Galaxy |

Changeset 0:5db064bbb3be (2014-07-15)

Next changeset 1:593bb8f5488b (2018-02-07)

Commit message:
Imported from capsule None

added:
antismash.xml
readme.rst
repository_dependencies.xml
static/images/antismash_html_overview.png
static/images/antismash_user_interface.png
tool-data/antismash.loc.sample
tool_data_table_conf.xml.sample
tool_dependencies.xml

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

b'@@ -0,0 +1,253 @@\n+<tool id="antismash" name="Secondary Metabolites" version="2.0.2.2">\n+ <description>and Antibiotics Analysis (antiSMASH)</description>\n+ <requirements>\n+ <requirement type="package" version="3.0">hmmer</requirement>\n+ <requirement type="package">hmmer</requirement>\n+ <requirement type="package" version="2.2.28">blast+</requirement>\n+ <requirement type="package">blast+</requirement>\n+ <requirement type="package" version="3.8.31">muscle</requirement>\n+ <requirement type="package">muscle</requirement>\n+ <requirement type="package" version="1.4.0-post-1">straight.plugin</requirement>\n+ <requirement type="package">straight.plugin</requirement>\n+ <requirement type="package" version="1.62">biopython</requirement>\n+ <requirement type="package">biopython</requirement>\n+ <requirement type="package" version="1.2.6">pyquery</requirement>\n+ <requirement type="package">pyquery</requirement>\n+ <requirement type="package" version="0.1.2">helperlibs</requirement>\n+ <requirement type="package">helperlibs</requirement>\n+ <requirement type="package" version="0.9">cssselect</requirement>\n+ <requirement type="package">cssselect</requirement>\n+ <requirement type="package" version="2.0.2">antismash</requirement>\n+ <requirement type="package">antismash</requirement>\n+ <requirement type="package">glimmer</requirement>\n+ </requirements>\n+ <command>\n+ #import os, glob\n+ #set $outputfolder = $html.files_path\n+ #if str($infile.ext) == \'genbank\':\n+ #set $file_extension = \'gb\'\n+ #else:\n+ ## TODO add embl as input file\n+ #set $file_extension = \'gb\'\n+ #end if\n+\n+ ln -s $infile #echo \'input_tempfile.\' + $file_extension#;\n+ mkdir -p $outputfolder;\n+ run_antismash.py \n+ --cpus "\\${GALAXY_SLOTS:-12}"\n+ --enable $types\n+ --input-type \'nucl\'\n+ $smcogs\n+ $clusterblast\n+ $subclusterblast\n+ $inclusive\n+ $full_hmmer\n+ $full_blast\n+ $eukaryotic\n+\n+\n+ #if str($pfam_database) != "None":\n+ --pfamdir $pfam_database.fields.path\n+ #end if\n+\n+ ##--debug\n+\n+ --disable-embl\n+ --outputfolder $outputfolder\n+\n+ #echo \'input_tempfile.\' + $file_extension#\n+\n+ ## leave out the start and end features, it can be easily replaced with Galaxy tools\n+ ##--from START Start analysis at nucleotide specified\n+ ##--to END\n+\n+ 2>&1\n+\n+ ##\n+ ## shuffling files to create the correct outputs for Galaxy\n+ ##\n+\n+ ## html output\n+ ;\n+ cp #echo os.path.join($outputfolder, \'index.html\')# $html 2> /dev/null\n+ \n+ ## gene clusters\n+ #if \'geneclusterprots_tabular\' in str($outputs).split(\',\'):\n+ ;\n+ cp #echo os.path.join($outputfolder, \'geneclusters.txt\')# $geneclusterprots_tabular 2> /dev/null\n+ #end if\n+\n+ #if \'geneclusterprots_fasta\' in str($outputs).split(\',\'):\n+ ;\n+ cp #echo os.path.join($outputfolder, \'*_genecluster_proteins.fa\')# $geneclusterprots_fasta 2> /dev/null\n+ #end if\n+\n+\n+ ##SVG images\n+ #if \'archive_svgs\' in str($outputs).split(\',\'):\n+ ;\n+ cd #echo os.path.join($outputfolder, \'svg\')#\n+ #if $clusterblast:\n+ ;\n+ tar cfz $archive_svgs *_all.svg genecluster* 2> /dev/null\n+ #else:\n+ ;\n+ tar cfz $archive_svgs genecluster*\n+ #end if\n+ #end if\n+\n+ ##all files in a archive\n+ #if \'archive\' in str($outputs).split(\',\'):\n+ ;\n+ cd $outputfolder;\n+ tar cf $archive *.zip 2> /dev/null\n+ #end if\n+\n+ ## g'..b'ters as image (compressed)</option>\n+ <option value="archive">All files compressed</option>\n+ <option value="gb">Annotated genome (GenBank)</option>\n+ </param>\n+\n+ </inputs>\n+ <outputs>\n+ <data format="fasta" name="geneclusterprots_fasta" label="${tool.name} on ${on_string} (Gen Cluster Proteins)">\n+ <filter>\'geneclusterprots_fasta\' in outputs</filter>\n+ </data>\n+ <data format="tabular" name="geneclusterprots_tabular" label="${tool.name} on ${on_string} (Gen Cluster Proteins)">\n+ <filter>\'geneclusterprots_tabular\' in outputs</filter>\n+ </data>\n+ <data format="tar" name="archive" label="${tool.name} on ${on_string} (all files compressed)">\n+ <filter>\'archive\' in outputs</filter>\n+ </data>\n+ <data format="tar.gz" name="archive_svgs" label="${tool.name} on ${on_string} (SVG images)">\n+ <filter>\'archive_svgs\' in outputs</filter>\n+ </data>\n+ <data format="html" name="html" label="${tool.name} on ${on_string} (html report)">\n+ \n+ </data>\n+ <data name="genbank" format="genbank" label="${tool.name} on ${on_string} (genbank)">\n+ <filter>\'gb\' in outputs</filter>\n+ </data>\n+ </outputs>\n+ <help>\n+ \n+.. class:: infomark\n+\n+**What it does**\n+\n+antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. \n+It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.\n+\n+\n+**Input**\n+\n+The ideal input for antiSMASH is an annotated nucleotide file in Genbank format. If no annotation is available, \n+we recommend running your sequence through an annotation pipeline like RAST are the one included in Galaxy.\n+\n+\n+There are several optional analyses that may or may not be run on your sequence.\n+Highly recommended is the Gene Cluster Blast Comparative Analysis, which runs BlastP using each amino acid sequence from a detected gene cluster as a \n+query on a large database of predicted protein sequences from secondary metabolite biosynthetic gene clusters, and pools the results to identify \n+the gene clusters that are most homologous to the gene cluster that was detected in your query nucleotide sequence.\n+\n+\n+Also available is the analysis of secondary metabolism gene families (smCOGs). \n+This analysis attempts to allocate each gene in the detected gene clusters to a secondary metabolism-specific gene \n+family using profile hidden Markov models specific for the conserved sequence region characteristic of this family. \n+Additionally, a phylogenetic tree is constructed of each gene together with the (max. 100) sequences of the smCOG seed alignment.\n+\n+\n+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. \n+Of course, some regions important to secondary metabolism may have been missed in the gene cluster identification stage \n+(e.g. because they represent the biosynthetic pathway of a yet unknown secondary metabolite). \n+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.\n+\n+\n+**References**\n+\n+Marnix H. Medema, Kai Blin, Peter Cimermancic, Victor de Jager, Piotr Zakrzewski, Michael A. Fischbach, Tilmann Weber, \n+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.\n+\n+http://antismash.secondarymetabolites.org/help.html\n+\n+\n+Bjoern A. Gruening: https://github.com/bgruening/galaxytools/tree/master/antismash\n+\n+ </help>\n+</tool>\n'

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 @@
+<?xml version="1.0"?>
+<repositories description="AntiSmash requires the Galaxy applicable data formats used by Emboss tools, especially genbank.">
+ <repository changeset_revision="a89163f31369" name="emboss_datatypes" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
+</repositories>

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:
+#
+#<unique_id> <PFAM name> <path>
+#
+#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 @@
+
+<tables>
+    
+    <table name="antismash_pfam" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/antismash.loc" />
+    </table>
+</tables>

diff -r 000000000000 -r 5db064bbb3be tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Tue Jul 15 14:34:55 2014 -0400

b'@@ -0,0 +1,217 @@\n+<?xml version="1.0"?>\n+<tool_dependency>\n+ <package name="blast+" version="2.2.28">\n+ <repository changeset_revision="23b9ba41ad00" name="package_blast_plus_2_2_28" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />\n+ </package>\n+ <package name="hmmer" version="3.0">\n+ <repository changeset_revision="bae6be83ada5" name="package_hmmer_3_0" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />\n+ </package>\n+ <package name="muscle" version="3.8.31">\n+ <repository changeset_revision="8f20b47725d8" name="package_muscle_3_8_31" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />\n+ </package>\n+ <package name="biopython" version="1.62">\n+ <repository changeset_revision="3e82cbc44886" name="package_biopython_1_62" owner="biopython" toolshed="http://toolshed.g2.bx.psu.edu" />\n+ </package>\n+ <package name="helperlibs" version="0.1.2">\n+ <install version="1.0">\n+ <actions>\n+ <action type="download_by_url">https://pypi.python.org/packages/source/h/helperlibs/helperlibs-0.1.2.tar.gz</action>\n+ <action type="make_directory">$INSTALL_DIR/lib/python</action>\n+ <action type="shell_command">\n+ export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && \n+ python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin\n+ </action>\n+ <action type="set_environment">\n+ <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>\n+ <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>\n+ </action>\n+ </actions>\n+ </install>\n+ <readme>\n+ helperlibs python library\n+ </readme>\n+ </package>\n+ <package name="cssselect" version="0.9">\n+ <install version="1.0">\n+ <actions>\n+ <action type="download_by_url">https://pypi.python.org/packages/source/c/cssselect/cssselect-0.9.tar.gz</action>\n+ <action type="make_directory">$INSTALL_DIR/lib/python</action>\n+ <action type="shell_command">\n+ export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && \n+ python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin\n+ </action>\n+ <action type="set_environment">\n+ <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>\n+ <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>\n+ </action>\n+ </actions>\n+ </install>\n+ <readme>\n+ cssselect python library\n+ </readme>\n+ </package>\n+ <package name="pyquery" version="1.2.6">\n+ <install version="1.0">\n+ <actions>\n+ <action type="download_by_url">https://github.com/gawel/pyquery/archive/1.2.6.tar.gz</action>\n+ <action type="make_directory">$INSTALL_DIR/lib/python</action>\n+ <action type="shell_command">\n+ export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && \n+ python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin\n+ </action>\n+ <action type="set_environment">\n+ <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>\n+ <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>\n+ </action>\n+ </actions>\n+ </install>\n+ <readme>\n+ pyquery python library\n+ </readme>\n+ </package>\n+ <'..b' <action type="make_directory">$INSTALL_DIR/antismash/output_modules/genecluster_sequence/</action>\n+ <action type="move_file">\n+ <source>__init__.py</source>\n+ <destination>$INSTALL_DIR/antismash/output_modules/genecluster_sequence/</destination>\n+ </action>\n+ \n+ <action type="shell_command">sed -i \'s/check_prereqs(plugins, options) > 0/False/g\' $INSTALL_DIR/run_antismash.py</action>\n+ <action type="download_file">https://bitbucket.org/antismash/antismash2/downloads/clusterblast.tar.gz</action>\n+ <action type="shell_command">tar xfvz clusterblast.tar.gz -C $INSTALL_DIR/antismash/generic_modules/clusterblast</action>\n+ </actions>\n+ \n+ <actions architecture="i386" os="linux">\n+ <action type="download_by_url">https://bitbucket.org/antismash/antismash2/downloads/antismash-2.0.2.i686.tar.bz2</action>\n+ <action type="move_directory_files">\n+ <source_directory>.</source_directory>\n+ <destination_directory>$INSTALL_DIR</destination_directory>\n+ </action>\n+ <action type="chmod">\n+ <file mode="750">$INSTALL_DIR/run_antismash.py</file>\n+ </action>\n+ \n+ <action type="download_file">https://raw.github.com/bgruening/galaxytools/master/antismash/src/genecluster_sequence/__init__.py</action>\n+ <action type="make_directory">$INSTALL_DIR/antismash/output_modules/genecluster_sequence/</action>\n+ <action type="move_file">\n+ <source>__init__.py</source>\n+ <destination>$INSTALL_DIR/antismash/output_modules/genecluster_sequence/</destination>\n+ </action>\n+ \n+ <action type="shell_command">sed -i \'s/check_prereqs(plugins, options) > 0/False/g\' $INSTALL_DIR/run_antismash.py</action>\n+ <action type="download_file">https://bitbucket.org/antismash/antismash2/downloads/clusterblast.tar.gz</action>\n+ <action type="shell_command">tar xfvz clusterblast.tar.gz -C $INSTALL_DIR/antismash/generic_modules/clusterblast</action>\n+ </actions>\n+ <actions>\n+\n+ </actions>\n+ \n+ <action type="set_environment">\n+ <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>\n+ <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR</environment_variable>\n+ </action>\n+ </actions_group>\n+ </install>\n+ <readme>\n+ AntiSmash installation with all dependencies.\n+ Java needs to be installed.\n+ </readme>\n+ </package>\n+</tool_dependency>\n'