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author bjoern-gruening
date Sun, 23 Jun 2013 07:38:53 -0400
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1 <tool id="interproscan" name="Interproscan functional predictions of ORFs" version="1.1"> 1 <tool id="interproscan" name="Interproscan functional predictions of ORFs" version="1.2">
2 <description>Interproscan functional predictions of ORFs</description> 2 <description>Interproscan functional predictions of ORFs</description>
3 <command> 3 <command>
4 ## The command is a Cheetah template which allows some Python based syntax. 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 5 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
6 6
7 ## create temp directory 7 ## create temp directory
9 #set $tfile = tempfile.mkstemp()[1] 9 #set $tfile = tempfile.mkstemp()[1]
10 10
11 sed 's/ /_/g' $input > $tfile; 11 sed 's/ /_/g' $input > $tfile;
12 12
13 ## Hack, because interproscan does not seem to produce gff output even if it is configured 13 ## Hack, because interproscan does not seem to produce gff output even if it is configured
14 #if str($oformat)=="gff": 14 #if str($oformat) == "gff":
15 #set $tfile2 = tempfile.mkstemp()[1] 15 #set $tfile2 = tempfile.mkstemp()[1]
16 iprscan -cli -nocrc -i $tfile -o $tfile2 -goterms -seqtype p -altjobs -format raw -appl $appl > /dev/null 2> /dev/null; 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 17 converter.pl -format gff3 -input $tfile2 -output $output;
18 rm $tfile2 18 rm $tfile2;
19 #else 19 #else
20 iprscan -cli -nocrc -i $tfile -o $output -goterms -seqtype p -altjobs -format $oformat -appl $appl > /dev/null 2> /dev/null; 20 iprscan -cli -nocrc -i $tfile -o $output -goterms -seqtype p -altjobs -format $oformat -appl $appl 2>&#38;1;
21 #end if 21 #end if
22 22
23 rm $tfile; 23 rm $tfile
24 24
25 </command> 25 </command>
26 <inputs> 26 <inputs>
27 <param name="input" type="data" format="fasta" label="Protein Fasta File"/> 27 <param name="input" type="data" format="fasta" label="Protein Fasta File"/>
28 28
29 <param name="appl" type="select" format="text" help="Select your programm."> 29 <param name="appl" type="select" format="text" label="Applications to run" help="Select your programm.">
30 <label>Applications to run ...</label>
31 <option value="blastprodom+coils+gene3d+hamap+hmmpanther+hmmpir+hmmpfam+hmmsmart+hmmtigr+fprintscan+patternscan+profilescan+superfamily+seg+signalp+tmhmm" selected="true">all</option> 30 <option value="blastprodom+coils+gene3d+hamap+hmmpanther+hmmpir+hmmpfam+hmmsmart+hmmtigr+fprintscan+patternscan+profilescan+superfamily+seg+signalp+tmhmm" selected="true">all</option>
32 <option value="seg">seg</option> 31 <option value="seg">seg</option>
33 <option value="signalp">signalp</option> 32 <option value="signalp">signalp</option>
34 <option value="tmhmm">tmhmm</option> 33 <option value="tmhmm">tmhmm</option>
35 <option value="fprintscan">fprintscan</option> 34 <option value="fprintscan">fprintscan</option>
43 <option value="hmmpanther">hmmpanther</option> 42 <option value="hmmpanther">hmmpanther</option>
44 <option value="hamap">hamap</option> 43 <option value="hamap">hamap</option>
45 <option value="gene3d">gene3d</option> 44 <option value="gene3d">gene3d</option>
46 <option value="coils">coils</option> 45 <option value="coils">coils</option>
47 <option value="blastprodom">blastprodom</option> 46 <option value="blastprodom">blastprodom</option>
48 </param> 47 </param>
49 48
50 <param name="oformat" type="select" label="Output format" help="Please select a output format."> 49 <param name="oformat" type="select" label="Output format" help="Please select a output format.">
51 <option value="gff" selected="true">gff</option> 50 <option value="gff">gff</option>
52 <option value="raw">raw</option> 51 <option value="raw" selected="true">raw</option>
53 <option value="txt">txt</option> 52 <option value="txt">txt</option>
54 <option value="html">html</option> 53 <option value="html">html</option>
55 <option value="xml">xml</option> 54 <option value="xml">xml</option>
56 <option value="ebixml">EBI header on top of xml</option> 55 <option value="ebixml">EBI header on top of xml</option>
57 </param> 56 </param>
70 69
71 </outputs> 70 </outputs>
72 <requirements> 71 <requirements>
73 </requirements> 72 </requirements>
74 <help> 73 <help>
75
76 **What it does** 74 **What it does**
77
78 75
79 Interproscan is a batch tool to query the Interpro database. It provides annotations based on multiple searches of profile and other functional databases. 76 Interproscan is a batch tool to query the Interpro database. It provides annotations based on multiple searches of profile and other functional databases.
80 These include SCOP, CATH, PFAM and SUPERFAMILY. 77 These include SCOP, CATH, PFAM and SUPERFAMILY.
81 78
82 **Input** 79 **Input**
83 A FASTA file containing ORF predictions is required. This file must NOT contain any spaces in the FASTA headers - any spaces will be convereted to underscores (_) by this tool before submission to Interproscan. 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.
84 82
85 **Output** 83 **Output**
86 84
87 Example for the raw format. 85 Example for the raw format.
88 This is a basic tab delimited format useful for uploading the data into a relational database or concatenation of different runs. 86 The output will consist of a tabular file in galaxy with 14 columns and can be easily concatenated or filtered.
89 is all on one line.
90 87
91 ====== ================================================================ ====================================================================== 88 ====== ================================================================ ======================================================================
92 column example description 89 column example description
93 ====== ================================================================ ====================================================================== 90 ====== ================================================================ ======================================================================
94 c1 NF00181542 the id of the input sequence. 91 c1 NF00181542 the id of the input sequence
95 c2 27A9BBAC0587AB84 the crc64 (checksum) of the protein sequence (supposed to be unique). 92 c2 27A9BBAC0587AB84 the crc64 (checksum) of the protein sequence (supposed to be unique)
96 c3 272 the length of the sequence (in AA). 93 c3 272 the length of the sequence (in AA)
97 c4 HMMPIR the anaysis method launched. 94 c4 HMMPIR the anaysis method launched.
98 c5 PIRSF001424 the database members entry for this match. 95 c5 PIRSF001424 the database members entry for this match
99 c6 Prephenate dehydratase the database member description for the entry. 96 c6 Prephenate dehydratase the database member description for the entry
100 c7 1 the start of the domain match. 97 c7 1 the start of the domain match
101 c8 270 the end of the domain match. 98 c8 270 the end of the domain match
102 c9 6.5e-141 the evalue of the match (reported by member database method). 99 c9 6.5e-141 the evalue of the match (reported by member database method)
103 c10 T the status of the match (T: true, ?: unknown). 100 c10 T the status of the match (T: true, ?: unknown)
104 c11 06-Aug-2005 the date of the run. 101 c11 06-Aug-2005 the date of the run.
105 c12 IPR008237 the corresponding InterPro entry (if iprlookup requested by the user). 102 c12 IPR008237 the corresponding InterPro entry (if iprlookup requested by the user)
106 c13 Prephenate dehydratase with ACT region the description of the InterPro entry. 103 c13 Prephenate dehydratase with ACT region the description of the InterPro entry
107 c14 Molecular Function:prephenate dehydratase activity (GO:0004664) the GO (gene ontology) description for the InterPro entry. 104 c14 Molecular Function:prephenate dehydratase activity (GO:0004664) the GO (gene ontology) description for the InterPro entry
108 ====== ================================================================ ====================================================================== 105 ====== ================================================================ ======================================================================
109 106
110
111 **Database updates** 107 **Database updates**
112 108
113 Typically these take place 2-3 times a year. 109 Typically these take place 2-3 times a year. Please contact your Galaxy administrator to update the databases.
114 110
115 111 -----
116 **Tools** 112 Tools
117 113 -----
118 PROSITE patterns 114
119 115 **PROSITE patterns**::
120 ::
121 116
122 Some biologically significant amino acid patterns can be summarised in 117 Some biologically significant amino acid patterns can be summarised in
123 the form of regular expressions. 118 the form of regular expressions.
124 ScanRegExp (by Wolfgang.Fleischmann@ebi.ac.uk), 119 ScanRegExp (by Wolfgang.Fleischmann@ebi.ac.uk).
125 120
126 PROSITE profiles 121 **PROSITE profiles**::
127
128 ::
129 122
130 There are a number of protein families as well as functional or 123 There are a number of protein families as well as functional or
131 structural domains that cannot be detected using patterns due to their extreme 124 structural domains that cannot be detected using patterns due to their extreme
132 sequence divergence, so the use of techniques based on weight matrices 125 sequence divergence, so the use of techniques based on weight matrices
133 (also known as profiles) allows the detection of such proteins or domains. 126 (also known as profiles) allows the detection of such proteins or domains.
134 A profile is a table of position-specific amino acid weights and gap costs. 127 A profile is a table of position-specific amino acid weights and gap costs.
135 The profile structure used in PROSITE is similar to but slightly more general 128 The profile structure used in PROSITE is similar to but slightly more general
136 (Bucher P. et al., 1996 [7]) than the one introduced by M. Gribskov and 129 (Bucher P. et al., 1996) than the one introduced by M. Gribskov and
137 co-workers. 130 co-workers.
138 pfscan from the Pftools package (by Philipp.Bucher@isrec.unil.ch). 131 pfscan from the Pftools package (by Philipp.Bucher@isrec.unil.ch).
139 132
140 PRINTS 133 **PRINTS**::
141
142 ::
143 134
144 The PRINTS database houses a collection of protein family fingerprints. 135 The PRINTS database houses a collection of protein family fingerprints.
145 These are groups of motifs that together are diagnostically more 136 These are groups of motifs that together are diagnostically more
146 powerful than single motifs by making use of the biological context inherent in a 137 powerful than single motifs by making use of the biological context inherent in a
147 multiple-motif method. The fingerprinting method arose from the need for 138 multiple-motif method. The fingerprinting method arose from the need for
148 a reliable technique for detecting members of large, highly divergent 139 a reliable technique for detecting members of large, highly divergent
149 protein super-families. 140 protein super-families.
150 FingerPRINTScan (Scordis P. et al., 1999 [8]). 141 FingerPRINTScan (Scordis P. et al., 1999).
151 142
152 PFAM 143 **PFAM**::
153
154 ::
155 144
156 Pfam is a database of protein domain families. Pfam contains curated 145 Pfam is a database of protein domain families. Pfam contains curated
157 multiple sequence alignments for each family and corresponding hidden 146 multiple sequence alignments for each family and corresponding hidden
158 Markov models (HMMs) (Eddy S.R., 1998 [9]). 147 Markov models (HMMs) (Eddy S.R., 1998).
159 Profile hidden Markov models are statistical models of the primary 148 Profile hidden Markov models are statistical models of the primary
160 structure consensus of a sequence family. The construction and use 149 structure consensus of a sequence family. The construction and use
161 of Pfam is tightly tied to the HMMER software package. 150 of Pfam is tightly tied to the HMMER software package.
162 hmmpfam from the HMMER2.3.2 package (by Sean Eddy, 151 hmmpfam from the HMMER2.3.2 package (by Sean Eddy,
163 eddy@genetics.wustl.edu, http://hmmer.wustl.edu). 152 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
164 153
165 PRODOM 154 **PRODOM**::
166
167 ::
168
169 155
170 ProDom is a database of protein domain families obtained by automated 156 ProDom is a database of protein domain families obtained by automated
171 analysis of the SWISS-PROT and TrEMBL protein sequences. It is useful 157 analysis of the SWISS-PROT and TrEMBL protein sequences. It is useful
172 for analysing the domain arrangements of complex protein families and the 158 for analysing the domain arrangements of complex protein families and the
173 homology relationships in modular proteins. ProDom families are built by 159 homology relationships in modular proteins. ProDom families are built by
174 an automated process based on a recursive use of PSI-BLAST homology 160 an automated process based on a recursive use of PSI-BLAST homology
175 searches. 161 searches.
176 ProDomBlast3i.pl (by Emmanuel Courcelle emmanuel.courcelle@toulouse.inra.fr 162 ProDomBlast3i.pl (by Emmanuel Courcelle emmanuel.courcelle@toulouse.inra.fr
177 and Yoann Beausse beausse@toulouse.inra.fr) 163 and Yoann Beausse beausse@toulouse.inra.fr)
178 a wrapper on top of the Blast package (Altschul S.F. et al., 1997 [10]). 164 a wrapper on top of the Blast package (Altschul S.F. et al., 1997).
179 165
180 166 **SMART**::
181 SMART
182
183 ::
184 167
185 SMART (a Simple Modular Architecture Research Tool) allows the 168 SMART (a Simple Modular Architecture Research Tool) allows the
186 identification and annotation of genetically mobile domains and the 169 identification and annotation of genetically mobile domains and the
187 analysis of domain architectures. These domains are extensively 170 analysis of domain architectures. These domains are extensively
188 annotated with respect to phyletic distributions, functional class, tertiary 171 annotated with respect to phyletic distributions, functional class, tertiary
189 structures and functionally important residues. SMART alignments are 172 structures and functionally important residues. SMART alignments are
190 optimised manually and following construction of corresponding hidden Markov models (HMMs). 173 optimised manually and following construction of corresponding hidden Markov models (HMMs).
191 hmmpfam from the HMMER2.3.2 package (by Sean Eddy, 174 hmmpfam from the HMMER2.3.2 package (by Sean Eddy,
192 eddy@genetics.wustl.edu, http://hmmer.wustl.edu). 175 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
193 176
194 177 **TIGRFAMs**::
195 TIGRFAMs
196
197 ::
198 178
199 TIGRFAMs are a collection of protein families featuring curated multiple 179 TIGRFAMs are a collection of protein families featuring curated multiple
200 sequence alignments, Hidden Markov Models (HMMs) and associated 180 sequence alignments, Hidden Markov Models (HMMs) and associated
201 information designed to support the automated functional identification 181 information designed to support the automated functional identification
202 of proteins by sequence homology. Classification by equivalog family 182 of proteins by sequence homology. Classification by equivalog family
205 for automatic assignment of specific functions to proteins from large 185 for automatic assignment of specific functions to proteins from large
206 scale genome sequencing projects. 186 scale genome sequencing projects.
207 hmmpfam from the HMMER2.3.2 package (by Sean Eddy, 187 hmmpfam from the HMMER2.3.2 package (by Sean Eddy,
208 eddy@genetics.wustl.edu, http://hmmer.wustl.edu). 188 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
209 189
210 PIR SuperFamily 190 **PIR SuperFamily**::
211
212 ::
213 191
214 PIR SuperFamily (PIRSF) is a classification system based on evolutionary 192 PIR SuperFamily (PIRSF) is a classification system based on evolutionary
215 relationship of whole proteins. 193 relationship of whole proteins.
216 hmmpfam from the HMMER2.3.2 package (by Sean Eddy, 194 hmmpfam from the HMMER2.3.2 package (by Sean Eddy,
217 eddy@genetics.wustl.edu, http://hmmer.wustl.edu). 195 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
218 196
219 SUPERFAMILY 197 **SUPERFAMILY**::
220
221 ::
222 198
223 SUPERFAMILY is a library of profile hidden Markov models that represent 199 SUPERFAMILY is a library of profile hidden Markov models that represent
224 all proteins of known structure, based on SCOP. 200 all proteins of known structure, based on SCOP.
225 hmmpfam/hmmsearch from the HMMER2.3.2 package (by Sean Eddy, 201 hmmpfam/hmmsearch from the HMMER2.3.2 package (by Sean Eddy,
226 eddy@genetics.wustl.edu, http://hmmer.wustl.edu). 202 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
227 Optionally, predictions for coiled-coil, signal peptide cleavage sites 203 Optionally, predictions for coiled-coil, signal peptide cleavage sites
228 (SignalP v3) and TM helices (TMHMM v2) are supported (See the FAQs file 204 (SignalP v3) and TM helices (TMHMM v2) are supported (See the FAQs file
229 for details). 205 for details).
230 206
231 207 **GENE3D**::
232 GENE3D 208
233 209 Gene3D is supplementary to the CATH database. This protein sequence database
234 :: 210 contains proteins from complete genomes which have been clustered into protein
235 211 families and annotated with CATH domains, Pfam domains and functional
236 Gene3D is supplementary to the CATH database. This protein sequence database 212 information from KEGG, GO, COG, Affymetrix and STRINGS.
237 contains proteins from complete genomes which have been clustered into protein 213 hmmpfam from the HMM2.3.2 package (by Sean Eddy,
238 families and annotated with CATH domains, Pfam domains and functional 214 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
239 information from KEGG, GO, COG, Affymetrix and STRINGS. 215
240 hmmpfam from the HMM2.3.2 package (by Sean Eddy, 216 **PANTHER**::
241 eddy@genetics.wustl.edu, http://hmmer.wustl.edu). 217
242 218 The PANTHER (Protein ANalysis THrough Evolutionary Relationships)
243 219 Classification System was designed to classify proteins (and their genes)
244 PANTHER 220 in order to facilitate high-throughput analysis.
245 221 hmmsearch from the HMM2.3.2 package (by Sean Eddy,
246 :: 222 eddy@genetics.wustl.edu, http://hmmer.wustl.edu).
247 223 and blastall from the Blast package (Altschul S.F. et al., 1997).
248 The PANTHER (Protein ANalysis THrough Evolutionary Relationships) 224
249 Classification System was designed to classify proteins (and their genes) 225 ----------
250 in order to facilitate high-throughput analysis. 226 References
251 hmmsearch from the HMM2.3.2 package (by Sean Eddy, 227 ----------
252 eddy@genetics.wustl.edu, http://hmmer.wustl.edu). 228
253 and blastall from the Blast package (Altschul S.F. et al., 1997 [10]). 229 Zdobnov EM, Apweiler R (2001)
254 230 InterProScan an integration platform for the signature-recognition methods in InterPro.
255 231 Bioinformatics 17, 847-848.
256 232 http://dx.doi.org/10.1093/bioinformatics/17.9.847
257 **References** 233
258 234 Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R (2005)
259 Quevillon E., Silventoinen V., Pillai S., Harte N., Mulder N., Apweiler R., Lopez R. 235 InterProScan: protein domains identifier.
260 InterProScan: protein domains identifier (2005). 236 Nucleic Acids Research 33 (Web Server issue), W116-W120.
261 Nucleic Acids Res. 33 (Web Server issue) :W116-W120 237 http://dx.doi.org/10.1093/nar/gki442
262 238
263 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. 239 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)
264 InterPro: the integrative protein signature database (2009). 240 InterPro: the integrative protein signature database.
265 Nucleic Acids Res. 37 (Database Issue) :D224-228 241 Nucleic Acids Research 37 (Database Issue), D224-228.
266 242 http://dx.doi.org/10.1093/nar/gkn785
267 Galaxy Wrapper Author: 243
268 244
269 * Bjoern Gruening, Pharmaceutical Bioinformatics, University of Freiburg 245 **Galaxy Wrapper Author**::
270 * Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter 246
271 247 * Bjoern Gruening, Pharmaceutical Bioinformatics, University of Freiburg
272 248 * Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter
273 249
274 </help> 250 </help>
275 </tool> 251 </tool>