# HG changeset patch
# User morinlab
# Date 1480552330 18000
# Node ID cf3f1adb1a554ae5e906d3c5c91f8a6065fa3eea

Uploaded

diff -r 000000000000 -r cf3f1adb1a55 igv2gistic.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/igv2gistic.xml	Wed Nov 30 19:32:10 2016 -0500
@@ -0,0 +1,68 @@
+<tool id="igv2gistic" name="IGV2Gistic" version="1.0">
+  <description>
+    Converts an IGV formatted segment file into an GISTIC2.0 compatible segment file. Requires exon BED file. Also produces an accompanying marker file in order to run GISTIC2.0.
+  </description>
+  <requirements>
+    <requirement type="package" version="14.2">morinlab_scripts</requirement>
+    <requirement type="set_environment">MORINLAB_SCRIPTS</requirement>
+  </requirements>
+  <command>
+    python \$MORINLAB_SCRIPTS/generate_gistic_inputs/generate_gistic_files_v4.0.py -o $out_seg -m $markers -c $igv_seg -b $bed_file
+  </command>
+  <inputs>
+    <param type="data" format="tabular" name="igv_seg" label="IGV segment file" help="IGV formatted segment file." />
+    <param type="data" format="tabular" name="bed_file" label="BED file" help="BED file for creating markers file." /> 
+  </inputs>
+  <outputs>
+    <data format="tabular" name="out_seg" />
+    <data format="tabular" name="markers" />
+  </outputs>
+  
+  <help>
+
+IGV2Gistic converts an IGV-formatted segment file into a GISTIC2.0 compatible segment file. This script is intended for segment files produced by Copy Number Variation (CNV) callers. This script effectively allows for running GISTIC2.0 on copy number segments derived from sequencing data (as opposed to array derived copy number segments).
+
+Additionally, this script requires a BED file containing coordinates of exons. 
+
+Both the IGV-formatted segment file and the BED file must have the "chr" prefix for any chromosomes. Both files must not have a header line.
+
+IGV-formatted segment file is a tabular file with the following columns: 
+  (1) Sample
+  (2) Chromsome (chr prefix required)
+  (3) Start position
+  (4) End position
+  (5) Copy number 
+
+Minimum exon BED file should contain the following columns:
+  (1) Chromosome
+  (2) Start position
+  (3) End position
+
+  </help>
+  <citations>
+    <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+      @unpublished{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>
+    <citation type="bibtex">
+      @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>
+  </citations>
+</tool>