# HG changeset patch
# User cmonjeau
# Date 1433518802 14400
# Node ID dbd6e370c8910b58622d94f889c43f90428152d0
Imported from capsule None
diff -r 000000000000 -r dbd6e370c891 TakeABreak.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/TakeABreak.xml Fri Jun 05 11:40:02 2015 -0400
@@ -0,0 +1,96 @@
+
+ is a tool that can detect inversion breakpoints directly from raw NGS reads
+
+ takeabreak
+
+
+TakeABreak_wrapper.py
+#if str( $options_usage.options_usage_selector ) == "graph"
+-g $options_usage.graph_file
+#end if
+#if str( $options_usage.options_usage_selector ) == "reads"
+-i $options_usage.data_files
+-k $options_usage.kmer
+-S $options_usage.kmersolid
+#end if
+-c $complexity
+-m $maxsimprct
+-r $optimization_param
+--output_graph $output_graph
+--output_fasta $output_fasta
+--output_log $output_log
+
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+ options_usage['options_usage_selector'] == 'reads'
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+**Description**
+
+TakeABreak is a tool that can detect inversion breakpoints directly from raw NGS reads, without the need of any reference genome and without de novo assembling the genomes. Its implementation has a very limited memory impact allowing its usage on common desktop computers and acceptable runtime (Illumina reads simulated at 2x40x coverage from human chromosome 22 can be treated in less than two hours, with less than 1GB of memory).
+
+-------
+
+**Web site**
+
+http://colibread.inria.fr/takeabreak/
+
+-------
+
+**Integrated by**
+
+Yvan Le Bras and Cyril Monjeaud
+
+GenOuest Bio-informatics Core Facility
+
+UMR 6074 IRISA INRIA-CNRS-UR1 Rennes (France)
+
+support@genouest.org
+
+If you use this tool in Galaxy, please cite :
+
+`Y. Le Bras, A. Roult, C. Monjeaud, M. Bahin, O. Quenez, C. Heriveau, A. Bretaudeau, O. Sallou, O. Collin, Towards a Life Sciences Virtual Research Environment : an e-Science initiative in Western France. JOBIM 2013. <https://www.e-biogenouest.org/resources/128>`_
+
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+
+10.1007/978-3-319-07953-0_10
+@INPROCEEDINGS{JOBIM2013,
+ author = {Le Bras, Y. and ROULT, A. and Monjeaud, C. and Bahin, M. and Quenez, O. and Heriveau, C. and Bretaudeau, A. and Sallou, O. and Collin, O.},
+ title = {Towards a Life Sciences Virtual Research Environment: An e-Science initiative in Western France},
+ booktitle = {JOBIM 2013 Proceedings},
+ year = {2013},
+ url = {https://www.e-biogenouest.org/resources/128},
+ pages = {97-106}
+ }
+
+
+
+
diff -r 000000000000 -r dbd6e370c891 TakeABreak_wrapper.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/TakeABreak_wrapper.py Fri Jun 05 11:40:02 2015 -0400
@@ -0,0 +1,83 @@
+import sys, tempfile, subprocess, glob
+import os, re, shutil
+import optparse
+from os.path import basename
+
+"""
+
+Created by Cyril Monjeaud
+Cyril.Monjeaud@irisa.fr
+
+WARNING :
+
+TakeABreak_wrapper.py needs:
+
+- dbgh5 & TakeABreak binaries in your $PATH
+
+All these files are available after compiling the sources of TakeABreak :
+
+http://colibread.inria.fr/files/2014/01/TakeABreak-1.1.0-Source.tar_.gz
+
+or with the package_takeabreak dependency in the toolshed
+
+"""
+
+def __main__():
+
+ # create a special dir inside job working dir
+ tmp_dir = tempfile.mkdtemp()
+ os.chdir(tmp_dir)
+
+ # retrieve arguments
+ parser = optparse.OptionParser()
+ parser.add_option("-i", dest="reads_files")
+ parser.add_option("-k", dest="kmer")
+ parser.add_option("-S", dest="kmersolid")
+
+ parser.add_option("-g", dest="graph_file")
+ parser.add_option("-c", dest="complexity")
+ parser.add_option("-m", dest="maxsimprct")
+ parser.add_option("-r", dest="optimization")
+
+ parser.add_option("--output_graph")
+ parser.add_option("--output_fasta")
+ parser.add_option("--output_log")
+
+ (options, args) = parser.parse_args()
+
+ cmd_line=[]
+ if options.reads_files:
+ # start the command line
+ cmd_line.append("TakeABreak")
+ cmd_line.extend(["-in",options.reads_files,"-kmer-size",options.kmer,"-abundance",options.kmersolid])
+ else:
+ # start the command line
+ os.symlink(options.graph_file, "graph.h5")
+ cmd_line.append("TakeABreak")
+ cmd_line.extend(["-graph", "graph.h5"])
+
+ cmd_line.extend(["-out","galaxy","-lct",options.complexity,"-max-sim",options.maxsimprct,"-repeat",options.optimization])
+
+ # execute command line
+ p=subprocess.Popen(cmd_line,
+ stdout=subprocess.PIPE,stderr=subprocess.PIPE)
+
+ stdoutput, stderror = p.communicate()
+
+ # log file
+ logfile=open(options.output_log, "w")
+ logfile.write("[COMMAND LINE]"+' '.join(cmd_line)+"\n\n")
+ logfile.write(stdoutput)
+ logfile.write(stderror)
+ logfile.close()
+
+ if options.reads_files:
+
+ # create output h5
+ shutil.copy("galaxy.h5", options.output_graph)
+
+ # create output fasta
+ shutil.copy("galaxy.fasta", options.output_fasta)
+
+if __name__ == "__main__": __main__()
+
diff -r 000000000000 -r dbd6e370c891 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Fri Jun 05 11:40:02 2015 -0400
@@ -0,0 +1,6 @@
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