<tool profile="16.07" id="mothur_biom_info" name="Biom.info" version="@WRAPPER_VERSION@.0">
    <description>create shared and taxonomy files from biom</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>
    <command><![CDATA[
@SHELL_OPTIONS@

ln -s '$biom' input.biom &&

echo 'biom.info(
    biom=input.biom,
    #if str($label) != '':
        label=$label,
    #end if
    basis=$basis,
    output=$output,
    relabund=$relabund,
    printlevel=$printlevel
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <param argument="biom" type="data" format="biom1" label="Biom input dataset"/>
        <!-- TODO: read label options from biom file -->
        <param argument="label" type="text" value="userLabel" label="label - OTU Labels"
            help="Enter a distance label to be used in the shared file created from your biom file (e.g. 0.03)"/>
        <param argument="basis" type="select" label="Summary type"
            help="indicate what you want the summary file to represent, options are otu and sequence. Default is otu.
            For example consider the following basis=sequence could give Clostridiales 3 105, where 105 is the total
            number of sequences whose otu classified to Clostridiales. Now for basis=otu could give Clostridiales 3 7,
            where 7 is the number of otus that classified to Clostridiales. ">
            <option value="otu" selected="true">OTU</option>
            <option value="sequence">Sequence</option>
        </param>
        <param argument="relabund" type="boolean" truevalue="T" falsevalue="F" label="Relative abundance values"
            help="use relative abundances rather than raw abundances for the tax.summary file"/>
        <expand macro="param-output"/>
        <expand macro="param-printlevel"/>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="shared" format="mothur.shared" from_work_dir="input*.shared" label="${tool.name} on ${on_string}: shared"/>
        <data name="taxonomy" format="mothur.cons.taxonomy" from_work_dir="input*.cons.taxonomy" label="${tool.name} on ${on_string}: cons.taxonomy"/>
        <data name="tax.summary" format="mothur.tax.summary" from_work_dir="input*.tax.summary" label="${tool.name} on ${on_string}: tax.summary"/>
    </outputs>
    <tests>
        <test><!-- test with biom without metadata -->
            <param name="biom" value="samplebiom.biom1"/>
            <output name="shared" ftype="mothur.shared">
                <assert_contents>
                    <expand macro="test-shared-format"/>
                </assert_contents>
            </output>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with biom file with metadata -->
            <param name="biom" value="example.biom"/>
            <output name="shared" ftype="mothur.shared">
                <assert_contents>
                    <expand macro="test-shared-format"/>
                </assert_contents>
            </output>
            <output name="taxonomy" ftype="mothur.cons.taxonomy">
                <assert_contents>
                    <expand macro="test-taxonomy-format"/>
                    <has_text text="GG_OTU_1"/>
                </assert_contents>
            </output>
            <output name="tax.summary" ftype="mothur.tax.summary">
                <assert_contents>
                    <expand macro="test-taxsummary-format"/>
                </assert_contents>
            </output>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with some more parameters -->
            <param name="biom" value="example.biom"/>
            <param name="label" value="0.03"/>
            <param name="output" value="detail"/>
            <param name="basis" value="sequence"/>
            <param name="printlevel" value="4"/>
            <output name="shared" ftype="mothur.shared">
                <assert_contents>
                    <expand macro="test-shared-format"/>
                </assert_contents>
            </output>
            <output name="taxonomy" ftype="mothur.cons.taxonomy">
                <assert_contents>
                    <expand macro="test-taxonomy-format"/>
                    <has_text text="GG_OTU_1"/>
                </assert_contents>
            </output>
            <output name="tax.summary" ftype="mothur.tax.summary">
                <assert_contents>
                    <expand macro="test-taxsummary-format"/>
                    <has_text text="Euryarchaeota"/>
                </assert_contents>
            </output>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The biom.info command reads a biom file creates a shared file. If your biom file contains metadata mothur will also
create taxonomy or constaxonomy along with tax.summary files.

    ]]></help>
    <expand macro="citations"/>
</tool>