<?xml version="1.0"?>
<tool id="askomics_integrate" name="AskOmics" version="@WRAPPER_VERSION@">
    <description>Data integration</description>

    <macros>
        <import>macros.xml</import>
    </macros>

    <expand macro='requirements' />

    <stdio>
        <exit_code range="1:" />
    </stdio>

    <command><![CDATA[
        askocli integrate

        #if @URL@
            -a @URL@
        #else
            -a @ENV_URL@
        #end if

        --file-type '$input_format.format'

        #if $input_format.format == "csv"

            #if $input_format.opt.headers
                --headers $input_format.opt.headers
            #end if

            #if $input_format.opt.col_type
                -c $input_format.opt.col_type
            #end if

            #if $input_format.opt.key_col
                --key-columns $input_format.opt.key_col
            #end if

            #if $input_format.opt.dis_col
                --disabled-columns $input_format.opt.dis_col
            #end if

        #end if

        #if $input_format.format == "gff"
            -e $input_format.ent
            -t '$input_format.tax'
        #end if

        #if $input_format.format == "bed"
            --entity-name $input_format.ent_name
            -t '$input_format.tax'
        #end if

        #if $advanced.uri
            --uri $advanced.uri
        #end if

        $advanced.public

        -k @APIKEY@

        '$input'
        > '$output'
    ]]></command>

    <inputs>
        <expand macro='askomics_loc' />
        <expand macro='askomics_auth' />

       <conditional name="input_format">
           <param type="select" name="format" label="Input format">
               <option value="csv">CSV/TSV</option>
               <option value="gff">GFF</option>
               <option value="ttl">Turtle</option>
               <option value="bed">BED</option>
            </param>
           <when value="csv">
               <param format="tabular" name="input" type="data" label="Dataset to integrate" />
               <section name='opt' title='Optional fields' expanded='false'>
                   <param name="headers" type="text" value="" optional="true" label="Headers (separated with spaces)" argument="--headers" />
                   <param name="col_type" type="text" value="" optional="true" label="Columns types (separated with spaces)" argument="-c" />
                   <param name="key_col" type="text" value="" optional="true" label="Key columns (separated with spaces)" argument="--key-columns" />
                   <param name="dis_col" type="text" value="" optional="true" label="Disabled columns (separated with spaces)" argument="--disabled-columns" />
                </section>
            </when>
            <when value="gff">
                <param format="gff3" name="input" type="data" label="Dataset to integrate" />
                <param name="ent" type="text" value="transcript gene" label="Entities (separated with space)" argument="-e" />
                <param name="tax" type="text" value="" label="Taxon" argument="-t" />
            </when>
            <when value="bed">
                <param format="bed" name="input" type="data" label="Dataset to integrate" />
                <param name="ent_name" type="text" value="" label="Entity name" argument="--entity-name" />
                <param name="tax" type="text" value="" label="Taxon" argument="-t" />
            </when>
            <when value="ttl">
                <param format="ttl" name="input" type="data" label="Dataset to integrate" />
            </when>
        </conditional>

        <!-- Advanced fonctionalities -->
        <section name="advanced" title="Advanced features" expanded="false">
            <param name="uri" type="text" value="" label="Custom URI" argument="--uri" />
            <param name="public" type="boolean" checked="false" truevalue="--public" falsevalue="" label="Integrate as a public dataset" argument="--public" />
        </section>

    </inputs>

    <outputs>
        <data format="txt" name="output" label="Integration of ${input_format.input.name}" />
    </outputs>

    <tests>
        <test expect_failure='true' expect_exit_code='1'>
            <expand macro='test_asko_loc' />
            <expand macro='test_asko_auth' />
            <conditional name='input_format'>
                <param name='format' value='csv' />
                <param name='input' value='people.tsv' />
            </conditional>
        </test>
    </tests>

    <help><![CDATA[
        @HELP@
    ]]></help>

    <expand macro='citation' />
</tool>