# HG changeset patch
# User bgruening
# Date 1405449295 14400
# Node ID 5db064bbb3be283d2f7af720b13306065d667f09
Imported from capsule None
diff -r 000000000000 -r 5db064bbb3be antismash.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/antismash.xml Tue Jul 15 14:34:55 2014 -0400
@@ -0,0 +1,253 @@
+
+ and Antibiotics Analysis (antiSMASH)
+
+ hmmer
+ hmmer
+ blast+
+ blast+
+ muscle
+ muscle
+ straight.plugin
+ straight.plugin
+ biopython
+ biopython
+ pyquery
+ pyquery
+ helperlibs
+ helperlibs
+ cssselect
+ cssselect
+ antismash
+ antismash
+ glimmer
+
+
+ #import os, glob
+ #set $outputfolder = $html.files_path
+ #if str($infile.ext) == 'genbank':
+ #set $file_extension = 'gb'
+ #else:
+ ## TODO add embl as input file
+ #set $file_extension = 'gb'
+ #end if
+
+ ln -s $infile #echo 'input_tempfile.' + $file_extension#;
+ mkdir -p $outputfolder;
+ run_antismash.py
+ --cpus "\${GALAXY_SLOTS:-12}"
+ --enable $types
+ --input-type 'nucl'
+ $smcogs
+ $clusterblast
+ $subclusterblast
+ $inclusive
+ $full_hmmer
+ $full_blast
+ $eukaryotic
+
+
+ #if str($pfam_database) != "None":
+ --pfamdir $pfam_database.fields.path
+ #end if
+
+ ##--debug
+
+ --disable-embl
+ --outputfolder $outputfolder
+
+ #echo 'input_tempfile.' + $file_extension#
+
+ ## leave out the start and end features, it can be easily replaced with Galaxy tools
+ ##--from START Start analysis at nucleotide specified
+ ##--to END
+
+ 2>&1
+
+ ##
+ ## shuffling files to create the correct outputs for Galaxy
+ ##
+
+ ## html output
+ ;
+ cp #echo os.path.join($outputfolder, 'index.html')# $html 2> /dev/null
+
+ ## gene clusters
+ #if 'geneclusterprots_tabular' in str($outputs).split(','):
+ ;
+ cp #echo os.path.join($outputfolder, 'geneclusters.txt')# $geneclusterprots_tabular 2> /dev/null
+ #end if
+
+ #if 'geneclusterprots_fasta' in str($outputs).split(','):
+ ;
+ cp #echo os.path.join($outputfolder, '*_genecluster_proteins.fa')# $geneclusterprots_fasta 2> /dev/null
+ #end if
+
+
+ ##SVG images
+ #if 'archive_svgs' in str($outputs).split(','):
+ ;
+ cd #echo os.path.join($outputfolder, 'svg')#
+ #if $clusterblast:
+ ;
+ tar cfz $archive_svgs *_all.svg genecluster* 2> /dev/null
+ #else:
+ ;
+ tar cfz $archive_svgs genecluster*
+ #end if
+ #end if
+
+ ##all files in a archive
+ #if 'archive' in str($outputs).split(','):
+ ;
+ cd $outputfolder;
+ tar cf $archive *.zip 2> /dev/null
+ #end if
+
+ ## genbank
+ #if 'gb' in str($outputs).split(','):
+ ;
+ cat #echo os.path.join($outputfolder, '*.gbk')# > $genbank 2> /dev/null
+ #end if
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 'geneclusterprots_fasta' in outputs
+
+
+ 'geneclusterprots_tabular' in outputs
+
+
+ 'archive' in outputs
+
+
+ 'archive_svgs' in outputs
+
+
+
+
+
+ 'gb' in outputs
+
+
+
+
+.. class:: infomark
+
+**What it does**
+
+antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes.
+It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.
+
+
+**Input**
+
+The ideal input for antiSMASH is an annotated nucleotide file in Genbank format. If no annotation is available,
+we recommend running your sequence through an annotation pipeline like RAST are the one included in Galaxy.
+
+
+There are several optional analyses that may or may not be run on your sequence.
+Highly recommended is the Gene Cluster Blast Comparative Analysis, which runs BlastP using each amino acid sequence from a detected gene cluster as a
+query on a large database of predicted protein sequences from secondary metabolite biosynthetic gene clusters, and pools the results to identify
+the gene clusters that are most homologous to the gene cluster that was detected in your query nucleotide sequence.
+
+
+Also available is the analysis of secondary metabolism gene families (smCOGs).
+This analysis attempts to allocate each gene in the detected gene clusters to a secondary metabolism-specific gene
+family using profile hidden Markov models specific for the conserved sequence region characteristic of this family.
+Additionally, a phylogenetic tree is constructed of each gene together with the (max. 100) sequences of the smCOG seed alignment.
+
+
+For the most thorough genome analysis, we provide genome-wide PFAM HMM analysis of all genes in the genome through modules of the CLUSEAN pipeline.
+Of course, some regions important to secondary metabolism may have been missed in the gene cluster identification stage
+(e.g. because they represent the biosynthetic pathway of a yet unknown secondary metabolite).
+Therefore, when genome-wide PFAM HMM analysis is selected, the PFAM frequencies are also used to find all genome regions in which PFAM domains typical for secondary metabolism are overrepresented.
+
+
+**References**
+
+Marnix H. Medema, Kai Blin, Peter Cimermancic, Victor de Jager, Piotr Zakrzewski, Michael A. Fischbach, Tilmann Weber,
+Rainer Breitling and Eriko Takano (2011). antiSMASH: Rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters. Nucleic Acids Research, doi: 10.1093/nar/gkr466.
+
+http://antismash.secondarymetabolites.org/help.html
+
+
+Bjoern A. Gruening: https://github.com/bgruening/galaxytools/tree/master/antismash
+
+
+
diff -r 000000000000 -r 5db064bbb3be readme.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.rst Tue Jul 15 14:34:55 2014 -0400
@@ -0,0 +1,65 @@
+Galaxy wrapper for AntiSmash
+=====================================
+
+This wrapper is copyright 2012-2014 by Björn Grüning.
+
+This is a wrapper for the command line tool of antiSMASH.
+
+antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes.
+It integrates and cross-links with a large number of in silico secondary metabolite analysis tools.
+
+http://antismash.secondarymetabolites.org/
+
+Marnix H. Medema, Kai Blin, Peter Cimermancic, Victor de Jager, Piotr Zakrzewski, Michael A. Fischbach, Tilmann Weber, Rainer Breitling & Eriko Takano (2011).
+antiSMASH: Rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters. Nucleic Acids Research 39: W339-W346.
+
+
+Installation
+============
+
+Galaxy should be able to automatically install the dependencies, i.e. the
+'package_hmmer_3_0' or 'package_blast_plus_2_2_28' repository.
+
+You must tell Galaxy about any system level Pfam databases using the configuration
+file antismash.loc.
+
+You can download the Pfam provided databases as compressed archives from here:
+
+* ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/
+
+
+External Data
+=============
+
+The antismash.loc file contains the path to a Pfam database.
+For any other tool that also uses a Pfam database *.log file, you can sync or link both *.loc files.
+
+
+
+History
+=======
+
+v0.1 - Initial public release
+
+
+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:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the 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.
+
diff -r 000000000000 -r 5db064bbb3be repository_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml Tue Jul 15 14:34:55 2014 -0400
@@ -0,0 +1,4 @@
+
+
+
+
diff -r 000000000000 -r 5db064bbb3be static/images/antismash_html_overview.png
Binary file static/images/antismash_html_overview.png has changed
diff -r 000000000000 -r 5db064bbb3be static/images/antismash_user_interface.png
Binary file static/images/antismash_user_interface.png has changed
diff -r 000000000000 -r 5db064bbb3be tool-data/antismash.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/antismash.loc.sample Tue Jul 15 14:34:55 2014 -0400
@@ -0,0 +1,16 @@
+#This is a sample file distributed with Galaxy that is used to define a
+#list of PFAM hmms, using three columns tab separated
+#(longer whitespace are TAB characters):
+#
+#The entries are as follows:
+#
+#
+#
+#Your antismash.loc file should include an entry per line. For example:
+#
+#pfam01 PFAM 27 08 Aug 2013 /data/0/galaxy_data/antismash/pfam/08_08_2013/
+#
+#...etc...
+#
+
+
diff -r 000000000000 -r 5db064bbb3be tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Tue Jul 15 14:34:55 2014 -0400
@@ -0,0 +1,8 @@
+
+
+
+