<tool id="antiSMASH" name="Secondary Metabolites" version="0.1">
  <description>and Antibiotics Analysis (antiSMASH)</description>
  <command interpreter="python">antiSMASH_wrapper.py 
## The command is a Cheetah template which allows some Python based syntax.
## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
## ./antismash.py Tue6071_genome.fasta --geneclustertypes 1 --fullblast y --fullhmm y
    --input $infile
    --glimmer_prediction $glimmer_prediction
    $eukaryotic 
    $genecluster 
    $smCOG 
    $wg_blast 
    --geneclustertypes $geneclustertypes
    --geneclusterprots $geneclusterprots
    --zip $zip
    --html_file $html
    --html_path $html.files_path
    --embl_path $embl
    > /dev/null 2> /dev/null
  </command>
  <inputs>
    <param name="infile" type="data" format="fasta" label="Sequence File"/>
    <param name="glimmer_prediction" type="data" format="tabular" label="Glimmer Prediction File"/>
    <param name="eukaryotic" type="boolean" label="is the DNA of Eukaryotic origin" truevalue="--eukaryotic" falsevalue="" checked="false" />

    <param name="smCOG" type="boolean" label="smCOG analysis for functional prediction and phylogenetic analysis of genes" falsevalue="" truevalue="--smcogs" checked="false" />
    <param name="genecluster" type="boolean" label="Gene Cluster Blast Comparative Analysis" truevalue="--clusterblast" falsevalue="" checked="false" />
    <param name="wg_blast" type="boolean" label="Whole genome BLAST results in EMBL output" truevalue="--fullblast" falsevalue="" checked="false" />
    <param name="pfam" type="boolean" label="Whole genome PFAM results in EMBL output" truevalue="--fullhmm" falsevalue="" checked="false" />

        <param name="geneclustertypes" type="select" display="checkboxes" multiple="true" label="Gene cluster types to search">
            <option value="1" selected="True">all</option>
            <option value="2">type I polyketide synthases</option>
            <option value="3">type II polyketide synthases</option>
            <option value="4">type III polyketide synthases</option>
            <option value="5">nonribosomal peptide synthetases</option>
            <option value="6">terpene synthases</option>
            <option value="7">lantibiotics</option>
            <option value="8">bacteriocins</option>
            <option value="9">beta-lactams</option>
            <option value="10">aminoglycosides / aminocyclitols</option>
            <option value="11">aminocoumarins</option>
            <option value="12">siderophores</option>
            <option value="13">ectoines</option>
            <option value="14">butyrolactones</option>
            <option value="15">indoles</option>
            <option value="16">nucleosides</option>
            <option value="17">phosphoglycolipids</option>
            <option value="18">melanins</option>
            <option value="19">others</option>
        </param>
  </inputs>
  <outputs>
    <data format="fasta" name="geneclusterprots" label="${tool.name} on ${on_string} (Gen Cluster Proteins)" />
    <data format="tabular" name="zip" label="${tool.name} on ${on_string} (all files compressed)" />
    <data format="html" name="html" label="${tool.name} on ${on_string} (html report)" />
    <data name="embl" format="text" label="${tool.name} on ${on_string} EMBL Output Format">
      <filter>(wg_blast == True or pfam == True)</filter>
    </data>
  </outputs>
  <help>
    
.. class:: infomark

That version of antiSMASH can only handle one sequence. So multi-sequence FASTA files are not supported.
For multiple sequences please use multi-antiSMASH. The advantage of that tool is that it will provide you with a 
archive of all results created from antiSMASH (It can be large!) and a HTML output, for better inspection.


**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**

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.


**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

  </help>
</tool>