<tool id="blobtools_view" name="Blobtools view" version="1.1" >
    <description>Transform BlobDB json file into view format</description>
    <xrefs>
        <xref type='bio.tools'>blobtools</xref>
    </xrefs>	
    <macros>
	  <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" /> 
    <command><![CDATA[
	    cp $input_json input.json &&
	    blobtools view 
	    $adv_options.hits
	    -x $adv_options.taxrule
	    -r $adv_options.rank
	    #if $adv_options.cov:
	        '$cov'
	    #end if
	    #if $adv_options.concoct:
	        '$concoct'
	    #end if
	    -i input.json 
	    -o output 
	    && mv output.input.table.txt '$blobDB_table'
	    2>&1

	    ]]></command>
    <inputs>
	    <param name="input_json" type="data" format="json" label="json File" help="Input BlobDB json file"/>
	    <section name="adv_options" title="Advance Options" expanded="False">
		    <param name="taxrule" type="select" display="radio" label="Taxonomy Rule" help="Taxonomy rule for computing taxonomy: default bestsum">
		        <option selected="true" value="bestsum">best sum</option>
		        <option value="bestsumorder">best sum order</option>
		    </param>
		    <param name="rank" type="select" display="radio" label="Taxonomic rank">
			  <option value="species">Species</option>
			  <option value="genus">Genus</option>
		          <option value="family">Family</option>
                          <option value="order">Order</option>
                          <option value="phylum" selected="true">Phylum</option>
			  <option value="superkingdom">Superkingdom</option>
                          <option value="all">All</option>
		    </param>
		    <param name="hits" type="boolean" truevalue="--hits" falsevalue="" checked="False" label="Displays taxonomic hits from tax files that contributed to the taxonomy"/>
		    <param argument="--concoct" type="boolean" truevalue="--concoct" falsevalue="" checked="false" label="Generate concoct files" help="default: False"/>
		    <param argument="--cov" type="boolean" truevalue="--cov" falsevalue="" checked="false" label="Generate cov files" help="Generate cov files"/>
	    </section>
    </inputs>
    <outputs>
	    <data name="blobDB_table" format="tabular" label="${tool.name} on ${on_string}"/>
    </outputs>

    <tests>
	 <test>
	     <!-- #1 blobtools view test -->
	    <param name="input_json" value="test.blobDB.json" ftype="json"/>
	    <output name="blobDB_table" file="test.blobDB.table.txt" ftype="tabular"/>
         </test>
    </tests>
    <help><![CDATA[
	    
.. class:: infomark

*Blobtools view is used to generate a blobDB.table.json before creating a plot using blobtools plot.*

**Input**

- a json file - output file created with Blobtools create.

**Parameters**

- taxrule - Taxrule used for computing taxonomy (supported: "bestsum", "bestsumorder") [ default: bestsum ]
- rank - Taxonomic rank(s) at which output will be written. (supported: 'species', 'genus', 'family', 'order', 'phylum', 'superkingdom', 'all') [default: phylum]
- hits - Displays taxonomic hits from tax files that contributed to the taxonomy.
- concoct - Generate cov files [default: False]
- calculate_cov - Legacy coverage when getting coverage from BAM file

**Command line example:**

- blobtools view -i prefix.blobDB.json

**Output**

- prefix.blobDB.table.json - a text base output file
- coverage file - a text base coverage file output file with column # contig_id  read_cov  base_cov #  - if cov is specified 
- prefix.blobDB.concoct_coverage_info.tsv - a text base coverage output file with base cov column only - if concoct is specified.


.. class:: infomark

**Contributor**

Galaxy Australia wrapped the Blobtools: the original software is available in this `Github repository <https://github.com/DRL/blobtools>`_.

**References**

     ]]></help>
     <citations>
        <citation type="doi">DOI: 10.12688/f1000research.12232.1</citation>
    </citations>
</tool>