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author bzeitouni
date Mon, 11 Jun 2012 12:31:50 -0400
parents f6ccaaed3654
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<tool id="svdetect_compare" name="Compare">

<description>structural variants between two samples</description>

<command interpreter="perl">SVDetect_compare.pl links2compare -conf '$config_file' -l '$log_file' -N '$sample_name.$reference_name'

#if $links2SV
-out1 '$common_sv_file'
-out2 '$sample_sv_file'
-out3 '$reference_sv_file'
#end if

#if $file_conversion.file_conversion_select=="convert" and $file_conversion.links2circos
-out4 '$common_circos_file'
-out5 '$sample_circos_file'
-out6 '$reference_circos_file'
#end if

#if $file_conversion.file_conversion_select=="convert" and $file_conversion.links2bed
-out7 '$common_bed_file'
-out8 '$sample_bed_file'
-out9 '$reference_bed_file'
#end if

</command>

<inputs>
	<param name="sample_name" type="text" size="20" value="sample" label="Sample Name"/>
	<param name="sample_read1_length" type="integer" size="10" value="50" label="Sample read 1 length (bp)"/>
	<param name="sample_read2_length" type="integer" size="10" value="50" label="Sample read 2 length (bp)"/>
   	<param name="sample_mates_file" type="data" format="sv" label="Sample input file" help=".sv file"/>
	
	<param name="reference_name" type="text" size="20" value="reference" label="Reference Name"/>
	<param name="reference_read1_length" type="integer" size="10" value="50" label="Reference read 1 length (bp)"/>
	<param name="reference_read2_length" type="integer" size="10" value="50" label="Reference read 2 length (bp)"/>
   	<param name="reference_mates_file" type="data" format="sv" label="Reference input file" help=".sv file"/>
	
	<param name="min_overlap" type="float" size="10"  value="0.05" label="Minimum overlap of links required as a fraction"/>
	<param name="same_sv_type" label="Comparison of SVs with the same type only ?" type="boolean" truevalue="1" falsevalue="0" checked="True"/>

	<param name="links2SV" label="Do you want to have filtered links in a tabulated file format showing significant SVs?" type="boolean" truevalue="1" falsevalue="0" checked="True"/>
		
	<conditional name="file_conversion">
		<param name="file_conversion_select" type="select" label="Output file conversion" help="Converts filtered links to Circos/BED files format for graphical view of SVs">
			<option value="do_not_convert">No</option>
			<option value="convert">Yes</option>
		</param>
		<when value="do_not_convert">
				<!-- do nothing here -->
		</when>
		<when value="convert">
			<param name="links2circos" label="Converts the link list to the Circos link format" type="boolean" truevalue="1" falsevalue="0" checked="True"/>
			<param name="links2bed" label="Converts the link list to the UCSC BED format" type="boolean" truevalue="1" falsevalue="0" checked="False"/>
			<param name="organism_id" type="text" size="10" value="hs" label="Organism ID"/>
			<repeat name="color_code" title="Color-code" min="1" max="7">
				<param name="color" type="select" label="Color">
					<option value="grey">grey</option>
					<option value="black">black</option>
					<option value="blue">blue</option>
					<option value="green">green</option>
					<option value="purple">purple</option>
					<option value="orange">orange</option>
					<option value="red">red</option>
				</param>
				<param name="interval" type="text" value="1,3" label="Interval"/>
			</repeat>
		</when>
	</conditional>
</inputs>



<outputs>
	<data format="sv" name="common_sv_file" label="common.compared.sv">
		<filter>links2SV is True</filter>
	</data>
	<data format="sv" name="sample_sv_file" label="${sample_name}.compared.sv">
		<filter>links2SV is True</filter>
	</data>
	<data format="sv" name="reference_sv_file" label="${reference_name}.compared.sv">
		<filter>links2SV is True</filter>
	</data>

	<data format="segdup" name="common_circos_file" label="common.compared.segdup">
		<filter>(
			file_conversion['file_conversion_select']=="convert" and
			file_conversion['links2circos'] is True
			)
		</filter>
	</data>
	<data format="segdup" name="sample_circos_file" label="${sample_name}.compared.segdup">
		<filter>(
			file_conversion['file_conversion_select']=="convert" and
			file_conversion['links2circos'] is True
			)
		</filter>
	</data>
	<data format="segdup" name="reference_circos_file" label="${reference_name}.compared.segdup">
		<filter>(
			file_conversion['file_conversion_select']=="convert" and
			file_conversion['links2circos'] is True
			)
		</filter>
	</data>

	<data format="bed" name="common_bed_file" label="common.compared.bed">
		<filter>(
			file_conversion['file_conversion_select']=="convert" and
			file_conversion['links2bed'] is True
			)
		</filter>
	</data>
	<data format="bed" name="sample_bed_file" label="${sample_name}.compared.bed">
		<filter>(
			file_conversion['file_conversion_select']=="convert" and
			file_conversion['links2bed'] is True
			)
		</filter>
	</data>
	<data format="bed" name="reference_bed_file" label="${reference_name}.compared.bed">
		<filter>(
			file_conversion['file_conversion_select']=="convert" and
			file_conversion['links2bed'] is True
			)
		</filter>
	</data>

	<data format="txt" name="log_file" label="${sample_name}.${reference_name}.svdetect_compare.log"/>
</outputs>



<configfiles>
	<configfile name="config_file">
&lt;general&gt;
output_dir=$__new_file_path__/svdetect
&lt;/general&gt; 

#if $file_conversion.file_conversion_select == "convert"
#if $file_conversion.links2circos
&lt;circos&gt;
organism_id=${file_conversion.organism_id}
&lt;colorcode&gt;
#for $color_repeat in $file_conversion.color_code
${color_repeat.color}=${color_repeat.interval}
#end for
&lt;/colorcode&gt;
&lt;/circos&gt;
#end if
#if $file_conversion.links2bed
&lt;bed&gt;
&lt;colorcode&gt;
#for $color_repeat in $file_conversion.color_code
#if str($color_repeat.color)== "grey"
190,190,190=${color_repeat.interval}
#end if
#if str($color_repeat.color)== "black"
0,0,0=${color_repeat.interval}
#end if
#if str($color_repeat.color)== "blue"
0,0,255=${color_repeat.interval}
#end if
#if str($color_repeat.color)== "green"
0,255,0=${color_repeat.interval}
#end if
#if str($color_repeat.color)== "purple"
153,50,205=${color_repeat.interval}
#end if
#if str($color_repeat.color)== "orange"
255,140,0=${color_repeat.interval}
#end if
#if str($color_repeat.color)== "red"
255,0,0=${color_repeat.interval}
#end if
#end for
&lt;/colorcode&gt;
&lt;/bed&gt;
#end if
#end if

&lt;compare&gt;
list_samples=${sample_name},${reference_name}
list_read_lengths=${sample_read1_length}-${sample_read2_length},${reference_read1_length}-${reference_read2_length}
sample_link_file=${sample_mates_file}
reference_link_file=${reference_mates_file}
min_overlap=${min_overlap}
same_sv_type=${same_sv_type}
sv_output=${links2SV}
#if $file_conversion.file_conversion_select == "convert"
circos_output=${$file_conversion.links2circos}
bed_output=${$file_conversion.links2bed}
#end if
&lt;/compare&gt; 

	</configfile>
</configfiles>

  <help>
**What it does**

SVDetect - Version : 0.8

Comparison of clusters between two samples to get common or sample-specific SVs

This program is designed to compare filtered links between two anomalously mapped mate-pair/paired-end datasets
and to identify common and sample-specific SVs (like the usual sample/reference design).
Overlaps between coordinates of clusters and types of SVs are used as parameters of comparison.

Manual documentation available at the http://svdetect.sourceforge.net/Site/Manual.html

-----

.. class:: infomark

Contact Bruno Zeitouni (bruno.zeitouni@curie.fr) for any questions or concerns about the Galaxy implementation of SVDetect.
  </help>

</tool>