changeset 4:2877b1ba1250 draft default tip

planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/oncoprintplus commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty

--- a/citations.xml	Mon Sep 12 15:46:13 2016 -0400
+++ b/citations.xml	Tue Oct 11 14:26:04 2016 -0400
@@ -10,9 +10,39 @@
             }
         </citation>
     </xml>
+    <xml name="vardict_citation">
+        <citation type="bibtex">
+            @article{
+            Lai20062016,
+            title = {VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research},
+            author = {Lai, Zhongwu and Markovets, Aleksandra and Ahdesmaki, Miika and Chapman, Brad and Hofmann, Oliver and McEwen, Robert and Johnson, Justin and Dougherty, Brian and Barrett, J. Carl and Dry, Jonathan R.}, 
+            journal = {Nucleic Acids Research} 
+            volume = {44}, 
+            number = {11}, 
+            pages = {e108}, 
+            year = {2016}, 
+            doi = {10.1093/nar/gkw227}
+            }
+        </citation>
+    </xml>
+    <xml name="somatic_sniper_citation">
+        <citation>
+            @article{
+            Larson01022012,
+            author = {Larson, David E. and Harris, Christopher C. and Chen, Ken and Koboldt, Daniel C. and Abbott, Travis E. and Dooling, David J. and Ley, Timothy J. and Mardis, Elaine R. and Wilson, Richard K. and Ding, Li}, 
+            title = {SomaticSniper: identification of somatic point mutations in whole genome sequencing data},
+            volume = {28}, 
+            number = {3}, 
+            pages = {311-317}, 
+            year = {2012}, 
+            doi = {10.1093/bioinformatics/btr665}, 
+            journal = {Bioinformatics} 
+            }
+        </citation>
+    </xml>
     <xml name="galaxy_citation">
         <citation>
-        @ARTICLE{Goecks2010-ra,
+          @ARTICLE{Goecks2010-ra,
           title    = "Galaxy: a comprehensive approach for supporting accessible,
                       reproducible, and transparent computational research in the life
                       sciences",
@@ -22,11 +52,47 @@
           volume   =  11,
           number   =  8,
           pages    = "R86",
-          month    =  "25~" # aug,
+          month    =  "25~",
           year     =  2010
         }
         </citation>
     </xml>
+
+    <xml name="delly_citation">
+      <citation>
+      @ARTICLE{Rausch2012-yi,
+  title    = "{DELLY}: structural variant discovery by integrated paired-end
+              and split-read analysis",
+  author   = "Rausch, Tobias and Zichner, Thomas and Schlattl, Andreas and
+              St{\"{u}}tz, Adrian M and Benes, Vladimir and Korbel, Jan O",
+  journal  = "Bioinformatics",
+  volume   =  28,
+  number   =  18,
+  pages    = "i333--i339",
+  month    =  "15~",
+  year     =  2012
+}
+      </citation>
+    </xml>
+    <xml name="mutationseq_citation">
+        <citation type="bibtex">
+@ARTICLE{Ding2012-jq,
+  title    = "Feature-based classifiers for somatic mutation detection in
+              tumour-normal paired sequencing data",
+  author   = "Ding, Jiarui and Bashashati, Ali and Roth, Andrew and Oloumi,
+              Arusha and Tse, Kane and Zeng, Thomas and Haffari, Gholamreza and
+              Hirst, Martin and Marra, Marco A and Condon, Anne and Aparicio,
+              Samuel and Shah, Sohrab P",
+  journal  = "Bioinformatics",
+  volume   =  28,
+  number   =  2,
+  pages    = "167--175",
+  month    =  "15~" # jan,
+  year     =  2012
+}
+        </citation>
+    </xml>
+
     <xml name="strelka_citation">
         <citation type="bibtex">
         @ARTICLE{Saunders2012-nh,
@@ -61,4 +127,27 @@
             }
         </citation>
     </xml>
+    <xml name="titan_citation">
+      <citation type="bibtex">
+          @ARTICLE{Ha2014-pu,
+  title       = "{TITAN}: inference of copy number architectures in clonal cell
+                 populations from tumor whole-genome sequence data",
+  author      = "Ha, Gavin and Roth, Andrew and Khattra, Jaswinder and Ho,
+                 Julie and Yap, Damian and Prentice, Leah M and Melnyk,
+                 Nataliya and McPherson, Andrew and Bashashati, Ali and Laks,
+                 Emma and Biele, Justina and Ding, Jiarui and Le, Alan and
+                 Rosner, Jamie and Shumansky, Karey and Marra, Marco A and
+                 Gilks, C Blake and Huntsman, David G and McAlpine, Jessica N
+                 and Aparicio, Samuel and Shah, Sohrab P",
+  journal     = "Genome Res.",
+  publisher   = "Cold Spring Harbor Lab",
+  volume      =  24,
+  number      =  11,
+  pages       = "1881--1893",
+  month       =  "1~" # nov,
+  year        =  2014,
+  keywords    = "computational method"
+}
+      </citation>
+    </xml>
 </macros>

--- a/oncoprintplus.xml	Mon Sep 12 15:46:13 2016 -0400
+++ b/oncoprintplus.xml	Tue Oct 11 14:26:04 2016 -0400
@@ -4,6 +4,10 @@
     creates a summary matrix plot of cohort wide mutations
   </description>
 
+  <macros>
+      <import>citations.xml</import>
+  </macros>
+
   <requirements>
     <requirement type="binary">Rscript</requirement>    
     <requirement type="package" version="3.2.1">R</requirement>
@@ -158,4 +162,11 @@
   <outputs>
     <data format="pdf" name="output"/>
   </outputs>
+  <help>
+  https://labs.oicr.on.ca/boutros-lab/software/bpg
+  </help>
+  <citations>
+      <expand macro="morinlab_citation"/>
+      <expand macro="galaxy_citation"/>
+  </citations>  
 </tool>