Mercurial > repos > konradpaszkiewicz > interproscan

annotate interproscan.xml @ 1:3c57a8767bb8 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
3c57a8767bb8 Uploaded v1.0.1, updates the help text, renamed readme file to display on the ToolShed.
peterjc
parents: 0
diff changeset
1 <tool id="interproscan" name="Interproscan functional predictions of ORFs" version="1.0.1">
0
49e20fa2c66d Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
2 <description>Interproscan functional predictions of ORFs</description>
49e20fa2c66d Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
3 <command interpreter="python">
49e20fa2c66d Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
4 interproscan.py
49e20fa2c66d Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
5 '$__app__.config.new_file_path'
49e20fa2c66d Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
6 '$input'
49e20fa2c66d Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
7 '$format'
49e20fa2c66d Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
8 '$output'
49e20fa2c66d Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
9 </command>
49e20fa2c66d Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
10 <inputs>
49e20fa2c66d Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
11 <param name="input" type="data" format="fasta" label="ORFs in protein FASTA format"/>
49e20fa2c66d Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
12 <param name="format" type="boolean" format="gff" label="GFF format?" truevalue="gff" falsevalue="raw"/>
49e20fa2c66d Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
13 </inputs>
49e20fa2c66d Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
14 <outputs>
49e20fa2c66d Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
15 <data format="tabular" name="output" label="Interproscan output"/>
49e20fa2c66d Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
16
49e20fa2c66d Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
17 </outputs>
49e20fa2c66d Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
18 <requirements>
49e20fa2c66d Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
19 </requirements>
49e20fa2c66d Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
20 <help>
1
3c57a8767bb8 Uploaded v1.0.1, updates the help text, renamed readme file to display on the ToolShed.
peterjc
parents: 0
diff changeset
21
3c57a8767bb8 Uploaded v1.0.1, updates the help text, renamed readme file to display on the ToolShed.
peterjc
parents: 0
diff changeset
22 **Interproscan**
0
49e20fa2c66d Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
23
49e20fa2c66d Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
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.
49e20fa2c66d Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
25
49e20fa2c66d Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
26 **Input**
1
3c57a8767bb8 Uploaded v1.0.1, updates the help text, renamed readme file to display on the ToolShed.
peterjc
parents: 0
diff changeset
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.
0
49e20fa2c66d Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
28
49e20fa2c66d Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
29 **Output**
49e20fa2c66d Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
30
1
3c57a8767bb8 Uploaded v1.0.1, updates the help text, renamed readme file to display on the ToolShed.
peterjc
parents: 0
diff changeset
31 The output will consist of a file in Interproscan raw format, a tabular file in galaxy with 14 columns.
3c57a8767bb8 Uploaded v1.0.1, updates the help text, renamed readme file to display on the ToolShed.
peterjc
parents: 0
diff changeset
32 This can be use to upload the data into a relational database or concatenation of different runs.
0
49e20fa2c66d Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
33
1
3c57a8767bb8 Uploaded v1.0.1, updates the help text, renamed readme file to display on the ToolShed.
peterjc
parents: 0
diff changeset
34 ====== ============================================================================================================================= ===========================================
3c57a8767bb8 Uploaded v1.0.1, updates the help text, renamed readme file to display on the ToolShed.
peterjc
parents: 0
diff changeset
35 Column Example Description
3c57a8767bb8 Uploaded v1.0.1, updates the help text, renamed readme file to display on the ToolShed.
peterjc
parents: 0
diff changeset
36 ------ ----------------------------------------------------------------------------------------------------------------------------- -------------------------------------------
3c57a8767bb8 Uploaded v1.0.1, updates the help text, renamed readme file to display on the ToolShed.
peterjc
parents: 0
diff changeset
37 c1 NF00181542 Identifier of the input sequence
3c57a8767bb8 Uploaded v1.0.1, updates the help text, renamed readme file to display on the ToolShed.
peterjc
parents: 0
diff changeset
38 c2 0A5FDCE74AB7C3AD crc64 checksum of the protein sequence
3c57a8767bb8 Uploaded v1.0.1, updates the help text, renamed readme file to display on the ToolShed.
peterjc
parents: 0
diff changeset
39 c3 272 Length of sequence (in amino acids)
3c57a8767bb8 Uploaded v1.0.1, updates the help text, renamed readme file to display on the ToolShed.
peterjc
parents: 0
diff changeset
40 c4 HMMPIR Analysis metho launched
3c57a8767bb8 Uploaded v1.0.1, updates the help text, renamed readme file to display on the ToolShed.
peterjc
parents: 0
diff changeset
41 c5 PIRSF001424 Database members entry for match
3c57a8767bb8 Uploaded v1.0.1, updates the help text, renamed readme file to display on the ToolShed.
peterjc
parents: 0
diff changeset
42 c6 Prephenate dehydratase Description from the database
3c57a8767bb8 Uploaded v1.0.1, updates the help text, renamed readme file to display on the ToolShed.
peterjc
parents: 0
diff changeset
43 c7 1 Start of the domain match
3c57a8767bb8 Uploaded v1.0.1, updates the help text, renamed readme file to display on the ToolShed.
peterjc
parents: 0
diff changeset
44 c8 270 End of the domain match
3c57a8767bb8 Uploaded v1.0.1, updates the help text, renamed readme file to display on the ToolShed.
peterjc
parents: 0
diff changeset
45 c9 6.5e-141 e-value (reported by the database method)
3c57a8767bb8 Uploaded v1.0.1, updates the help text, renamed readme file to display on the ToolShed.
peterjc
parents: 0
diff changeset
46 c10 T Status of match (Tfor true, ? forunknown)
3c57a8767bb8 Uploaded v1.0.1, updates the help text, renamed readme file to display on the ToolShed.
peterjc
parents: 0
diff changeset
47 c11 06-Aug-2005 Date of the run
3c57a8767bb8 Uploaded v1.0.1, updates the help text, renamed readme file to display on the ToolShed.
peterjc
parents: 0
diff changeset
48 c12 IPR008237 InterPro entry (if iprlookup requested)
3c57a8767bb8 Uploaded v1.0.1, updates the help text, renamed readme file to display on the ToolShed.
peterjc
parents: 0
diff changeset
49 c13 Prephenate dehydratase with ACT region Description of the InterPro entry
3c57a8767bb8 Uploaded v1.0.1, updates the help text, renamed readme file to display on the ToolShed.
peterjc
parents: 0
diff changeset
50 c14 Molecular Function:prephenate dehydratase activity (GO:0004664), Biological Process:L-phenylalanine biosynthesis (GO:0009094) GO (gene ontology) description
3c57a8767bb8 Uploaded v1.0.1, updates the help text, renamed readme file to display on the ToolShed.
peterjc
parents: 0
diff changeset
51 ====== ============================================================================================================================= ===========================================
3c57a8767bb8 Uploaded v1.0.1, updates the help text, renamed readme file to display on the ToolShed.
peterjc
parents: 0
diff changeset
52
0
49e20fa2c66d Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
53 **Database updates**
49e20fa2c66d Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
54
49e20fa2c66d Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
55 Typically these take place 2-3 times a year.
49e20fa2c66d Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
56
49e20fa2c66d Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
57 **References**
49e20fa2c66d Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
58
1
3c57a8767bb8 Uploaded v1.0.1, updates the help text, renamed readme file to display on the ToolShed.
peterjc
parents: 0
diff changeset
59 Zdobnov EM, Apweiler R (2001)
3c57a8767bb8 Uploaded v1.0.1, updates the help text, renamed readme file to display on the ToolShed.
peterjc
parents: 0
diff changeset
60 InterProScan an integration platform for the signature-recognition methods in InterPro.
3c57a8767bb8 Uploaded v1.0.1, updates the help text, renamed readme file to display on the ToolShed.
peterjc
parents: 0
diff changeset
61 Bioinformatics 17, 847-848.
3c57a8767bb8 Uploaded v1.0.1, updates the help text, renamed readme file to display on the ToolShed.
peterjc
parents: 0
diff changeset
62 http://dx.doi.org/10.1093/bioinformatics/17.9.847
0
49e20fa2c66d Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
63
1
3c57a8767bb8 Uploaded v1.0.1, updates the help text, renamed readme file to display on the ToolShed.
peterjc
parents: 0
diff changeset
64 Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R (2005)
3c57a8767bb8 Uploaded v1.0.1, updates the help text, renamed readme file to display on the ToolShed.
peterjc
parents: 0
diff changeset
65 InterProScan: protein domains identifier.
3c57a8767bb8 Uploaded v1.0.1, updates the help text, renamed readme file to display on the ToolShed.
peterjc
parents: 0
diff changeset
66 Nucleic Acids Research 33 (Web Server issue), W116-W120.
3c57a8767bb8 Uploaded v1.0.1, updates the help text, renamed readme file to display on the ToolShed.
peterjc
parents: 0
diff changeset
67 http://dx.doi.org/10.1093/nar/gki442
0
49e20fa2c66d Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
68
1
3c57a8767bb8 Uploaded v1.0.1, updates the help text, renamed readme file to display on the ToolShed.
peterjc
parents: 0
diff changeset
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)
3c57a8767bb8 Uploaded v1.0.1, updates the help text, renamed readme file to display on the ToolShed.
peterjc
parents: 0
diff changeset
70 InterPro: the integrative protein signature database.
3c57a8767bb8 Uploaded v1.0.1, updates the help text, renamed readme file to display on the ToolShed.
peterjc
parents: 0
diff changeset
71 Nucleic Acids Research 37 (Database Issue), D224-228.
3c57a8767bb8 Uploaded v1.0.1, updates the help text, renamed readme file to display on the ToolShed.
peterjc
parents: 0
diff changeset
72 http://dx.doi.org/10.1093/nar/gkn785
0
49e20fa2c66d Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
73
1
3c57a8767bb8 Uploaded v1.0.1, updates the help text, renamed readme file to display on the ToolShed.
peterjc
parents: 0
diff changeset
74 This wrapper is available to install into other Galaxy Instances via the Galaxy Tool Shed at
3c57a8767bb8 Uploaded v1.0.1, updates the help text, renamed readme file to display on the ToolShed.
peterjc
parents: 0
diff changeset
75 http://toolshed.g2.bx.psu.edu/view/konradpaszkiewicz/interproscan
0
49e20fa2c66d Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
76
49e20fa2c66d Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
77 </help>
49e20fa2c66d Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
konradpaszkiewicz
parents:
diff changeset
78 </tool>