view antismash.xml @ 9:b11e1dfbc7c9 draft

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−<tool id="antismash" name="Secondary Metabolites" version="2.0.2.0">
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−    <description>and Antibiotics Analysis (antiSMASH)</description>
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−    <requirements>
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−        <requirement type="package" version="3.0">hmmer</requirement>
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−        <requirement type="package" version="2.3.2">hmmer</requirement>
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−        <requirement type="package" version="2.2.28">blast+</requirement>
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−        <requirement type="package" version="3.8.31">muscle</requirement>
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−        <requirement type="package" version="1.62">biopython</requirement>
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−        <requirement type="package" version="2.0.2">antismash_python_deps</requirement>
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−        <requirement type="package" version="2.0.2">antismash</requirement>
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−    </requirements>
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−    <command>
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−        run_antismash.py 
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−
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−            --input $infile
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−            --cpus 4
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−            #set $type_list = ','.join([$type for $type in $types])
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−            --enable $type_list
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−            --input-type nucl
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−            $smcogs
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−            $clusterblast
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−            $subclusterblast
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−            $inclusive
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−            $full_hmmer
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−            $full_blast
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−
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−            --pfamdir  $pfam_database.fields.path
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−
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−            ## leave out the start and end features, it can be easily replaced with Galaxy tools
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−            ##--from START          Start analysis at nucleotide specified
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−            ##--to END  
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−
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−    </command>
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−    <inputs>
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−        <param name="infile" type="data" format="gb,embl" label="Nucleotide sequence file in GenBank or EMBL format"/>
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−
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−        <param name="smcogs" type="boolean" label="Look for sec.met. clusters of orthologous groups" falsevalue="" truevalue="--smcogs" checked="false" />
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−        <param name="clusterblast" type="boolean" label="BLAST identified clusters against known clusters" truevalue="--clusterblast" falsevalue="" checked="false" />
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−        <param name="subclusterblast" type="boolean" label="BLAST identified clusters against known subclusters" truevalue="--subclusterblast" falsevalue="" checked="false" />
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−
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−        <param name="inclusive" type="boolean" label="Use inclusive algorithm for cluster detection" truevalue="--inclusive" falsevalue="" checked="false" />
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−        <param name="full_hmmer" type="boolean" label="Run a whole-genome HMMer analysis" truevalue="--full-hmmer" falsevalue="" checked="false" />
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−        <param name="full_blast" type="boolean" label="Run a whole-genome BLAST analysis" truevalue="--full-blast" falsevalue="" checked="false" />
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−
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−        <param name="pfam_database" type="select" label="Pfam database" help="Pfam Covariance models">
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−            <options from_file="antismash.loc">
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−              <column name="value" index="0"/>
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−              <column name="name" index="1"/>
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−              <column name="path" index="2"/>
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−            </options>
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−        </param>
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−
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−        <param name="types" type="select" display="checkboxes" multiple="true" label="Gene cluster types to search">
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−            <option value="t1pks" selected="True">type I polyketide synthases</option>
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−            <option value="t2pks" selected="True">type II polyketide synthases</option>
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−            <option value="t3pks" selected="True">type III polyketide synthases</option>
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−            <option value="t4pks" selected="True">type IV polyketide synthases</option>
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−            <option value="transatpks" selected="True">trans-AT PKS</option>
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−            <option value="nrps" selected="True">nonribosomal peptide synthetases</option>
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−            <option value="terpene" selected="True">terpene synthases</option>
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−            <option value="lantipeptide" selected="True">lantipeptides</option>
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−            <option value="bacteriocin" selected="True">bacteriocins</option>
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−            <option value="blactam" selected="True">beta-lactams</option>
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−            <option value="amglyccycl" selected="True">aminoglycosides / aminocyclitols</option>
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−            <option value="aminocoumarin" selected="True">aminocoumarins</option>
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−            <option value="siderophore" selected="True">siderophores</option>
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−            <option value="ectoine" selected="True">ectoines</option>
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−            <option value="butyrolactone" selected="True">butyrolactones</option>
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−            <option value="indole" selected="True">indoles</option>
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−            <option value="nucleoside" selected="True">nucleosides</option>
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−            <option value="phosphoglycolipid" selected="True">phosphoglycolipids</option>
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−            <option value="oligosaccharide" selected="True">oligosaccharides</option>
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−            <option value="furan" selected="True">furans</option>
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−            <option value="hserlactone" selected="True">hserlactones</option>
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−            <option value="thiopeptide" selected="True">thiopeptides</option>
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−            <option value="phenazine" selected="True">phenazines</option>
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−            <option value="phosphonate" selected="True">phosphonates</option>
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−            <option value="others" selected="True">others</option>
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−        </param>
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−
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−    </inputs>
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−    <outputs>
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−        <data format="fasta" name="geneclusterprots" label="${tool.name} on ${on_string} (Gen Cluster Proteins)" />
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−        <data format="tabular" name="zip" label="${tool.name} on ${on_string} (all files compressed)" />
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−        <data format="html" name="html" label="${tool.name} on ${on_string} (html report)" />
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−        <data name="embl" format="text" label="${tool.name} on ${on_string} EMBL Output Format">
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−          <filter>(wg_blast == True or pfam == True)</filter>
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−        </data>
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−    </outputs>
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−  <help>
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−    
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−.. class:: infomark
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−
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−That version of antiSMASH can only handle one sequence. So multi-sequence FASTA files are not supported.
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−For multiple sequences please use multi-antiSMASH. The advantage of that tool is that it will provide you with a 
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−archive of all results created from antiSMASH (It can be large!) and a HTML output, for better inspection.
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−
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−
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−**What it does**
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−
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−antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. 
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−It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.
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−
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−
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−**Input**
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−
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−If you don't have an annotated GenBank or embl file you also can provide a glimmer prediction output. You can created it with glimmer or glimmerHMM.
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−
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−
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−**References**
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−
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−Marnix H. Medema, Kai Blin, Peter Cimermancic, Victor de Jager, Piotr Zakrzewski, Michael A. Fischbach, Tilmann Weber, 
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−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.
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−
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−http://antismash.secondarymetabolites.org/help.html
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−
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−  </help>
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−</tool>