Mercurial > repos > bgruening > iprscan
changeset 3:a773b8eaccce draft default tip
Uploaded
| author | bgruening |
|---|---|
| date | Tue, 08 Oct 2013 10:22:00 -0400 |
| parents | 32ae2da3a3e4 |
| children | |
| files | interproscan.xml readme.rst |
| diffstat | 2 files changed, 73 insertions(+), 56 deletions(-) [+] |
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--- a/interproscan.xml Sun Jun 23 07:40:45 2013 -0400 +++ b/interproscan.xml Tue Oct 08 10:22:00 2013 -0400 @@ -83,25 +83,25 @@ **Output** Example for the raw format. -The output will consist of a tabular file in galaxy with 14 columns and can be easily concatenated or filtered. +The output will consist of a tabular file with 14 columns and can be easily concatenated or filtered. ====== ================================================================ ====================================================================== column example description ====== ================================================================ ====================================================================== -c1 NF00181542 the id of the input sequence -c2 27A9BBAC0587AB84 the crc64 (checksum) of the protein sequence (supposed to be unique) -c3 272 the length of the sequence (in AA) -c4 HMMPIR the anaysis method launched. -c5 PIRSF001424 the database members entry for this match -c6 Prephenate dehydratase the database member description for the entry -c7 1 the start of the domain match -c8 270 the end of the domain match -c9 6.5e-141 the evalue of the match (reported by member database method) -c10 T the status of the match (T: true, ?: unknown) -c11 06-Aug-2005 the date of the run. -c12 IPR008237 the corresponding InterPro entry (if iprlookup requested by the user) -c13 Prephenate dehydratase with ACT region the description of the InterPro entry -c14 Molecular Function:prephenate dehydratase activity (GO:0004664) the GO (gene ontology) description for the InterPro entry +c1 NF00181542 id of the input sequence +c2 27A9BBAC0587AB84 crc64 (checksum) of the protein sequence (supposed to be unique) +c3 272 length of the sequence (in AA) +c4 HMMPIR anaysis method launched. +c5 PIRSF001424 database members entry for this match +c6 Prephenate dehydratase database member description for the entry +c7 1 start of the domain match +c8 270 end of the domain match +c9 6.5e-141 evalue of the match (reported by member database method) +c10 T status of the match (T: true, ?: unknown) +c11 06-Aug-2005 date of the run. +c12 IPR008237 corresponding InterPro entry (if iprlookup requested by the user) +c13 Prephenate dehydratase with ACT region description of the InterPro entry +c14 Molecular Function:prephenate dehydratase activity (GO:0004664) GO (gene ontology) description for the InterPro entry ====== ================================================================ ====================================================================== **Database updates** @@ -230,6 +230,10 @@ http://dx.doi.org/10.1093/nar/gkn785 +This wrapper is available to install into other Galaxy Instances via the Galaxy Tool Shed at +http://toolshed.g2.bx.psu.edu/view/bgruening/interproscan + + **Galaxy Wrapper Author**:: * Bjoern Gruening, Pharmaceutical Bioinformatics, University of Freiburg
--- a/readme.rst Sun Jun 23 07:40:45 2013 -0400 +++ b/readme.rst Tue Oct 08 10:22:00 2013 -0400 @@ -1,17 +1,25 @@ -================================================ -Galaxy wrapper for InterProScan prediction tools -================================================ +================================================== +Galaxy wrapper for InterProScan 4 prediction tools +================================================== + +**Note**: + +This wrapper is for InterProScan 4.x if you want to use InterProScan 5 please have a look at: +http://toolshed.g2.bx.psu.edu/view/bgruening/interproscan5 + +----- InterProScan is a tool that combines different protein signature recognition methods native to the InterPro member databases into one resource with look up of corresponding InterPro and GO annotation. -This wrapper is copyright 2012-2013 by -* Bjoern Gruening, Pharmaceutical Bioinformatics, University of Freiburg -* Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter +This wrapper is copyright 2012-2013 by: + * Bjoern Gruening, Pharmaceutical Bioinformatics, University of Freiburg + * Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter -This prepository contains wrapper for the InterProScan command line tool. -http://www.ebi.ac.uk/interpro/ +This prepository contains wrapper for the InterProScan_ command line tool. + +.. _InterProScan: http://www.ebi.ac.uk/interpro/ Zdobnov E.M. and Apweiler R. "InterProScan - an integration platform for the signature-recognition methods in InterPro" Bioinformatics, 2001, 17(9): p. 847-8. @@ -28,21 +36,25 @@ Please see also: ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/index.html -And rebuild the indizes if necessary: +And rebuild the indizes if necessary + +.. code:: -index_data.pl -f interpro.xml -inx -v -bin -bforce -index_data.pl -f match_complete.xml -inx -v -bin -bforce -index_data.pl -f Pfam-A.seed -inx -v -bin -bforce -index_data.pl -f Pfam-C -inx -v -bin -bforce -index_data.pl -f prints.pval -inx -v -bin -bforce -index_data.pl -f sf.seq -inx -v -bin -bforce -index_data.pl -f sf_hmm -inx -v -bin -bforce -index_data.pl -f smart.HMMs -inx -v -bin -bforce -index_data.pl -f superfamily.hmm -inx -v -bin -bforce -index_data.pl -f TIGRFAMs_HMM.LIB -inx -v -bin -bforce + index_data.pl -f interpro.xml -inx -v -bin -bforce + index_data.pl -f match_complete.xml -inx -v -bin -bforce + index_data.pl -f Pfam-A.seed -inx -v -bin -bforce + index_data.pl -f Pfam-C -inx -v -bin -bforce + index_data.pl -f prints.pval -inx -v -bin -bforce + index_data.pl -f sf.seq -inx -v -bin -bforce + index_data.pl -f sf_hmm -inx -v -bin -bforce + index_data.pl -f smart.HMMs -inx -v -bin -bforce + index_data.pl -f superfamily.hmm -inx -v -bin -bforce + index_data.pl -f TIGRFAMs_HMM.LIB -inx -v -bin -bforce -Add the tool definition to your tool_conf.xml file under Galaxy root. +Add the tool definition to your tool_conf.xml file under Galaxy root: +.. code:: + <tool file="iprscan/interproscan.xml" /> ============= @@ -60,29 +72,30 @@ ======= interproscan: -- v1.1: Initial public release -- v1.2: Merge with Konrad Paszkiewicz repository + + - v1.1: Initial public release + - v1.2: Merge with Konrad Paszkiewicz repository -=============================== -Wrapper Licence (MIT/BSD style) -=============================== +============= +Licence (MIT) +============= + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: -Permission to use, copy, modify, and distribute this software and its -documentation with or without modifications and for any purpose and -without fee is hereby granted, provided that any copyright notices -appear in all copies and that both those copyright notices and this -permission notice appear in supporting documentation, and that the -names of the contributors or copyright holders not be used in -advertising or publicity pertaining to distribution of the software -without specific prior permission. +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. -THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL -WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED -WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE -CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT -OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS -OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE -OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE -OR PERFORMANCE OF THIS SOFTWARE. +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE.