TSV format presents the match data in columns as follows:
195
196 - Protein Accession (e.g. P51587)
197 - Sequence MD5 digest (e.g. 14086411a2cdf1c4cba63020e1622579)
198 - Sequence Length (e.g. 3418)
199 - Analysis (e.g. Pfam / PRINTS / Gene3D)
200 - Signature Accession (e.g. PF09103 / G3DSA:2.40.50.140)
201 - Signature Description (e.g. BRCA2 repeat profile)
202 - Start location
203 - Stop location
204 - Score - is the e-value of the match reported by member database method (e.g. 3.1E-52)
205 - Status - is the status of the match (T: true)
206 - Date - is the date of the run
207 - (InterProScan_ annotations - accession (e.g. IPR002093) - optional column; only displayed if -iprscan option is switched on)
208 - (InterProScan_ annotations - description (e.g. BRCA2 repeat) - optional column; only displayed if -iprscan option is switched on)
209 - (GO annotations (e.g. GO:0005515) - optional column; only displayed if --goterms option is switched on)
210 - (Pathways annotations (e.g. REACT_71) - optional column; only displayed if --pathways option is switched on)
211
212
213 Extensible Markup Language (XML)
214 ================================
215
216 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].
217
218 Example Output
219 --------------
220
221 .. image:: $PATH_TO_IMAGES/example_xml_output.png
222
223
224
225 Generic Feature Format Version 3 (GFF3)
226 =======================================
227
228 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].
229
230 Example Output
231 --------------
232
233 ::
234
235 ##gff-version 3
236 ##feature-ontology http://song.cvs.sourceforge.net/viewvc/song/ontology/sofa.obo?revision=1.269
237 ##sequence-region AACH01000027 1 1347
238 ##seqid|source|type|start|end|score|strand|phase|attributes
239 AACH01000027 provided_by_user nucleic_acid 1 1347 . + . Name=AACH01000027;md5=b2a7416cb92565c004becb7510f46840;ID=AACH01000027
240 AACH01000027 getorf ORF 1 1347 . + . Name=AACH01000027.2_21;Target=pep_AACH01000027_1_1347 1 449;md5=b2a7416cb92565c004becb7510f46840;ID=orf_AACH01000027_1_1347
241 AACH01000027 getorf polypeptide 1 449 . + . md5=fd0743a673ac69fb6e5c67a48f264dd5;ID=pep_AACH01000027_1_1347
242 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"
243 ##sequence-region 2
244 ...
245 >pep_AACH01000027_1_1347
246 LVLLAAFDCIDDTKLVKQIIISEIINSLPNIVNDKYGRKVLLYLLSPRDPAHTVREIIEV
247 LQKGDGNAHSKKDTEIRRREMKYKRIVFKVGTSSLTNEDGSLSRSKVKDITQQLAMLHEA
248 GHELILVSSGAIAAGFGALGFKKRPTKIADKQASAAVGQGLLLEEYTTNLLLRQIVSAQI
249 LLTQDDFVDKRRYKNAHQALSVLLNRGAIPIINENDSVVIDELKVGDNDTLSAQVAAMVQ
250 ADLLVFLTDVDGLYTGNPNSDPRAKRLERIETINREIIDMAGGAGSSNGTGGMLTKIKAA
251 TIATESGVPVYICSSLKSDSMIEAAEETEDGSYFVAQEKGLRTQKQWLAFYAQSQGSIWV
252 DKGAAEALSQYGKSLLLSGIVEAEGVFSYGDIVTVFDKESGKSLGKGRVQFGASALEDML
253 RSQKAKGVLIYRDDWISITPEIQLLFTEF
254 ...
255 >match$8_84_314
256 KRIVFKVGTSSLTNEDGSLSRSKVKDITQQLAMLHEAGHELILVSSGAIAAGFGALGFKK
257 RPTKIADKQASAAVGQGLLLEEYTTNLLLRQIVSAQILLTQDDFVDKRRYKNAHQALSVL
258 LNRGAIPIINENDSVVIDELKVGDNDTLSAQVAAMVQADLLVFLTDVDGLYTGNPNSDPR
259 AKRLERIETINREIIDMAGGAGSSNGTGGMLTKIKAATIATESGVPVYICS
260
261
262 Scalable Vector Graphics (SVG) and HyperText Markup Language (HTML)
263 ====================================================================
264
265 InterProScan_ 5 outputs a single HTML/SVG file for each protein sequence analysed.
266
267
268 Example Output
269 --------------
270
271 .. image:: $PATH_TO_IMAGES/P51587.svg.png
272
273 .. _InterProScan: http://www.ebi.ac.uk/interpro
274
275
276 ----------
277 References
278 ----------
279
280
281 If you use this Galaxy tool in work leading to a scientific publication please
282 cite the following papers:
283
284 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
285 Galaxy tools and workflows for sequence analysis with applications
286 in molecular plant pathology. PeerJ 1:e167
287 http://dx.doi.org/10.7717/peerj.167
288
289 Zdobnov EM, Apweiler R (2001)
290 InterProScan an integration platform for the signature-recognition methods in InterPro.
291 Bioinformatics 17, 847-848.
292 http://dx.doi.org/10.1093/bioinformatics/17.9.847
293
294 Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R (2005)
295 InterProScan: protein domains identifier.
296 Nucleic Acids Research 33 (Web Server issue), W116-W120.
297 http://dx.doi.org/10.1093/nar/gki442
298
299 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)
300 InterPro: the integrative protein signature database.
301 Nucleic Acids Research 37 (Database Issue), D224-228.
302 http://dx.doi.org/10.1093/nar/gkn785
303
304
305 This wrapper is available to install into other Galaxy Instances via the Galaxy Tool Shed at
306 http://toolshed.g2.bx.psu.edu/view/bgruening/interproscan5
307
308
309 **Galaxy Wrapper Author**::
310
311 * Bjoern Gruening, University of Freiburg
312 * Konrad Paszkiewicz, University of Exeter
313
314 </help>
315 </tool>