--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SVDetect_compare.xml	Mon Jun 11 12:31:19 2012 -0400
@@ -0,0 +1,218 @@
+<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>