# HG changeset patch
# User bzonnedda
# Date 1487590350 18000
# Node ID 5dcedbe7edff4f0f0452c118e5386691131bee5d
# Parent  063348f7c3e495e87325622b80d291abe488546b
Uploaded

diff -r 063348f7c3e4 -r 5dcedbe7edff c_calls.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/c_calls.xml	Mon Feb 20 06:32:30 2017 -0500
@@ -0,0 +1,48 @@
+<tool id="conifer_call" name="CoNIFER CNVs caller" version="1.0">
+  <description></description>
+  <command interpreter="python">
+       conifer.py call
+	--input $input
+	--output temporary
+    --threshold $threshold
+	2&gt;&amp;1
+    &amp;&amp; awk '{print \$2,\$3,\$4,\$5,\$1}' OFS="\t" temporary &gt; $outputFile
+  </command>
+  <inputs>
+    <param format="hdf5" name="input" type="data" label="CoNIFER output analysis file (HDF5)" />
+    <param name="threshold" type="float" value="1.5" label="Threshold" />
+  </inputs>
+  <outputs>
+    <data format="bed" name="outputFile" label="${tool.name} on ${on_string}" />
+  </outputs>
+ <help>
+**What it does**
+
+This tool is a CNVs caller using SVD-ZRPKM thresholding.
+
+**License and citation**
+
+This Galaxy tool is Copyright © 2014 `CRS4 Srl.`_ and is released under the `MIT license`_.
+
+.. _CRS4 Srl.: http://www.crs4.it/
+.. _MIT license: http://opensource.org/licenses/MIT
+
+You can use this tool only if you agree to the license terms of: `CoNIFER`_.
+
+.. _CoNIFER: http://conifer.sourceforge.net/
+
+If you use this tool, please cite:
+
+- |Cuccuru2014|_
+- |Krumm2012|_.
+
+.. |Cuccuru2014| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. *Bioinformatics* 30(13), 1928-1929
+.. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/30/13/1928
+.. |Krumm2012| replace::  Krumm, N., Sudmant, P. H., Ko, A., O'Roak, B. J., Malig, M., Coe, B. P., NHLBI Exome Sequencing Project, Quinlan, A. R., Nickerson, D. A., Eichler, E. E. (2012) Copy number variation detection and genotyping from exome sequence data. *Genome Res.* 22(8), 1525-1532
+.. _Krumm2012: http://genome.cshlp.org/content/22/8/1525
+  </help>
+  <citations>
+    <citation type="doi">10.1093/bioinformatics/btu135</citation>
+    <citation type="doi">10.1101/gr.138115.112</citation>
+  </citations>
+</tool>