<tool id="purge_haplotigs_hist" name="Purge Haplotigs Hist" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" >
    <description>Generate a coverage histogram</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[
	    cp $input_bam input.bam &&
	    purge_haplotigs hist
	    -t \${GALAXY_SLOTS:-4}
	    #if $options.depth
	        --depth '$options.depth'
	    #end if
	    -b input.bam
	    -g $genome &&
	    cp input.bam.histogram.png '$output_histogram' &&
	    cp input.bam.gencov '$output_coverage' 
	    2>&1

	    ]]></command>
    <inputs>
	    <param name="input_bam" type="data" format="bam" label="BAM file" help="Input BAM file"/>
	    <param name="genome" type="data" format="fasta" label="FASTA file" help="Input Genome File"/>
	    <section name="options" title="Options" expanded="False">
		    <param name="depth" argument="--depth" type="integer" value="200" label="Maximum cutoff for depth" help="default=200, increase if needed."/>
	    </section>
    </inputs>
    <outputs>
	    <data name="output_histogram" format="png" label="${tool.name} on ${on_string}: histogram"/>
	    <data name="output_coverage" format="tabular" label="${tool.name} on ${on_string}: Coverage"/>
    </outputs>

    <tests>
	 <test>
	      <!-- #1 test with common parameters -->
	      <param name="input_bam" value="aligned.bam" ftype="bam"/>
	      <param name="genome" value="contigs.fa" ftype="fasta"/>
	      <output name="output_histogram" file="aligned.bam.histogram.png" ftype="png">
                       <assert_content>
                           <has_size value="135878" delta="100"/>
                       </assert_content>
              </output>
	      <output name="output_coverage">
		      <assert_contents>
			   <has_n_lines n="2613"/>
		      </assert_contents>
	      </output>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

**What it does**
	    
Purge Haplotigs Histogram is part of purge_haplotigs for generate a coverage histogram.
	    
**Input**
	    
- input file 1 - BAM file.
- input file 2 - FASTA file.    

**Example:**

- purge_haplotigs hist -b input.bam -g genome.fa

**Output**

- input.bam.histogram.png 
- input.bam.gencov

.. class:: infomark

**References**

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