Mercurial > repos > bgruening > antismash
changeset 25:99435bb90725 draft
Uploaded
| author | bgruening |
|---|---|
| date | Fri, 18 Oct 2013 03:35:17 -0400 |
| parents | b942dfd80819 |
| children | a5eb6fad2a76 |
| files | antismash.xml src/genecluster_sequence/__init__.py tool_dependencies.xml |
| diffstat | 3 files changed, 99 insertions(+), 24 deletions(-) [+] |
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--- a/antismash.xml Tue Oct 15 04:19:33 2013 -0400 +++ b/antismash.xml Fri Oct 18 03:35:17 2013 -0400 @@ -2,14 +2,18 @@ <description>and Antibiotics Analysis (antiSMASH)</description> <requirements> <requirement type="package" version="3.0">hmmer</requirement> + <requirement type="package">hmmer</requirement> <requirement type="package" version="2.2.28">blast+</requirement> + <requirement type="package">blast+</requirement> <requirement type="package" version="3.8.31">muscle</requirement> + <requirement type="package">muscle</requirement> <requirement type="package" version="1.4.0-post-1">straight.plugin</requirement> <requirement type="package" version="1.62">biopython</requirement> <requirement type="package" version="1.2.6">pyquery</requirement> <requirement type="package" version="0.1.2">helperlibs</requirement> <requirement type="package" version="0.9">cssselect</requirement> <requirement type="package" version="2.0.2">antismash</requirement> + <requirement type="package">antismash</requirement> </requirements> <command> #import os, glob @@ -24,7 +28,7 @@ ln -s $infile #echo 'input_tempfile.' + $file_extension#; mkdir -p $outputfolder; run_antismash.py - --cpus 4 + --cpus 12 --enable $types --input-type 'nucl' $smcogs @@ -33,11 +37,15 @@ $inclusive $full_hmmer $full_blast + $eukaryotic + #if str($pfam_database) != "None": --pfamdir $pfam_database.fields.path #end if + --debug + --disable-embl --outputfolder $outputfolder @@ -47,49 +55,63 @@ ##--from START Start analysis at nucleotide specified ##--to END - ; + 2>&1 + + ## ## shuffling files to create the correct outputs for Galaxy - + ## + ## html output - #if 'html' in str($outputs).split(','): - cp #echo os.path.join($outputfolder, 'index.html')# $html 2>/dev/null; - #end if + ; + cp #echo os.path.join($outputfolder, 'index.html')# $html 2> /dev/null ## gene clusters #if 'geneclusterprots_tabular' in str($outputs).split(','): - cp #echo os.path.join($outputfolder, 'geneclusters.txt')# $geneclusterprots_tabular 2>/dev/null; + ; + cp #echo os.path.join($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')# $geneclusterprots_fasta 2>/dev/null; + ; + cp #echo os.path.join($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($outputfolder, 'svg')#; + ; + cd #echo os.path.join($outputfolder, 'svg')# #if $clusterblast: - tar cfz $archive_svgs *_all.svg genecluster* 2>/dev/null; + ; + tar cfz $archive_svgs *_all.svg genecluster* 2> /dev/null #else: - tar cfz $archive_svgs genecluster*; + ; + 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; + tar cf $archive *.zip 2> /dev/null #end if ## genbank #if 'gb' in str($outputs).split(','): - cat #echo os.path.join($outputfolder, '*.gbk')# > $genbank 2>/dev/null; + ; + cat #echo os.path.join($outputfolder, '*.gbk')# > $genbank 2> /dev/null #end if </command> <inputs> <param name="infile" type="data" format="genbank" label="Nucleotide sequence file in GenBank format"/> + <param name="eukaryotic" type="select" label="Origin of DNA"> + <option value="" selected="True">Prokaryotic</option> + <option value="--eukaryotic">Eukaryotic</option> + </param> + <param name="clusterblast" type="boolean" label="BLAST identified clusters against known clusters" help="(--clusterblast)" truevalue="--clusterblast" falsevalue="" checked="True" /> @@ -146,10 +168,9 @@ <option value="other" selected="True">others</option> </param> - <param name="outputs" type="select" multiple="true" label="Output formats"> + <param name="outputs" type="select" multiple="true" label="Additional outputs"> <option value="geneclusterprots_fasta" selected="True">Gene cluster proteins (FASTA)</option> <option value="geneclusterprots_tabular">Gene cluster proteins (Tabular)</option> - <option value="html" selected="True">Interactive summary page (html)</option> <option value="archive_svgs">All clusters as image (compressed)</option> <option value="archive">All files compressed</option> <option value="gb">Annotated genome (GenBank)</option> @@ -170,7 +191,9 @@ <filter>'archive_svgs' in outputs</filter> </data> <data format="html" name="html" label="${tool.name} on ${on_string} (html report)"> + <!-- html is default output at any time. <filter>'html' in outputs</filter> + --> </data> <data name="genbank" format="genbank" label="${tool.name} on ${on_string} (genbank)"> <filter>'gb' in outputs</filter> @@ -217,5 +240,8 @@ http://antismash.secondarymetabolites.org/help.html + +Bjoern A. Gruening: https://github.com/bgruening/galaxytools/tree/master/antismash + </help> </tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/src/genecluster_sequence/__init__.py Fri Oct 18 03:35:17 2013 -0400 @@ -0,0 +1,37 @@ +#!/usr/bin/env python + +""" + antiSMASH 2.0 output plugin to write all cluster proteins to a file (*_genecluster_proteins.fa) +""" +import logging +import textwrap +from os import path +from antismash import utils + +name = "genecluster_proteins" +short_description = "Ouptut gene clusters as FASTA sequences" +# Output plugins are sorted by priority, lower numbers get run first +priority = 9 + +def write(seq_records, options): + """Write all cluster proteins to a file + + Args: + seq_records (iterable): An iterable containing Bio.SeqRecords + options (argparse.Namespace): The options passed to the program + """ + basename = seq_records[0].id + output_name = path.join(options.outputfoldername, "%s_genecluster_proteins.fa" % basename) + logging.debug("Writing seq_records to %r" % output_name) + + with open(output_name, 'w+') as handle: + for seq_record in seq_records: + clusters = utils.get_cluster_features(seq_record) + for cluster in clusters: + clustertype = utils.get_cluster_type(cluster) + clusternr = utils.get_cluster_number(cluster) + for feature in utils.get_cluster_cds_features(cluster, seq_record): + qual = feature.qualifiers + fasta_header = '>%s:%s %s #%s - %s\n' % (qual['locus_tag'][0], qual['protein_id'][0], clustertype, clusternr, qual['product'][0]) + handle.write( fasta_header ) + handle.write( '%s\n' % '\n'.join( textwrap.wrap(qual['translation'][0], 60) ) )
--- a/tool_dependencies.xml Tue Oct 15 04:19:33 2013 -0400 +++ b/tool_dependencies.xml Fri Oct 18 03:35:17 2013 -0400 @@ -7,7 +7,7 @@ <repository changeset_revision="a44693e3a2c4" name="package_hmmer_3_0" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </package> <package name="muscle" version="3.8.31"> - <repository changeset_revision="ce304c51f69b" name="package_muscle_3_8_31" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="83bd107a5300" name="package_muscle_3_8_31" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </package> <package name="biopython" version="1.62"> <repository changeset_revision="ac9cc2992b69" name="package_biopython_1_62" owner="biopython" toolshed="http://testtoolshed.g2.bx.psu.edu" /> @@ -18,7 +18,10 @@ <actions> <action type="download_by_url">https://pypi.python.org/packages/source/h/helperlibs/helperlibs-0.1.2.tar.gz</action> <action type="make_directory">$INSTALL_DIR/lib/python</action> - <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin</action> + <action type="shell_command"> + export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && + python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin + </action> <action type="set_environment"> <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> @@ -35,7 +38,10 @@ <actions> <action type="download_by_url">https://pypi.python.org/packages/source/c/cssselect/cssselect-0.9.tar.gz</action> <action type="make_directory">$INSTALL_DIR/lib/python</action> - <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin</action> + <action type="shell_command"> + export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && + python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin + </action> <action type="set_environment"> <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> @@ -52,7 +58,10 @@ <actions> <action type="download_by_url">https://github.com/gawel/pyquery/archive/1.2.6.tar.gz</action> <action type="make_directory">$INSTALL_DIR/lib/python</action> - <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin</action> + <action type="shell_command"> + export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && + python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin + </action> <action type="set_environment"> <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> @@ -69,7 +78,10 @@ <actions> <action type="download_by_url">https://pypi.python.org/packages/source/s/straight.plugin/straight.plugin-1.4.0-post-1.tar.gz</action> <action type="make_directory">$INSTALL_DIR/lib/python</action> - <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin</action> + <action type="shell_command"> + export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python && + python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin + </action> <action type="set_environment"> <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable> <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> @@ -83,8 +95,7 @@ <package name="antismash" version="2.0.2"> <install version="1.0"> <actions_group> - - <!-- Download the binaries for antiSMASH compatible with 64-bit OSX. --> + <!-- Download the binaries for MUSCLE compatible with 64-bit OSX. --> <actions architecture="x86_64" os="darwin"> <action type="download_by_url">https://bitbucket.org/antismash/antismash2/downloads/antiSMASH2.0.2_macosx.zip</action> <action type="move_directory_files"> @@ -109,10 +120,10 @@ --> <action type="shell_command">sed -i 's/check_prereqs(plugins, options) > 0/False/g' $INSTALL_DIR/run_antismash.py</action> <action type="download_file">https://bitbucket.org/antismash/antismash2/downloads/clusterblast.tar.gz</action> - <action type="shell_command">tar xfvz clusterblast.tar.gz -C $INSTALL_DIR/antismash/generic_modules/clusterblast</action>n> + <action type="shell_command">tar xfvz clusterblast.tar.gz -C $INSTALL_DIR/antismash/generic_modules/clusterblast</action> </actions> - <!-- Download the binaries for antiSMASH compatible with 64-bit OSX. --> + <!-- Download the binaries for MUSCLE compatible with 64-bit OSX. --> <actions architecture="i386" os="darwin"> <action type="download_by_url">https://bitbucket.org/antismash/antismash2/downloads/antiSMASH2.0.2_macosx.zip</action> <action type="move_directory_files"> @@ -209,6 +220,7 @@ </install> <readme> AntiSmash installation with all dependencies. + Java needs to be installed. </readme> </package> </tool_dependency>