Mercurial > repos > bgruening > interproscan

comparison interproscan.xml @ 0:c10e37cca7e3 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author bgruening
date Tue, 25 Jun 2013 06:29:45 -0400
parents
children eb12db502d3c
comparison
equal deleted inserted replaced
-1:000000000000 0:c10e37cca7e3
1 <tool id="interproscan" name="Interproscan functional predictions of ORFs" version="1.2">
2 <description>Interproscan functional predictions of ORFs</description>
3 <command>
4 ## The command is a Cheetah template which allows some Python based syntax.
5 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
6
7 ## create temp directory
8 #import tempfile, os
9 #set $tfile = tempfile.mkstemp()[1]
10
11 sed 's/ /_/g' $input > $tfile;
12
13 ## Hack, because interproscan does not seem to produce gff output even if it is configured
14 #if str($oformat) == "gff":
15 #set $tfile2 = tempfile.mkstemp()[1]
16 iprscan -cli -nocrc -i $tfile -o $tfile2 -goterms -seqtype p -altjobs -format raw -appl $appl 2>&#38;1;
17 converter.pl -format gff3 -input $tfile2 -output $output;
18 rm $tfile2;
19 #else
20 iprscan -cli -nocrc -i $tfile -o $output -goterms -seqtype p -altjobs -format $oformat -appl $appl 2>&#38;1;
21 #end if
22
23 rm $tfile
24
25 </command>
26 <inputs>
27 <param name="input" type="data" format="fasta" label="Protein Fasta File"/>
28
29 <param name="appl" type="select" format="text" label="Applications to run" help="Select your programm.">
30 <option value="blastprodom+coils+gene3d+hamap+hmmpanther+hmmpir+hmmpfam+hmmsmart+hmmtigr+fprintscan+patternscan+profilescan+superfamily+seg+signalp+tmhmm" selected="true">all</option>
31 <option value="seg">seg</option>
32 <option value="signalp">signalp</option>
33 <option value="tmhmm">tmhmm</option>
34 <option value="fprintscan">fprintscan</option>
35 <option value="patternscan">patternscan</option>
36 <option value="profilescan">profilescan</option>
37 <option value="superfamily">superfamily</option>
38 <option value="hmmpir">hmmpir</option>
39 <option value="hmmpfam">hmmpfam</option>
40 <option value="hmmsmart">hmmsmart</option>
41 <option value="hmmtigr">hmmtigr</option>
42 <option value="hmmpanther">hmmpanther</option>
43 <option value="hamap">hamap</option>
44 <option value="gene3d">gene3d</option>
45 <option value="coils">coils</option>
46 <option value="blastprodom">blastprodom</option>
47 </param>
48
49 <param name="oformat" type="select" label="Output format" help="Please select a output format.">
50 <option value="gff">gff</option>
51 <option value="raw" selected="true">raw</option>
52 <option value="txt">txt</option>
53 <option value="html">html</option>
54 <option value="xml">xml</option>
55 <option value="ebixml">EBI header on top of xml</option>
56 </param>
57
58 </inputs>
59 <outputs>
60
61 <data format="txt" name="output" label="Interproscan calculation on ${on_string}">
62 <change_format>
63 <when input="oformat" value="html" format="html"/>
64 <when input="oformat" value="xml" format="xml"/>
65 <when input="oformat" value="ebixml" format="xml"/>
66 <when input="oformat" value="gff" format="gff"/>
67 </change_format>
68 </data>
69
70 </outputs>
71 <requirements>
72 </requirements>
73 <help>
74 **What it does**
75
76 Interproscan is a batch tool to query the Interpro database. It provides annotations based on multiple searches of profile and other functional databases.
77 These include SCOP, CATH, PFAM and SUPERFAMILY.
78
79 **Input**
80
81 Required is a FASTA file containing ORF predictions. This file must NOT contain any spaces in the FASTA headers - any spaces will be convereted to underscores ``_`` by this tool before running with Interproscan.
82
83 **Output**
84
85 Example for the raw format.
86 The output will consist of a tabular file in galaxy with 14 columns and can be easily concatenated or filtered.
87
88 ====== ================================================================ ======================================================================
89 column example description
90 ====== ================================================================ ======================================================================
91 c1 NF00181542 the id of the input sequence
92 c2 27A9BBAC0587AB84 the crc64 (checksum) of the protein sequence (supposed to be unique)
93 c3 272 the length of the sequence (in AA)
94 c4 HMMPIR the anaysis method launched.
95 c5 PIRSF001424 the database members entry for this match
96 c6 Prephenate dehydratase the database member description for the entry
97 c7 1 the start of the domain match
98 c8 270 the end of the domain match
99 c9 6.5e-141 the evalue of the match (reported by member database method)
100 c10 T the status of the match (T: true, ?: unknown)
101 c11 06-Aug-2005 the date of the run.
102 c12 IPR008237 the corresponding InterPro entry (if iprlookup requested by the user)
103 c13 Prephenate dehydratase with ACT region the description of the InterPro entry
104 c14 Molecular Function:prephenate dehydratase activity (GO:0004664) the GO (gene ontology) description for the InterPro entry
105 ====== ================================================================ ======================================================================
106
107 **Database updates**
108
109 Typically these take place 2-3 times a year. Please contact your Galaxy administrator to update the databases.
110
111 -----
112 Tools
113 -----
114
115 **PROSITE patterns**
116 Some biologically significant amino acid patterns can be summarised in
117 the form of regular expressions.
118 ScanRegExp (by Wolfgang.Fleischmann@ebi.ac.uk).
119
120 **PROSITE profiles**
121 There are a number of protein families as well as functional or
122 structural domains that cannot be detected using patterns due to their extreme
123 sequence divergence, so the use of techniques based on weight matrices
124 (also known as profiles) allows the detection of such proteins or domains.
125 A profile is a table of position-specific amino acid weights and gap costs.
126 The profile structure used in PROSITE is similar to but slightly more general
127 (Bucher P. et al., 1996) than the one introduced by M. Gribskov and
128 co-workers.
129 pfscan from the Pftools package (by Philipp.Bucher@isrec.unil.ch).
130
131 **PRINTS**
132 The PRINTS database houses a collection of protein family fingerprints.
133 These are groups of motifs that together are diagnostically more
134 powerful than single motifs by making use of the biological context inherent in a
135 multiple-motif method. The fingerprinting method arose from the need for
136 a reliable technique for detecting members of large, highly divergent
137 protein super-families.
138 FingerPRINTScan (Scordis P. et al., 1999).
139
140 **PFAM**
141 Pfam is a database of protein domain families. Pfam contains curated
142 multiple sequence alignments for each family and corresponding hidden
143 Markov models (HMMs) (Eddy S.R., 1998).
144 Profile hidden Markov models are statistical models of the primary
145 structure consensus of a sequence family. The construction and use
146 of Pfam is tightly tied to the HMMER software package.
147 hmmpfam from the HMMER2.3.2 package (by Sean Eddy,
148 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
149
150 **PRODOM**
151 ProDom is a database of protein domain families obtained by automated
152 analysis of the SWISS-PROT and TrEMBL protein sequences. It is useful
153 for analysing the domain arrangements of complex protein families and the
154 homology relationships in modular proteins. ProDom families are built by
155 an automated process based on a recursive use of PSI-BLAST homology
156 searches.
157 ProDomBlast3i.pl (by Emmanuel Courcelle emmanuel.courcelle@toulouse.inra.fr
158 and Yoann Beausse beausse@toulouse.inra.fr)
159 a wrapper on top of the Blast package (Altschul S.F. et al., 1997).
160
161 **SMART**
162 SMART (a Simple Modular Architecture Research Tool) allows the
163 identification and annotation of genetically mobile domains and the
164 analysis of domain architectures. These domains are extensively
165 annotated with respect to phyletic distributions, functional class, tertiary
166 structures and functionally important residues. SMART alignments are
167 optimised manually and following construction of corresponding hidden Markov models (HMMs).
168 hmmpfam from the HMMER2.3.2 package (by Sean Eddy,
169 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
170
171 **TIGRFAMs**
172 TIGRFAMs are a collection of protein families featuring curated multiple
173 sequence alignments, Hidden Markov Models (HMMs) and associated
174 information designed to support the automated functional identification
175 of proteins by sequence homology. Classification by equivalog family
176 (see below), where achievable, complements classification by orthologs,
177 superfamily, domain or motif. It provides the information best suited
178 for automatic assignment of specific functions to proteins from large
179 scale genome sequencing projects.
180 hmmpfam from the HMMER2.3.2 package (by Sean Eddy,
181 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
182
183 **PIR SuperFamily**
184 PIR SuperFamily (PIRSF) is a classification system based on evolutionary
185 relationship of whole proteins.
186 hmmpfam from the HMMER2.3.2 package (by Sean Eddy,
187 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
188
189 **SUPERFAMILY**
190 SUPERFAMILY is a library of profile hidden Markov models that represent
191 all proteins of known structure, based on SCOP.
192 hmmpfam/hmmsearch from the HMMER2.3.2 package (by Sean Eddy,
193 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
194 Optionally, predictions for coiled-coil, signal peptide cleavage sites
195 (SignalP v3) and TM helices (TMHMM v2) are supported (See the FAQs file for details).
196
197 **GENE3D**
198 Gene3D is supplementary to the CATH database. This protein sequence database
199 contains proteins from complete genomes which have been clustered into protein
200 families and annotated with CATH domains, Pfam domains and functional
201 information from KEGG, GO, COG, Affymetrix and STRINGS.
202 hmmpfam from the HMM2.3.2 package (by Sean Eddy,
203 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
204
205 **PANTHER**
206 The PANTHER (Protein ANalysis THrough Evolutionary Relationships)
207 Classification System was designed to classify proteins (and their genes)
208 in order to facilitate high-throughput analysis.
209 hmmsearch from the HMM2.3.2 package (by Sean Eddy,
210 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
211 and blastall from the Blast package (Altschul S.F. et al., 1997).
212
213 ----------
214 References
215 ----------
216
217 Zdobnov EM, Apweiler R (2001)
218 InterProScan an integration platform for the signature-recognition methods in InterPro.
219 Bioinformatics 17, 847-848.
220 http://dx.doi.org/10.1093/bioinformatics/17.9.847
221
222 Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R (2005)
223 InterProScan: protein domains identifier.
224 Nucleic Acids Research 33 (Web Server issue), W116-W120.
225 http://dx.doi.org/10.1093/nar/gki442
226
227 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)
228 InterPro: the integrative protein signature database.
229 Nucleic Acids Research 37 (Database Issue), D224-228.
230 http://dx.doi.org/10.1093/nar/gkn785
231
232
233 **Galaxy Wrapper Author**::
234
235 * Bjoern Gruening, Pharmaceutical Bioinformatics, University of Freiburg
236 * Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter
237
238 </help>
239 </tool>