diff oncocircos.xml @ 0:b77ab858eac1 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/oncocircos.xml	Mon Sep 12 16:23:26 2016 -0400
@@ -0,0 +1,77 @@
+<tool id="oncocircos" name="Oncocircos" version="0.69">
+
+  <description>
+    creates a genome-centric visualization of SNV and CNV Data
+  </description>
+
+  <requirements>
+    <requirement type="package" version="0.69">circos_perl_environment</requirement>
+    <requirement type="package" version="0.69">circos</requirement>
+  </requirements>
+
+
+  <command error_checking="aggressive">
+
+  mkdir data;
+  mkdir circos;
+  mkdir circos/data;
+  mkdir circos/etc;
+
+  cp $__tool_directory__/etc/* circos/etc/;
+
+  mkdir etc;
+  
+  ln -s $input_maf data/snv.txt;
+  ln -s $input_seg data/cnv.txt;  
+  cat $__tool_directory__/parse.conf
+
+  #if $advancedOptions.filter_snvs != 1:
+    | sed 's/^SNV_FILTER$/sv = yes/g'
+    | sed 's/^SNV_FILTER_NUM$/sv_num = $advancedOptions.filter_snvs/g'
+  #else:
+    | sed 's/^SNV_FILTER$/sv = no/g'
+    | sed 's/^SNV_FILTER_NUM$//g'
+  #end if
+
+  #if $advancedOptions.chromosome != "":
+    | sed 's/^CHR$/chr = $advancedOptions.chromosome/g'
+  #else:
+    | sed 's/^CHR$//g'
+  #end if
+
+  | sed "s#^ROOT#root = \$(pwd)#g"
+  | sed 's#^CNV$#cnv = data/cnv.txt#g'
+  | sed 's#^SNV$#sv = data/snv.txt#g'
+  | sed 's#^MART#mart = $biomart#g'
+  | sed 's#^CIRCOS#circos = circos/data#g'
+
+  > ./etc/parse.conf;
+
+  perl $__tool_directory__/bin/parse --conf ./etc/parse.conf | perl $__tool_directory__/bin/make.circos.data --conf ./etc/parse.conf;
+
+  circos --conf ./circos/etc/circos.conf;
+
+  cp circos.png $png;
+  cp circos.svg $svg;
+  cp ./etc/parse.conf $tmp;
+
+  </command>
+
+  <inputs>
+    <param type="data" format="maf" name="input_maf" label="Cohort Wide MAF File"/>
+    <param type="data" format="segs" name="input_seg" label="Cohort Wide SEGS File"/>
+    <param type="data" format="" name="biomart" label="Biomart File"/>
+    <section name="advancedOptions">
+      <param type="integer" name="filter_snvs" 
+             min="1" value="1" max="100" 
+             label="Filter genes with a cohort wide snv tally below this value"/>
+      <param type="text" name="chromosome" value="" 
+            label="Restrict plot to the following chromosome"/>
+    </section>
+  </inputs>
+  <outputs>
+    <data format="png" name="png" />
+    <data format="svg" name="svg" />
+    <data format="txt" name="tmp" />
+  </outputs>
+</tool>    
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