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Uploaded v1.0.1, updates the help text, renamed readme file to display on the ToolShed.
author peterjc
date Wed, 05 Jun 2013 13:40:56 -0400
parents 49e20fa2c66d
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0:49e20fa2c66d 1:3c57a8767bb8
1 <tool id="interproscan" name="Interproscan functional predictions of ORFs" version="1.0.0"> 1 <tool id="interproscan" name="Interproscan functional predictions of ORFs" version="1.0.1">
2 <description>Interproscan functional predictions of ORFs</description> 2 <description>Interproscan functional predictions of ORFs</description>
3 <command interpreter="python"> 3 <command interpreter="python">
4 interproscan.py 4 interproscan.py
5 '$__app__.config.new_file_path' 5 '$__app__.config.new_file_path'
6 '$input' 6 '$input'
16 16
17 </outputs> 17 </outputs>
18 <requirements> 18 <requirements>
19 </requirements> 19 </requirements>
20 <help> 20 <help>
21 **Interproscan ** 21
22 **Interproscan**
22 23
23 Interproscan is a batch tool to query the Interpro database. It provides annotations based on multiple searches of profile and other functional databases. These include SCOP, CATH, PFAM and SUPERFAMILY. Currently due to resource limitations, only the PFAM database is searched however. 24 Interproscan is a batch tool to query the Interpro database. It provides annotations based on multiple searches of profile and other functional databases. These include SCOP, CATH, PFAM and SUPERFAMILY. Currently due to resource limitations, only the PFAM database is searched however.
24 25
25 **Input** 26 **Input**
26 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. 27 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.
27 28
28 **Output** 29 **Output**
29 The output will consist of a file in Interproscan raw format@
30 30
31 This is a basic tab delimited format useful for uploading the data into a relational database or concatenation of different runs. 31 The output will consist of a file in Interproscan raw format, a tabular file in galaxy with 14 columns.
32 is all on one line. 32 This can be use to upload the data into a relational database or concatenation of different runs.
33 33
34 Example here (with descriptions): 34 ====== ============================================================================================================================= ===========================================
35 NF00181542 0A5FDCE74AB7C3AD 272 HMMPIR PIRSF001424 Prephenate dehydratase 1 270 6.5e-141 T 06-Aug-2005\ 35 Column Example Description
36 IPR008237 Prephenate dehydratase with ACT region Molecular Function:prephenate dehydratase activity (GO:0004664), Biological Process\ 36 ------ ----------------------------------------------------------------------------------------------------------------------------- -------------------------------------------
37 :L-phenylalanine biosynthesis (GO:0009094) 37 c1 NF00181542 Identifier of the input sequence
38 38 c2 0A5FDCE74AB7C3AD crc64 checksum of the protein sequence
39 Key: 39 c3 272 Length of sequence (in amino acids)
40 c4 HMMPIR Analysis metho launched
41 c5 PIRSF001424 Database members entry for match
42 c6 Prephenate dehydratase Description from the database
43 c7 1 Start of the domain match
44 c8 270 End of the domain match
45 c9 6.5e-141 e-value (reported by the database method)
46 c10 T Status of match (Tfor true, ? forunknown)
47 c11 06-Aug-2005 Date of the run
48 c12 IPR008237 InterPro entry (if iprlookup requested)
49 c13 Prephenate dehydratase with ACT region Description of the InterPro entry
50 c14 Molecular Function:prephenate dehydratase activity (GO:0004664), Biological Process:L-phenylalanine biosynthesis (GO:0009094) GO (gene ontology) description
51 ====== ============================================================================================================================= ===========================================
40 52
41 NF00181542 is the id of the input sequence.
42 27A9BBAC0587AB84 is the crc64 (checksum) of the protein sequence (supposed to be unique).
43 272 is the length of the sequence (in AA).
44 HMMPIR is the anaysis method launched.
45 PIRSF001424 is the database members entry for this match.
46 Prephenate dehydratase is the database member description for the entry.
47 1 is the start of the domain match.
48 270 is the end of the domain match.
49 6.5e-141 is the evalue of the match (reported by member database method).
50 T is the status of the match (T: true, ?: unknown).
51 06-Aug-2005 is the date of the run.
52 IPR008237 is the corresponding InterPro entry (if iprlookup requested by the user).
53 Prephenate dehydratase with ACT region is the description of the InterPro entry.
54 Molecular Function:prephenate dehydratase activity (GO:0004664) is the GO (gene ontology) description for the InterPro entry.
55
56 **Database updates** 53 **Database updates**
57 54
58 Typically these take place 2-3 times a year. 55 Typically these take place 2-3 times a year.
59 56
60 **References** 57 **References**
61 58
62 Quevillon E., Silventoinen V., Pillai S., Harte N., Mulder N., Apweiler R., Lopez R. 59 Zdobnov EM, Apweiler R (2001)
63 InterProScan: protein domains identifier (2005). 60 InterProScan an integration platform for the signature-recognition methods in InterPro.
64 Nucleic Acids Res. 33 (Web Server issue) :W116-W120 61 Bioinformatics 17, 847-848.
62 http://dx.doi.org/10.1093/bioinformatics/17.9.847
65 63
64 Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R (2005)
65 InterProScan: protein domains identifier.
66 Nucleic Acids Research 33 (Web Server issue), W116-W120.
67 http://dx.doi.org/10.1093/nar/gki442
66 68
67 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. 69 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)
68 InterPro: the integrative protein signature database (2009). 70 InterPro: the integrative protein signature database.
69 Nucleic Acids Res. 37 (Database Issue) :D224-228 71 Nucleic Acids Research 37 (Database Issue), D224-228.
72 http://dx.doi.org/10.1093/nar/gkn785
70 73
71 74 This wrapper is available to install into other Galaxy Instances via the Galaxy Tool Shed at
75 http://toolshed.g2.bx.psu.edu/view/konradpaszkiewicz/interproscan
72 76
73 </help> 77 </help>
74 </tool> 78 </tool>