<tool id="draw_circos" name="draw_circos" version="0.1"> 
    <description> : Draw circos figure</description>  
	<requirements>
		<requirement type="binary">circos</requirement>
	</requirements>
	<stdio>
        <exit_code range="1:" />
    </stdio>
    <command>
		source $__tool_directory__/include_scaffremodler.sh ;
        python $__tool_directory__/draw_circos.py
		--config $config
		--draw $draw
		--cov $cov
		--scaff $scaff
		--discord $discord
		--frf $frf
		--ff $ff
		--rr $rr
		--ins $ins
		--delet $delet
		--chr_rr $chr_rr
		--chr_rf $chr_rf
		--chr_fr $chr_fr
		--chr_ff $chr_ff
		--read_fr $read_fr
		--read_rf $read_rf
		--read_ff $read_ff
		--read_rr $read_rr
		--read_ins $read_ins
		--read_delet $read_delet
		--read_chr_rr $read_chr_rr
		--read_chr_rf $read_chr_rf
		--read_chr_fr $read_chr_fr
		--read_chr_ff $read_chr_ff
		--text $text
		--out $circos_file
		
    </command>
    <inputs>
		<param name="config" type="data" label="The circos_conf file generated by conf4circos" />
		<param name="draw" type="text" value="all" label="Region to draw ('all' or potitions separated by ':' : chrX:start1:end1-chrY:start2:end2)" />
		
		<param name="cov" type="select" label="Draw coverage layer">
			<option selected="true" value="y">y</option>
			<option value="n">n</option>
		</param>
		
		<param name="scaff" type="select" label="Draw scaffold location layer">
			<option selected="true" value="y">y</option>
			<option value="n">n</option>
		</param>
		
		<param name="discord" type="select" label="Draw discordant proportion layer">
			<option selected="true" value="y">y</option>
			<option value="n">n</option>
		</param>
		
		
		<param name="frf" type="select" label="Draw fr/rf discordant regions links">
			<option selected="true" value="y">y</option>
			<option value="n">n</option>
		</param>
		
		<param name="ff" type="select" label="Draw ff discordant regions links">
			<option selected="true" value="y">y</option>
			<option value="n">n</option>
		</param>
		
		<param name="rr" type="select" label="Draw rr discordant regions links">
			<option selected="true" value="y">y</option>
			<option value="n">n</option>
		</param>
		
		<param name="ins" type="select" label="Draw ins discordant regions links">
			<option selected="true" value="y">y</option>
			<option value="n">n</option>
		</param>
		
		<param name="delet" type="select" label="Draw delet discordant regions links">
			<option selected="true" value="y">y</option>
			<option value="n">n</option>
		</param>
		
		<param name="chr_rf" type="select" label="Draw chr_rf discordant regions links">
			<option selected="true" value="y">y</option>
			<option value="n">n</option>
		</param>
		
		<param name="chr_rr" type="select" label="Draw chr_rr discordant regions links">
			<option selected="true" value="y">y</option>
			<option value="n">n</option>
		</param>
		
		<param name="chr_fr" type="select" label="Draw chr_fr discordant regions links">
			<option selected="true" value="y">y</option>
			<option value="n">n</option>
		</param>
		<param name="chr_ff" type="select" label="Draw chr_ff discordant regions links">
			<option selected="true" value="y">y</option>
			<option value="n">n</option>
		</param>
		
		
		
		<param name="read_rf" type="select" label="Draw rf read links">
			<option selected="true" value="y">y</option>
			<option value="n">n</option>
		</param>
		
		<param name="read_fr" type="select" label="Draw fr read links">
			<option selected="true" value="y">y</option>
			<option value="n">n</option>
		</param>
		
		<param name="read_ff" type="select" label="Draw ff read links">
			<option selected="true" value="y">y</option>
			<option value="n">n</option>
		</param>
		
		<param name="read_rr" type="select" label="Draw rr read links">
			<option selected="true" value="y">y</option>
			<option value="n">n</option>
		</param>
		
		<param name="read_ins" type="select" label="Draw ins read links">
			<option selected="true" value="y">y</option>
			<option value="n">n</option>
		</param>
		
		<param name="read_delet" type="select" label="Draw delet read links">
			<option selected="true" value="y">y</option>
			<option value="n">n</option>
		</param>
		
		<param name="read_chr_rf" type="select" label="Draw chr_rf read links">
			<option selected="true" value="y">y</option>
			<option value="n">n</option>
		</param>
		
		<param name="read_chr_rr" type="select" label="Draw chr_rr read links">
			<option selected="true" value="y">y</option>
			<option value="n">n</option>
		</param>
		
		<param name="read_chr_fr" type="select" label="Draw chr_fr read links">
			<option selected="true" value="y">y</option>
			<option value="n">n</option>
		</param>
		<param name="read_chr_ff" type="select" label="Draw chr_ff read links">
			<option selected="true" value="y">y</option>
			<option value="n">n</option>
		</param>
		
		<param name="text" type="select" label="Draw a text layer locating N regions">
			<option selected="true" value="y">y</option>
			<option value="n">n</option>
		</param>
		
		<param name="prefix" type="text" label="Identifier for output" value="circos" />
    </inputs>
    <outputs>
        <data name="circos_file" format="png" label="${tool.name} : $prefix .png" />
    </outputs>
    <help>
    
**Overview**

-----

.. class:: infomark

**Galaxy integration** Martin Guillaume (CIRAD), Droc Gaetan (CIRAD).

.. class:: infomark

**Support** For any questions about Galaxy integration, please send an e-mail to galaxy-dev-southgreen@cirad.fr

.. class:: infomark

**Program encapsulated in Galaxy by South Green**

	</help>
	<citations>
        <citation type="doi">10.1186/s12864-016-2579-4</citation> 
    </citations>
</tool>