# HG changeset patch
# User cmonjeau
# Date 1433518818 14400
# Node ID 1beb3ed9e1e38cc8a2b8cf3e6e56b41ad4a8e864
Imported from capsule None
diff -r 000000000000 -r 1beb3ed9e1e3 bbric_disco.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bbric_disco.py Fri Jun 05 11:40:18 2015 -0400
@@ -0,0 +1,126 @@
+import sys, tempfile, subprocess, glob
+import os, re, shutil, stat
+import optparse
+from os.path import basename
+
+"""
+
+Created by Cyril Monjeaud
+Cyril.Monjeaud@irisa.fr
+Modified by Fabrice Legeai
+fabrice.legeai@rennes.inra.fr
+
+Last modifications : 04/21/2015
+
+WARNING :
+
+discoSNP++.py needs:
+
+- run_discoSnp++.sh
+- discoSNP++_to_genotypes.py
+- the build repository next to the scripts
+
+All these files are available after compiling the sources of discoSNP :
+
+https://colibread.inria.fr/files/2013/10/DiscoSNPpp-2.0.6-Source.zip
+
+or with the package_discoSnp_plus_plus package in the toolshed
+
+"""
+
+
+def __main__():
+
+ # store inputs in an array
+ parser = optparse.OptionParser()
+ parser.add_option("-r", dest="data_files")
+ parser.add_option("-b", dest="branching_bubbles")
+ parser.add_option("-D", dest="deletions")
+ parser.add_option("-P", dest="min_snps")
+ parser.add_option("-l", action="store_true", dest="low_complexity")
+ parser.add_option("-k", dest="kmer")
+ parser.add_option("-t", action="store_true", dest="left_right_unitigs")
+ parser.add_option("-T", action="store_true", dest="left_right_contigs")
+ parser.add_option("-c", dest="coverage")
+ parser.add_option("-C", dest="maxcoverage")
+ parser.add_option("-d", dest="error_threshold")
+ parser.add_option("-n", action="store_true", dest="genotypes")
+ parser.add_option("-G", dest="reference")
+ parser.add_option("-M", dest="mapping_error")
+
+ (options, args) = parser.parse_args()
+
+ # create the working dir inside job_working_dir
+ output_dir = os.mkdir("job_outputs")
+
+ cmd_line=[]
+ cmd_line.append("/bin/bash")
+ #cmd_line.append("/home/genouest/inrarennes/flegeai/local/DiscoSNP/DiscoSNP++-2.1.4-Source/run_discoSnp++.sh")
+ cmd_line.append("run_discoSnp++.sh")
+ #cmd_line.append("-B /local/bwa/bwa-0.7.10/")
+
+ # transform .dat into .fasta or .fastq for kissreads2
+ link_files=[]
+ f = open(options.data_files, 'r')
+ files = f.readlines()
+ for file in files:
+ file=file.strip()
+ if re.search("^$",file): continue
+ tagfile=[]
+ tagfile=re.split('::', file)
+ number = int(tagfile[0])+1
+ if re.search("^>.*", open(tagfile[1]).readline()):
+ link_file = 'input'+str(number)+'.fasta'
+ else:
+ link_file = 'input'+str(number)+'.fastq'
+
+ os.symlink(tagfile[1], link_file)
+ link_files.append(link_file)
+
+
+ # edit the command line
+ cmd_line.extend(["-r",' '.join(link_files),"-b",options.branching_bubbles,"-D",options.deletions,"-P",options.min_snps,"-k",options.kmer,"-c",options.coverage,"-C",options.maxcoverage,"-d",options.error_threshold])
+ if options.low_complexity:
+ cmd_line.append("-l")
+ if options.left_right_unitigs:
+ cmd_line.append("-t")
+ if options.left_right_contigs:
+ cmd_line.append("-T")
+ if options.genotypes:
+ cmd_line.append("-n")
+
+ # genotype part
+ if options.reference:
+ cmd_line.extend(["-G", options.reference])
+ cmd_line.extend(["-M", options.mapping_error])
+
+ cmd_line.extend(["-p","job_outputs/galaxy"])
+
+ # execute job
+ p=subprocess.Popen(cmd_line,
+ stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+
+ stdoutput, stderror = p.communicate()
+
+ # report file
+ logfile=open("report.txt", "w")
+ logfile.write("[COMMAND LINE]"+' '.join(cmd_line)+"\n\n")
+ logfile.write(stdoutput)
+
+ # print stderror because it's informations
+ logfile.write(stderror)
+
+ # close logfile
+ logfile.close()
+
+ # change .fa extension to .fasta for a correct print inside Galaxy
+ fafiles = glob.glob("job_outputs/*_coherent.fa")
+ for fafile in fafiles:
+ shutil.move(fafile, "coherent.fasta")
+ vcffiles = glob.glob("job_outputs/*_coherent.vcf")
+ for vcffile in vcffiles:
+ shutil.move(vcffile, "coherent.vcf")
+
+
+if __name__ == "__main__": __main__()
+
diff -r 000000000000 -r 1beb3ed9e1e3 bbric_disco.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bbric_disco.xml Fri Jun 05 11:40:18 2015 -0400
@@ -0,0 +1,151 @@
+
+is an efficient tool for detecting SNPs without a reference genome.
+
+ discoSnp_plus_plus
+ bwa
+
+
+bbric_disco.py
+-r ${datfile}
+-b $branching_bubbles
+-D $deletions
+-P $limit_snp
+#if $low_complexity
+-l
+#end if
+-k $kmer
+#if (str($extension) == 't'):
+-t
+#end if
+#if (str($extension) == 'T'):
+-T
+#end if
+-c $coverage
+-C ${maxcoverage}
+-d $error_threshold
+#if (str($VCF_option.mapping) == 'reference'):
+-G ${VCF_option.reference}
+-M ${VCF_option.mapping_error}
+#end if
+
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+ #for $i, $lib in enumerate ($input_list)
+ ${i}::${lib.input}
+ #end for
+
+
+
+
+**Description**
+
+Software discoSnp is designed for discovering Single Nucleotide Polymorphism (SNP) from raw set(s) of reads obtained with Next Generation Sequencers (NGS).
+Note that number of input read sets is not constrained, it can be one, two, or more. Note also that no other data as reference genome or annotations are needed.
+The software is composed by two modules. First module, kissnp2, detects SNPs from read sets. A second module, kissreads, enhance the kissnp2 results by computing per read set and for each found SNP i/ its mean read coverage and ii/ the (phred) quality of reads generating the polymorphism.
+
+Note that from release of DiscoSnp++-2.0.6, the tool also detects close SNPs and indels.
+
+-------
+
+.. class:: warningmark
+
+**Input parameters**
+
+-Sequences files in fasta, fastq or fastq.gz, each allele will be counted in each file individually
+
+-Fasta sequence of a genome if case of you are willing to map the sequence extension on a reference in order to get a compliant VCF
+
+-------
+
+.. class:: warningmark
+
+**Ouput parameters**
+
+-VCF file with coordinates on the higher branch sequences or on a reference genome if provided
+
+-Fasta file with sequence extensions around the SNP.
+
+
+-------
+
+**Web site**
+
+https://colibread.inria.fr/software/discosnp/
+
+-------
+
+**Integrated by**
+
+Cyril Monjeaud and Fabrice Legeai
+
+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>`_
+
+
+
+10.1093/nar/gku1187
+@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 1beb3ed9e1e3 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Fri Jun 05 11:40:18 2015 -0400
@@ -0,0 +1,9 @@
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