<tool id="obi_convert" name="obiconvert" version="@TOOL_VERSION@" profile="@PROFILE@">
    <description>converts sequence files to different output formats</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <command><![CDATA[
        @GUNZIP_INPUT@
        
        obiconvert
        #if $db
            -d '$db'
        #end if
        #if $tax
            -t '$tax'
        #end if
        @INPUT_FORMAT@
        @OUT_FORMAT@
        ${uppercase}
        ${ecopcrdb}
        #if str( $ecopcrdb) == "--ecopcrdb"
            --ecopcrdb-output=${ecopcrdb_output}
        #end if
        input 
        @GZIP_OUTPUT@
        > '${output}'
        @GENERATE_GALAXY_JSON@
    ]]></command>
    <inputs>
        <param name="input" type="data" format="@INPUT_FORMATS@,txt,tabular" label="Input sequences file" help="database used for the in silico PCR. The database must be in the ecoPCR format (for example output of obiconvert)" />
        <param name="db" type="data" optional="true" format="txt,tabular" label="ecoPCR taxonomy database" />
        <param name="tax" type="data" optional="true" format="txt,tabular" label="NCBI taxonomy dump repository"/>
        <expand macro="input_format_options_macro"/>
        <expand macro="out_format_macro"/>
        <param name="ecopcrdb" type="boolean" truevalue="--ecopcrdb" falsevalue="" label="Do you want to create an ecoPCR database from sequence records results?"  help="Use this option if you want to generate an ecoPCR database output file" />
        <param name="uppercase" type="boolean" truevalue="--uppercase" falsevalue=""  label="Do you want to print sequences in upper case?" />
    </inputs>
    <outputs>
        <data format="txt" name="ecopcrdb_output" label="${tool.name} on ${on_string}: ecopcrdb">
            <filter>ecopcrdb == True</filter>
        </data>
        <data format="auto" name="output"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="output_obisort.fasta" />
            <param name="options_inputtype" value="--fasta"/>
            <param name="options_seqtype" value="--nuc"/>
            <param name="out_format" value="fasta"/>
            <param name="ecopcrdb" value="false"/>
            <param name="uppercase" value="true"/>
            <output name="output" file="output_obiconvert.fasta" ftype="fasta"/>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

**What it does**

obiconvert converts sequence files to different output formats. See the documentation for more details on the different formats.

Input files can be in :

fasta format

extended OBITools fasta format

Sanger fastq format

Solexa fastq format

ecoPCR format

ecoPCR database format

GenBank format

EMBL format

obiconvert converts those files to the :

extended OBITools fasta format

Sanger fastq format

ecoPCR database format

If no file name is specified, data is read from standard input.

@OBITOOLS_LINK@

    ]]>

    </help>
    <expand macro="citation" />
</tool>