# HG changeset patch
# User crs4
# Date 1490189803 14400
# Node ID 59989c9351470ac8cd7e07d95256ab8a9a4492f0
# Parent  e30af84e9ef5cc22673993751ba812b01b576714
Deleted selected files

diff -r e30af84e9ef5 -r 59989c935147 conifer3/c_calls.xml
--- a/conifer3/c_calls.xml	Wed Mar 22 09:19:49 2017 -0400
+++ /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>
-       python $__tool_directory__/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>
diff -r e30af84e9ef5 -r 59989c935147 conifer3/c_plotcalls.xml
--- a/conifer3/c_plotcalls.xml	Wed Mar 22 09:19:49 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,57 +0,0 @@
-<tool id="conifer_plotcalls" name="CoNIFER plot caller" version="1.0">
-	<description>cnv caller</description>
-	<command interpreter="perl">
-    conifer_wrapper.pl --input $input --regions $plot_option.regions --html_file $html_file --html_folder $html_file.files_path
-    #if str($plot_option.plot_option_select) == "single"
-        --sample "$plot_option.sample"
-    #else
-        --window $plot_option.window
-        --multiple
-    #end if
-    2&gt;&amp;1
-	</command>
-	<inputs>
-		<param format="hdf5" name="input" type="data" label="CoNIFER output analysis file (hdf5)"/>
-		<conditional name="plot_option">
-			<param name="plot_option_select" type="select" label="Single or multiple regions?">
-				<option value="single" selected="true">Single region</option>
-				<option value="multiple">Multiple regions</option>
-			</param>
-			<when value="single">
-				<param name="regions" type="text" size="50" optional="false" label="Region" help="Region for the plot (i.e. chr1:1000-2000)"/>
-				<param name="sample" type="text" size="50" optional="true" value="" label="Sample" help="Sample names to be highlighted in the plot (optional)"/>
-			</when>
-			<when value="multiple">
-				<param format="tabular" name="regions" type="data" label="CoNIFER output calls file (tabular)"/>
-                <param name="window" size="10" type="integer" value="50" label="Window"/>
-			</when>
-		</conditional>
-    </inputs>
-    <outputs>
-        <data format="html" name="html_file" label="${tool.name} on ${on_string}" />
-    </outputs>
-<help>
-**What it does**
-
-Draw a HTML page with CNV plots. It accepts as input either a single region or a file with CoNIFER calls.
-
-**License and citation**
-
-This Galaxy tool is Copyright © 2013 `CRS4 Srl.`_ and is released under the `MIT license`_.
-
-.. _CRS4 Srl.: http://www.crs4.it/
-.. _MIT license: http://opensource.org/licenses/MIT
-
-If you use this tool in Galaxy, please cite |Cuccuru2014|_.
-
-.. |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*, accepted
-.. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/early/2014/03/10/bioinformatics.btu135
-
-This tool uses CoNIFER, which is licensed separately. Please cite:
-
-- |Krumm2012|_.
-
-.. |Krumm2012| replace::  (Krumm et al., 2012) Copy number variation detection and genotyping from exome sequence data. Genome research.
-.. _Krumm2012: http://genome.cshlp.org/content/22/8/1525.full?sid=4a7a300a-b960-4544-8611-effc3315411c
-  </help>
-</tool>