Repository 'svdetect'
hg clone https://toolshed.g2.bx.psu.edu/repos/bzeitouni/svdetect

Changeset 6:f6ccaaed3654 (2012-06-11)
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SVDetect_compare.xml
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diff -r ba8c5e544948 -r f6ccaaed3654 SVDetect_compare.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/SVDetect_compare.xml Mon Jun 11 12:31:19 2012 -0400
[
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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>