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comparison interproscan5/ipsfaux.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="ipsfaux" name="Faux Interproscan" version="1.0.2a">
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 "Start timestamp: \$(date)";
16 python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/fake_ips.py
17 ## disables the precalculated lookup service, all calculation will be run locally
18 -dp
19 --input $infile
20 --seqtype $seqtype
21 -f tsv,$output_types
22 --applications $appl
23
24 $pathways
25 $goterms
26 $iprlookup
27 $mode
28 --output-file-base __base__
29 2>&#38;1;
30
31 mv __base__.tsv $tsv_file;
32
33 #if 'gff3' in str($output_types):
34 mv __base__.gff3 $gff3_file;
35 #end if
36
37 #if 'xml' in str($output_types):
38 mv __base__.xml $xml_file;
39 #end if
40
41 #if 'html' in str($output_types):
42 mkdir -p $html_file.files_path;
43 #set temp_archive_file = '__base__.html.tar.gz'
44 tar -C $html_file.files_path -xvmzf $temp_archive_file;
45 #if str($seqtype) == 'p' and not str($getorfed):
46 python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_html_index.py 0 $tsv_file $html_file $html_file.files_path;
47 #else
48 python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_html_index.py 1 $tsv_file $html_file $html_file.files_path;
49 #end if
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 $temp_archive_file;
57 #if str($seqtype) == 'p' and not str($getorfed):
58 python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_html_index.py 0 $tsv_file $svg_file $svg_file.files_path;
59 #else
60 python \$INTERPROSCAN_SCRIPT_PATH/interproscan5/create_html_index.py 1 $tsv_file $svg_file $svg_file.files_path;
61 #end if
62 rm $temp_archive_file;
63 #end if
64
65 echo "End timestamp: \$(date)"
66 </command>
67
68 <inputs>
69 <param name="infile" type="data" format="fasta" label="Sequence Fasta File (ignored -- faux mode)"/>
70
71 <param name="seqtype" type="select" label="Type of the input sequences" help="">
72 <option value="p" selected="true">Protein</option>
73 <option value="n">DNA / RNA</option>
74 </param>
75
76 <param name="getorfed" type="boolean" label="DNA/RNA was externally processed by getorf?" help="Ignored for DNA inputs."
77 truevalue="getorfed"
78 falsevalue=""/>
79
80 <param name="mode" type="boolean" label="Run on cluster?" help="Check to submit job to cluster."
81 truevalue="--mode=cluster --clusterrunid=gtdi-ips-analysis"
82 falsevalue=""/>
83
84 <param name="appl" type="select" multiple="True" display="checkboxes" label="Applications to run"
85 help="Select your programm.">
86 <option value="TIGRFAM"
87 selected="true">TIGRFAM: protein families based on Hidden Markov Models or HMMs</option>
88 <option value="PIRSF" selected="true">PIRSF: non-overlapping clustering of UniProtKB sequences into a hierarchical order (evolutionary relationships)</option>
89 <option value="ProDom"
90 selected="true">ProDom: set of protein domain families generated from the UniProtKB</option>
91 <option value="Panther"
92 selected="true">Panther: Protein ANalysis THrough Evolutionary Relationships</option>
93 <option value="SMART" selected="true">SMART: identification and analysis of domain architectures based on Hidden Markov Models or HMMs</option>
94 <option value="PrositeProfiles" selected="true">PROSITE Profiles: protein domains, families and functional sites as well as associated profiles to identify them</option>
95 <option value="PrositePatterns" selected="true">PROSITE Pattern: protein domains, families and functional sites as well as associated patterns to identify them</option>
96 <option value="HAMAP"
97 selected="true">HAMAP: High-quality Automated Annotation of Microbial Proteomes</option>
98 <option value="PfamA" selected="true">PfamA: protein families, each represented by multiple sequence alignments and hidden Markov models</option>
99 <option value="PRINTS" selected="true">PRINTS: group of conserved motifs (fingerprints) used to characterise a protein family</option>
100 <option value="SuperFamily"
101 selected="true">SUPERFAMILY: database of structural and functional annotation</option>
102 <option value="Coils" selected="true">Coils: Prediction of Coiled Coil Regions in Proteins</option>
103 <option value="Gene3d" selected="true">Gene3d: Structural assignment for whole genes and genomes using the CATH domain structure database</option>
104 <option value="SignalP-GRAM_POSITIVE" selected="false">SignalP Gram Positive Bacteria</option>
105 <option value="SignalP-GRAM_NEGATIVE" selected="false">SignalP Gram Negative Bacteria</option>
106 <option value="SignalP-EUK" selected="false">SignalP Eukaryotic Bacteria</option>
107 <option value="Phobius" selected="false">Phobius: combined transmembrane topology and signal peptide predictor</option>
108 <option value="TMHMM" selected="false">TMHMM: Prediction of transmembrane helices in proteins</option>
109 </param>
110
111 <param name="pathways" truevalue="--pathways" falsevalue="" checked="True" type="boolean"
112 label="Include pathway information"
113 help="Option that provides mappings from matches to pathway information, which is based on the matched manually curated InterPro entries. (--pathways)"/>
114 <param name="goterms" truevalue="--goterms" falsevalue="" checked="True" type="boolean"
115 label="Include Gene Ontology (GO) mappings"
116 help="Look up of corresponding Gene Ontology annotation. Implies -iprlookup option. (--goterms)"/>
117
118 <param name="iprlookup" truevalue="--iprlookup" falsevalue="" checked="False" type="boolean"
119 label="Provide additional mappings"
120 help="Provide mappings from matched member database signatures to the InterPro entries that they are integrated into (--iprlookup)"/>
121
122 <param name="output_types" type="select" display="checkboxes" multiple="true" label="Output formats (in addition to TSV)"
123 help="Select the output formats to generate (at least one)">
124 <option value="html" selected="true">HTML (Graphical)</option>
125 <option value="svg" selected="false">SVG (Scalable Vector Graphics)</option>
126 <option value="gff3" selected="true">GFF3</option>
127 <option value="xml" selected="false">XML</option>
128 </param>
129 </inputs>
130
131 <outputs>
132 <data format="tabular" name="tsv_file" label="Interproscan TSV on ${on_string}"/>
133 <data format="html" name="html_file" label="Interproscan HTML on ${on_string}">
134 <filter>'html' in output_types</filter>
135 </data>
136 <data format="html" name="svg_file" label="Interproscan SVG on ${on_string}">
137 <filter>'svg' in output_types</filter>
138 </data>
139 <data format="gff3" name="gff3_file" label="Interproscan GFF3 on ${on_string}">
140 <filter>'gff3' in output_types</filter>
141 </data>
142 <data format="xml" name="xml_file" label="Interproscan XML on ${on_string}">
143 <filter>'xml' in output_types</filter>
144 </data>
145 </outputs>
146
147 <requirements>
148 </requirements>
149
150 <help>
151
152 **What it does**
153
154 Interproscan is a batch tool to query the Interpro database. It provides annotations based on multiple searches of profile and other functional databases.
155
156
157 #####
158 Input
159 #####
160
161 Required is a FASTA file containing protein or nucleotide sequences.
162
163
164 ######
165 Output
166 ######
167
168 In this version of InterProScan_, you can retrieve output in any of the following five formats:
169
170 * TSV: a simple tab-delimited file format
171 * XML: the new "IMPACT" XML format (XSD available here_).
172 * GFF: The `GFF 3.0`_ format
173 * HTML: An HTML representation of the protein matches
174 * SVG: An Scalable Vector Graphics representation of the protein matches
175
176
177 .. _`GFF 3.0`: http://gmod.org/wiki/GFF#GFF3_Format
178 .. _here: http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5
179
180
181
182 Tab-separated values format (TSV)
183 =================================
184
185 Basic tab delimited format.
186
187
188 Example Output
189 --------------
190
191 ::
192
193 P51587 14086411a2cdf1c4cba63020e1622579 3418 Pfam PF09103 BRCA2, oligonucleotide/oligosaccharide-binding, domain 1 2670 2799 7.9E-43 T 15-03-2013
194 P51587 14086411a2cdf1c4cba63020e1622579 3418 ProSiteProfiles PS50138 BRCA2 repeat profile. 1002 1036 0.0 T 18-03-2013 IPR002093 BRCA2 repeat GO:0005515|GO:0006302
195 P51587 14086411a2cdf1c4cba63020e1622579 3418 Gene3D G3DSA:2.40.50.140 2966 3051 3.1E-52 T 15-03-2013
196 ...
197
198
199 The TSV format presents the match data in columns as follows:
200
201 - Protein Accession (e.g. P51587)
202 - Sequence MD5 digest (e.g. 14086411a2cdf1c4cba63020e1622579)
203 - Sequence Length (e.g. 3418)
204 - Analysis (e.g. Pfam / PRINTS / Gene3D)
205 - Signature Accession (e.g. PF09103 / G3DSA:2.40.50.140)
206 - Signature Description (e.g. BRCA2 repeat profile)
207 - Start location
208 - Stop location
209 - Score - is the e-value of the match reported by member database method (e.g. 3.1E-52)
210 - Status - is the status of the match (T: true)
211 - Date - is the date of the run
212 - (InterProScan_ annotations - accession (e.g. IPR002093) - optional column; only displayed if -iprscan option is switched on)
213 - (InterProScan_ annotations - description (e.g. BRCA2 repeat) - optional column; only displayed if -iprscan option is switched on)
214 - (GO annotations (e.g. GO:0005515) - optional column; only displayed if --goterms option is switched on)
215 - (Pathways annotations (e.g. REACT_71) - optional column; only displayed if --pathways option is switched on)
216
217
218 Extensible Markup Language (XML)
219 ================================
220
221 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].
222
223 Example Output
224 --------------
225
226 .. image:: $PATH_TO_IMAGES/example_xml_output.png
227
228
229
230 Generic Feature Format Version 3 (GFF3)
231 =======================================
232
233 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].
234
235 Example Output
236 --------------
237
238 ::
239
240 ##gff-version 3
241 ##feature-ontology http://song.cvs.sourceforge.net/viewvc/song/ontology/sofa.obo?revision=1.269
242 ##sequence-region AACH01000027 1 1347
243 ##seqid|source|type|start|end|score|strand|phase|attributes
244 AACH01000027 provided_by_user nucleic_acid 1 1347 . + . Name=AACH01000027;md5=b2a7416cb92565c004becb7510f46840;ID=AACH01000027
245 AACH01000027 getorf ORF 1 1347 . + . Name=AACH01000027.2_21;Target=pep_AACH01000027_1_1347 1 449;md5=b2a7416cb92565c004becb7510f46840;ID=orf_AACH01000027_1_1347
246 AACH01000027 getorf polypeptide 1 449 . + . md5=fd0743a673ac69fb6e5c67a48f264dd5;ID=pep_AACH01000027_1_1347
247 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"
248 ##sequence-region 2
249 ...
250 >pep_AACH01000027_1_1347
251 LVLLAAFDCIDDTKLVKQIIISEIINSLPNIVNDKYGRKVLLYLLSPRDPAHTVREIIEV
252 LQKGDGNAHSKKDTEIRRREMKYKRIVFKVGTSSLTNEDGSLSRSKVKDITQQLAMLHEA
253 GHELILVSSGAIAAGFGALGFKKRPTKIADKQASAAVGQGLLLEEYTTNLLLRQIVSAQI
254 LLTQDDFVDKRRYKNAHQALSVLLNRGAIPIINENDSVVIDELKVGDNDTLSAQVAAMVQ
255 ADLLVFLTDVDGLYTGNPNSDPRAKRLERIETINREIIDMAGGAGSSNGTGGMLTKIKAA
256 TIATESGVPVYICSSLKSDSMIEAAEETEDGSYFVAQEKGLRTQKQWLAFYAQSQGSIWV
257 DKGAAEALSQYGKSLLLSGIVEAEGVFSYGDIVTVFDKESGKSLGKGRVQFGASALEDML
258 RSQKAKGVLIYRDDWISITPEIQLLFTEF
259 ...
260 >match$8_84_314
261 KRIVFKVGTSSLTNEDGSLSRSKVKDITQQLAMLHEAGHELILVSSGAIAAGFGALGFKK
262 RPTKIADKQASAAVGQGLLLEEYTTNLLLRQIVSAQILLTQDDFVDKRRYKNAHQALSVL
263 LNRGAIPIINENDSVVIDELKVGDNDTLSAQVAAMVQADLLVFLTDVDGLYTGNPNSDPR
264 AKRLERIETINREIIDMAGGAGSSNGTGGMLTKIKAATIATESGVPVYICS
265
266
267 Scalable Vector Graphics (SVG) and HyperText Markup Language (HTML)
268 ====================================================================
269
270 InterProScan_ 5 outputs a single HTML/SVG file for each protein sequence analysed.
271
272
273 Example Output
274 --------------
275
276 .. image:: $PATH_TO_IMAGES/P51587.svg.png
277
278 .. _InterProScan: http://www.ebi.ac.uk/interpro
279
280
281 ----------
282 References
283 ----------
284
285
286 If you use this Galaxy tool in work leading to a scientific publication please
287 cite the following papers:
288
289 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
290 Galaxy tools and workflows for sequence analysis with applications
291 in molecular plant pathology. PeerJ 1:e167
292 http://dx.doi.org/10.7717/peerj.167
293
294 Zdobnov EM, Apweiler R (2001)
295 InterProScan an integration platform for the signature-recognition methods in InterPro.
296 Bioinformatics 17, 847-848.
297 http://dx.doi.org/10.1093/bioinformatics/17.9.847
298
299 Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R (2005)
300 InterProScan: protein domains identifier.
301 Nucleic Acids Research 33 (Web Server issue), W116-W120.
302 http://dx.doi.org/10.1093/nar/gki442
303
304 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)
305 InterPro: the integrative protein signature database.
306 Nucleic Acids Research 37 (Database Issue), D224-228.
307 http://dx.doi.org/10.1093/nar/gkn785
308
309
310 This wrapper is available to install into other Galaxy Instances via the Galaxy Tool Shed at
311 http://toolshed.g2.bx.psu.edu/view/bgruening/interproscan5
312
313
314 **Galaxy Wrapper Author**::
315
316 * Bjoern Gruening, University of Freiburg
317 * Konrad Paszkiewicz, University of Exeter
318
319 </help>
320 </tool>