<tool id="purge_haplotigs_cov" name="Purge Haplotigs Cov" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" >
    <description>Generate a coverage statistic</description>
    <xrefs>
        <xref type='bio.tools'>purgehaplotigs</xref>
    </xrefs>
    <macros>
	  <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" /> 
    <command><![CDATA[
	    purge_haplotigs cov
	    #if $options.j:
        	-j '$options.j'
	    #end if
	    #if $options.s:
	        -s '$options.s'
	    #end if
	    -i $genomecov
	    -l $low_cutoff
	    -m $mid_cutoff
	    -h $high_cutoff
	    cp coverage_stats.csv '$output_statistic'
	    2>&1

	    ]]></command>
    <inputs>
	    <param name="genomecov" type="data" format="tabular" label="Coverage file" help="Coverage file"/>
	    <param name="low_cutoff" type="integer" value="10" label="read depth low cutoff" help="obtain from the histogram"/>
	    <param name="mid_cutoff" type="integer" value="20" label="read depth high cutoff" help="Coverage file"/>
	    <param name="high_cutoff" type="integer" value="30" label="read depth mid cutoff" help="The low point between the haploid and diploid peaks"/>
	    <section name="options" title="Options" expanded="False">
		    <param argument="-j" type="integer" value="80" label="Auto-assign contig as j (junk)"/>
	            <param argument="-s" type="integer" value="80" label="Auto-assign contig as s (suspected haplogit)"/>		    
	    </section>
    </inputs>
    <outputs>
	    <data name="output_statistic" format="csv" label="${tool.name} on ${on_string}: Coverage Statistic" from_work_dir="coverage_stats.csv"/>
    </outputs>

    <tests>
	 <test>
              <!-- #1 test with common parameters -->
              <param name="genomecov" value="aligned.bam.gencov" ftype="tabular"/>
	      <param name="low_cutoff" value="10" />
	      <param name="mid_cutoff" value="20" />
	      <param name="high_cutoff" value="30" />
              <output name="output_statistic" file="coverage_stats.csv" ftype="csv"/>
        </test> 
    </tests>
    <help><![CDATA[
	    
.. class:: infomark

**What it does**
	    
Analyze the coverage on a contig by contig basis.

**Input**
	    
- input file: a genemecov output file (tabular format) that was produced from purge_haplotigs hist. 

**Parameters**

- l : The read depth low cutoff (use the histogram to eyeball these cutoffs)

- m : The low point between the haploid and diploid peaks

- h : The read depth high cutoff

- junk : Auto-assign contig as "j" (junk) if this percentage or greater of the contig is low/high coverage (DEFAULT = 80, > 100 = don't junk anything)

- suspect : Auto-assign contig as "s" (suspected haplotig) if this percentage or less of the contig is diploid level of coverage (DEFAULT = 80)

**Output**

- coverage_stats.csv

.. class:: infomark
	    
**References**
]]></help>
     <citations>
        <citation type="doi">DOI: 10.1186/s12859-018-2485-7</citation>
    </citations>
</tool>