Mercurial > repos > morinlab > somatic_sniper

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/citations.xml	Tue Oct 11 14:33:29 2016 -0400
@@ -0,0 +1,153 @@
+<macros>
+    <xml name="morinlab_citation">
+        <citation type="bibtex">
+            @unpublished{
+            albuquerque2016galaxy,
+            author = "Marco Albuquerque and Bruno Grande and Elie Ritch and Martin Krzywinski and Prasath Pararajalingam and Selin Jessa and Paul Boutros and Sohrab Shah and Ryan Morin",
+            title = "A Suite of Galaxy Tools for Cancer Mutational Analysis",
+            note = "Unpublished Manuscript",
+            year = "2016"
+            }
+        </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,
+          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
+                      {Galaxy Team}",
+          journal  = "Genome Biol.",
+          volume   =  11,
+          number   =  8,
+          pages    = "R86",
+          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,
+          title    = "Strelka: accurate somatic small-variant calling from sequenced
+                      tumor-normal sample pairs",
+          author   = "Saunders, Christopher T and Wong, Wendy S W and Swamy, Sajani and
+                      Becq, Jennifer and Murray, Lisa J and Cheetham, R Keira",
+          journal  = "Bioinformatics",
+          volume   =  28,
+          number   =  14,
+          pages    = "1811--1817",
+          month    =  "15~" # jul,
+          year     =  2012
+        }
+        </citation>
+    </xml>
+    <xml name="radia_citation">
+        <citation type="bibtex">
+            @article{
+            Radenbaugh2014-tj,
+            title={RADIA: RNA and DNA integrated analysis for somatic
+            mutation detection},
+            author={Radenbaugh, Amie J and Ma, Singer and Ewing, Adam and Stuart,
+            Joshua M and Collisson, Eric A and Zhu, Jingchun and Haussler,
+            David},
+            journal={PLoS One},
+            volume={9},
+            number={11},
+            pages={e111516},
+            year={2014},
+            publisher={PLoS}
+            }
+        </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>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/somatic_sniper.xml	Tue Oct 11 14:33:29 2016 -0400
@@ -0,0 +1,121 @@
+<tool id="somatic_sniper" name="SomaticSniper" version="1.0">
+  <description>calls SNVs for tumour-normal pairs.</description>
+  <requirements>
+    <requirement type="package" version="1.0.5.0">somatic_sniper</requirement>
+    <requirement type="set_environment">SOMATIC_SNIPER_ROOT_DIR</requirement>
+  </requirements>
+  <command detect_errors="aggressive"><![CDATA[
+
+  ## SYMLINK BAM FILES ALONGSIDE INDEX FILES
+  ln -s $normal normal.bam;
+  ln -s $normal.metadata.bam_index normal.bam.bai;
+  ln -s $tumor tumor.bam;
+  ln -s $tumor.metadata.bam_index tumor.bam.bai;
+
+  #if $interval:
+
+  for i in \$(cut -f1 $interval); do
+
+  #end if
+
+
+  ## BUILD SOMATICSNIPER COMMAND LINE
+  \$SOMATIC_SNIPER_ROOT_DIR/bin/bam-somaticsniper
+    -F vcf
+    -q $advancedsettings.q
+    -Q $advancedsettings.Q
+    -T $advancedsettings.T
+    -N $advancedsettings.N
+    -r $advancedsettings.r
+    -n $advancedsettings.n
+    -t $advancedsettings.t
+    $advancedsettings.L
+    $advancedsettings.G
+    $advancedsettings.p
+
+    #if $ref.ref_options == "cached"
+      -f ${ref.index.fields.path}
+    #else
+      -f ${ref.ownFile}
+    #end if
+
+    #if $interval:
+
+    <(samtools view -b tumor.bam \$i)
+    <(samtools view -b normal.bam \$i)
+
+    #else:
+      tumor.bam
+      normal.bam
+
+    #end if
+
+    #if $interval:
+      tmp_\$i.txt
+    #else:
+      $variants
+    #end if
+    ;
+
+    #if $interval:
+
+      done;
+
+      for i in \$(cut -f1 $interval); do
+
+      if [ \$i == \$(cut -f1 $interval | head -n1) ] ; then
+        cat tmp_\$i.txt > $variants;
+      else
+        grep -v ^#.* tmp_\$i.txt >> $variants;
+      fi ;
+
+      done;
+
+    #end if
+
+
+
+    ]]></command>
+	<inputs>
+		<conditional name="ref">
+			<param name="ref_options" type="select" label="Choose the source for the reference genome">
+				<option value="cached" selected="True">Use a built-in genome</option>
+				<option value="history">Use a genome from the history</option>
+			</param>
+			<when value="cached">
+				<param name="index" type="select" label="Reference Genome File" >
+					<options from_data_table="all_fasta" />
+				</param>
+      			</when>
+      			<when value="history">
+        			<param format="fasta" name="ownFile" type="data" metadata_name="dbkey" label="Reference Genome File" />
+      			</when>
+		</conditional>
+		<param format="bam" name="normal" type="data" label="Normal Alignment File" />
+		<param format="bam" name="tumor" type="data" label="Tumour Alignment File" />
+                <param type="data" format="txt" optional="true" name="interval" label="Specify Inteval"/>
+		<section name="advancedsettings" title="Advanced Settings" expanded="False" >
+			<param name="q" type="integer" value="0" label="Minimum read mapping quality"/>
+			<param name="Q" type="integer" value="15" label="Minimum somatic variant quality score"/>
+			<param name="T" type="float" value="0.850000" label="theta in maq consensus calling model (for -c/-g) [0.850000]"/>
+			<param name="N" type="integer" value="2" label="Ploidy (number of haplotypes)"/>
+			<param name="r" type="float" value="0.001000" label="Prior probability for differences between haplotypes"/>
+			<param name="n" type="text" value="NORMAL" label="Normal sample ID"/>
+			<param name="t" type="text" value="TUMOR" label="Tumour sample ID"/>
+  			<param name="L" type="boolean" truevalue="-L" falsevalue="" checked="true" label="Exclude LOH variants from output" />
+  			<param name="G" type="boolean"  truevalue="-G" falsevalue="" checked="true" label="Exclude gain of reference variants from output" />
+  			<param name="p" type="boolean"  truevalue="-p" falsevalue="" checked="true" label="Disable priors in somatic calculation (improved sensitivity for solid tumours)" />
+		</section>
+	</inputs>
+	<outputs>
+		<data name="variants" format="vcf" label="SomaticSniper SNVs" />
+	</outputs>
+	<help>
+		http://gmt.genome.wustl.edu/packages/somatic-sniper/
+	</help>
+	<citations>
+		<expand macro="morinlab_citation" />
+		<expand macro="galaxy_citation" />
+		<expand macro="somatic_sniper_citation" />
+	</citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Tue Oct 11 14:33:29 2016 -0400
@@ -0,0 +1,6 @@
+<tables>
+    <table name="fasta_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/all_fasta.loc"/>
+    </table>
+</tables>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Oct 11 14:33:29 2016 -0400
@@ -0,0 +1,6 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="somatic_sniper" version="1.0.5.0">
+    <repository changeset_revision="0059826b36e0" name="package_somatic_sniper_1_0_5_0" owner="morinlab" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+  </package>
+</tool_dependency>