# HG changeset patch
# User morinlab
# Date 1480530836 18000
# Node ID 55571b9980b031cc4148b3214207448818d226e6
# Parent  916c60c717a684a369623b57ae7cd77b741b562f
Uploaded

diff -r 916c60c717a6 -r 55571b9980b0 oncocircos.xml
--- a/oncocircos.xml	Tue Oct 11 14:23:01 2016 -0400
+++ b/oncocircos.xml	Wed Nov 30 13:33:56 2016 -0500
@@ -17,32 +17,47 @@
   mkdir circos/data;
   mkdir circos/etc;
 
+  touch data/cnv.large.scale.txt;
+  cat $sig_regions >> data/cnv.large.scale.txt;
+  touch data/genes_to_label.txt;
+  #if $advancedOptions.gene_label_input_type.gene_label_input_type_selector.value == "other":
+    echo $advancedOptions.gene_label_input_type.gene > data/genes_to_label.txt;
+  #else:
+    cat $advancedOptions.gene_label_input_type.gene_file > data/genes_to_label.txt;
+  #end if
+
+  touch data/genes_to_hide.txt;
+  #if $advancedOptions.gene_mask_input_type.gene_mask_input_type_selector.value == "other":
+      echo $advancedOptions.gene_mask_input_type.gene > data/genes_to_hide.txt;
+  #else:
+      cat $advancedOptions.gene_mask_input_type.gene_file > data/genes_to_hide.txt;
+  #end if
+      
   cp $__tool_directory__/etc/* circos/etc/;
 
   mkdir etc;
   
   ln -s $input_maf data/snv.txt;
   ln -s $input_seg data/cnv.txt;  
+  ln -s $biomart data/biomart.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$//g'
+    | sed 's/^SNV_FILTER$/sv = yes/g'
+    | sed 's/^SNV_FILTER_NUM$/sv_num = $advancedOptions.filter_snvs/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#^ROOT#root = \$(pwd)#g"  
   | sed 's#^CIRCOS#circos = circos/data#g'
 
   > ./etc/parse.conf;
@@ -60,13 +75,38 @@
   <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"/>
+    <param type="data" format="" name="biomart" label="Biomart File listing all genes (format: ENSG, chrom, start, end, Symbol"/>
+    <param type="data" format="bed" name="sig_regions" label="Regions of recurrent copy number gain/loss in bed format. 4th column must indicate the event type (e.g gain, hetd)" optional="true"/>
     <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"/>
+             label="Restrict plot to the following chromosome"/>
+      <conditional name="gene_label_input_type">
+	<param name="gene_label_input_type_selector" type="select" label="How will you supply genes of interest to label in the plot?">
+	  <option value="file" selected="True">Gene File</option>
+	  <option value="other">Other</option>
+	</param>
+	<when value="file">
+	  <param name="gene_file" type="data" format="txt" label="Gene File"  help="list of genes separated by newlines" />
+	</when>
+	<when value="other">
+	  <param name="gene" type="text" value="TP53" label="Gene" help="type the single gene" />
+	</when>
+      </conditional>
+      <conditional name="gene_mask_input_type">
+	<param name="gene_mask_input_type_selector" type="select" label="How will you supply blacklist genes to hide from plot?">
+	  <option value="file" selected="True">Gene Blacklist File</option>
+	  <option value="other">Other</option>
+	</param>
+	<when value="file">
+	  <param name="gene_file" type="data" format="txt" label="Gene File"  help="list of genes separated by newlines" />
+	</when>
+	<when value="other">
+	  <param name="gene" type="text" value="TP53" label="Gene" help="type the single gene" />
+	</when>
+      </conditional>
     </section>
   </inputs>
   <outputs>
@@ -74,4 +114,68 @@
     <data format="svg" name="svg" />
     <data format="txt" name="tmp" />
   </outputs>
-</tool>    
\ No newline at end of file
+  <citations>
+    <citation type="bibtex">
+      @article {Albuquerque089631,
+      author = {Albuquerque, Marco A and Grande, Bruno M and Ritch, Elie and Jessa, Selin and Krzywinski, Martin I and Grewal, Jasleen and Shah, Sohrab and Boutros, Paul and Morin, Ryan},
+      title = {Enhancing Knowledge Discovery from Cancer Genomics Data with Galaxy},
+      year = {2016},
+      doi = {10.1101/089631},
+      publisher = {Cold Spring Harbor Labs Journals},
+      URL = {http://biorxiv.org/content/early/2016/11/26/089631},
+      eprint = {http://biorxiv.org/content/early/2016/11/26/089631.full.pdf},
+      journal = {bioRxiv}
+      }
+
+    </citation>
+    <citation type="bibtex">
+      @misc{
+      goecks2010galaxy,
+      title={Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences},
+      author={Goecks, Jeremy and Nekrutenko, Anton and Taylor, James and others},
+      journal={Genome Biol},
+      volume={11},
+      number={8},
+      pages={R86},
+      year={2010}
+      }
+    </citation>
+    <citation type="bibtex">
+
+      @ARTICLE{Krzywinski2009-hn,
+      title       = "Circos: an information aesthetic for comparative genomics",
+      author      = "Krzywinski, Martin and Schein, Jacqueline and Birol, Inan\c{c}
+      and Connors, Joseph and Gascoyne, Randy and Horsman, Doug and
+      Jones, Steven J and Marra, Marco A",
+      affiliation = "Canada's Michael Smith Genome Sciences Center, Vancouver,
+      British Columbia V5Z 4S6, Canada. martink@bcgsc.ca",
+      abstract    = "We created a visualization tool called Circos to facilitate
+      the identification and analysis of similarities and
+      differences arising from comparisons of genomes. Our tool is
+      effective in displaying variation in genome structure and,
+      generally, any other kind of positional relationships between
+      genomic intervals. Such data are routinely produced by
+      sequence alignments, hybridization arrays, genome mapping, and
+      genotyping studies. Circos uses a circular ideogram layout to
+      facilitate the display of relationships between pairs of
+      positions by the use of ribbons, which encode the position,
+      size, and orientation of related genomic elements. Circos is
+      capable of displaying data as scatter, line, and histogram
+      plots, heat maps, tiles, connectors, and text. Bitmap or
+      vector images can be created from GFF-style data inputs and
+      hierarchical configuration files, which can be easily
+      generated by automated tools, making Circos suitable for rapid
+      deployment in data analysis and reporting pipelines.",
+      journal     = "Genome Res.",
+      volume      =  19,
+      number      =  9,
+      pages       = "1639--1645",
+      month       =  sep,
+      year        =  2009,
+      language    = "en"
+      }
+
+      
+    </citation>
+  </citations>
+</tool>