# HG changeset patch
# User bzonnedda
# Date 1487589853 18000
# Node ID 59fb4f2931df5d18a867f4b7b4b28e81242da067
# Parent  28d28bc2156a1b1ee2efc04e6f1f906f753011f1
Deleted selected files

diff -r 28d28bc2156a -r 59fb4f2931df c_calls.xml
--- a/c_calls.xml	Mon Feb 20 06:24:03 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,48 +0,0 @@
-<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>