<tool id="multi_antiSMASH" name="Secondary Metabolites" version="0.1">
  <description>and Antibiotics Analysis (multi antiSMASH)</description>
  <command interpreter="python">multi_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

    #if $input_opts.input_opts_selector == "fasta":
        --input $infile
        --glimmer_prediction $glimmer_prediction
    #else:
        --input $infile
    #end if

    --input_format $input_opts.input_opts_selector

    $eukaryotic 
    $genecluster 
    $smCOG 
    $wg_blast 
    --geneclustertypes $geneclustertypes
    --geneclusterprots $geneclusterprots
    --geneclusterprots_gff $geneclusterprots_gff
    --embl_path $embl
    > /dev/null 2> /dev/null
  </command>
  <inputs>

    <conditional name="input_opts">
        <param name="input_opts_selector" type="select" label="Input format">
          <option value="fasta" selected="True">FASTA file (not annotated)</option>
          <option value="genbank">GenBank file (annotated)</option>
          <option value="embl">embl file (annotated)</option>
        </param>
        <when value="fasta">
            <param name="infile" type="data" format="fasta" label="Sequence File"/>
            <param name="glimmer_prediction" type="data" format="tabular" label="Glimmer Prediction File"/>
        </when>
        <when value="embl">
            <param name="infile" type="data" format="embl" label="embl Sequence File"/>
        </when>
        <when value="genbank">
            <param name="infile" type="data" format="embl" label="GenBank Sequence File"/>
        </when>
    </conditional>




    <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="true" />
    <param name="genecluster" type="boolean" label="Gene Cluster Blast Comparative Analysis" truevalue="--clusterblast" falsevalue="" checked="true" />
    <param name="wg_blast" type="boolean" label="Whole genome BLAST results in EMBL output" truevalue="--fullblast" falsevalue="" checked="true" />
    <param name="pfam" type="boolean" label="Whole genome PFAM results in EMBL output" truevalue="--fullhmm" falsevalue="" checked="true" />

        <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 ${on_string} (Gen Cluster Proteins)" />
    <data format="gff3" name="geneclusterprots_gff" label="${tool.name} on ${on_string} (Gen Cluster Proteins)" />
    <data name="embl" format="text" label="${tool.name} on ${on_string} EMBL Output Format">
    </data>
  </outputs>
  <help>
    
.. class:: infomark

That version of antiSMASH can only handle multiple sequence files.
It will run antiSMASH automatically on each sequence and aggregate the most important information from all runs.
It will not provide an interactive HTML output file. If you need that please use the normal antiSMASH version on a single sequence.


.. class:: warningmark

**Warning on FASTA Header**

The FASTA header should not contain any special letters, like '|'. Please replace them with the 'sed-tool'.


**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. Created 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>