<tool id="mycrobiota-krona-mothur" name="Krona" version="1">
    <description>for mothur datasets</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="2.7">krona</requirement>
    </requirements>
    <command detect_errors="aggressive"><![CDATA[
        ## create symlinks to taxonomy files for nicer display names in output
        #if $input.haveshared == 'no':
            #for $tax in $input.taxonomy:
                ln -s '$tax' '$tax.name' &&
            #end for
        #end if

        python '$__tool_directory__/mycrobiota.py'
            #if $input.haveshared == 'yes':
                --command create_krona_plot_multisample
                --shared_file '$input.shared_file'
                #if $input.level == 'None':
                    --level '$input.taxonomy.name'
                #else:
                    --level '$input.level'
                #end if
                --taxonomy $input.taxonomy
            #else:
                --command create_krona_plot
                #for $tax in $input.taxonomy:
                    --taxonomy '$tax.name'
                #end for
            #end if
            ${with_otu}
    ]]></command>
    <inputs>
        <conditional name="input">
            <param name="haveshared" type="select" label="Would you like to supply a mothur shared file?"
                help="This will create a multisample plot. If you select 'no', you can still create a multisample plot by providing a taxonomy file per sample">
                <option value="no">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="no">
                <param argument="--taxonomy" type="data" multiple="true" format="mothur.ref.taxonomy,mothur.seq.taxonomy,mothur.cons.taxonomy" label="Select mothur taxonomy file" help=""/>
            </when>
            <when value="yes">
                <param argument="--taxonomy" type="data" format="mothur.ref.taxonomy,mothur.seq.taxonomy,mothur.cons.taxonomy" label="Select mothur taxonomy file" help=""/>
                <param argument="--shared_file" type="data" optional="true" format="mothur.shared" label="Supply a mothur shared file" help=""/>
                <param argument="--level" type="select" optional="true" label="label - pick (one) OTU Label" help="leave blank for collections, will try to determine level from element names">
                    <options>
                        <filter type="data_meta" ref="shared_file" key="labels"/>
                    </options>
                </param>
            </when>
        </conditional>
        <param argument="--with_otu" type="boolean" checked="false" truevalue="--with-otu" falsevalue="" label="differentiate between different OTUs of same taxonomy?" help=""/>
    </inputs>
    <outputs>
        <data name="krona_plot" format="html"  from_work_dir="text.krona.html" label="Krona plot of ${on_string}: HTML"/>
    </outputs>
    <tests>
        <test> <!-- test single sample -->
            <param name="haveshared" value="no"/>
            <param name="taxonomy" value="multisample.taxonomy"/>
            <param name="with_otu" value="--with-otu"/>
            <output name="krona_plot">
                <assert_contents>
                    <has_text text="Krona"/>
                    <has_text text="Actinobacteria"/>
                    <not_has_text text="F3D0"/>
                    <not_has_text text="F3D148"/>
                    <not_has_text text="krona.test1.mothur.cons"/>
                    <has_text text="Otu0127"/>
                </assert_contents>
            </output>
        </test>
        <test> <!-- test multi samples (multiple single-sample taxonomy files) -->
            <param name="haveshared" value="no"/>
            <param name="taxonomy" value="multisample.taxonomy,krona.test1.mothur.cons.taxonomy"/>
            <param name="with_otu" value=""/>
            <output name="krona_plot">
                <assert_contents>
                    <has_text text="Krona"/>
                    <has_text text="krona.test1.mothur.cons"/>
                    <has_text text="Actinobacteria"/>
                    <not_has_text text="F3D0"/>
                    <not_has_text text="F3D148"/>
                    <not_has_text text="Otu0127"/>
                </assert_contents>
            </output>
        </test>
        <test> <!-- test multi sample (single multisample taxonomy file with shared file) -->
            <param name="haveshared" value="yes"/>
            <param name="taxonomy" value="multisample.taxonomy"/>
            <param name="shared_file" ftype="mothur.shared" value="example.mothur.shared"/>
            <param name="with_otu" value="--with-otu"/>
            <param name="level" value="0.03"/>
            <output name="krona_plot">
                <assert_contents>
                    <has_text text="Krona"/>
                    <has_text text="Actinobacteria"/>
                    <has_text text="F3D0"/>
                    <has_text text="F3D148"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
**What it does**
    ]]></help>
    <expand macro="citations">
        <citation type="doi">10.1007/978-1-4614-6418-1_802-1</citation>
    </expand>
</tool>