# HG changeset patch
# User cmonjeau
# Date 1433518836 14400
# Node ID 131c36a303ee7bb644566f516ed74f77de14bb37
Imported from capsule None
diff -r 000000000000 -r 131c36a303ee kissplice.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/kissplice.xml Fri Jun 05 11:40:36 2015 -0400
@@ -0,0 +1,67 @@
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+ A local transcriptome assembler for SNPs, indels and AS events
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+ kissplice
+
+ kisspliceGWrapper.py $output1 $type0 $type1 $type2 $type3 $type4 $kmer $smallc $bigc $output_context $counts
+ #for $r in $reads
+ ${r.input}
+ ${r.input.extension}
+ #end for
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+**Website**
+
+References, documentation and FAQ here_.
+
+.. _here: http://kissplice.prabi.fr/
+
+------
+
+**Description**
+
+KisSplice is a piece of software that enables the **analysis of RNA-seq data with or without a reference genome**. It is an exact local transcriptome assembler that allows one to identify **SNPs, indels and alternative splicing events**. It can deal with an arbitrary number of biological conditions, and will quantify each variant in each condition. It has been tested on Illumina datasets of up to 1G reads. Its memory consumption is around 5Gb for 100M reads.
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+KisSplice is not a full-length transcriptome assembler. This means that it will output the variable regions of the transcripts, not reconstruct them entirely. However, KisSplice results can be further aligned to a reference transcriptome (if available), or to the output of a full-length transcriptome assembler like Trinity or Oases.
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diff -r 000000000000 -r 131c36a303ee kisspliceGWrapper.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/kisspliceGWrapper.py Fri Jun 05 11:40:36 2015 -0400
@@ -0,0 +1,75 @@
+import subprocess, os, sys, shutil, tempfile, os.path
+from os.path import basename, splitext
+
+## inputs
+kmer_value = sys.argv[7]
+smallc_value = sys.argv[8]
+bigc_value = sys.argv[9]
+output_contex_value = sys.argv[10]
+counts_value = sys.argv[11]
+input_dat = sys.argv[12:len(sys.argv):2] # contains filename1... filenameq
+input_ext = sys.argv[13:len(sys.argv):2] # contains extension1... extensionq
+
+## tmp directory
+tmp_dir = tempfile.mkdtemp(prefix='kissplice-galaxy.')
+
+## command line (init)
+command_line = []
+command_line.append("kissplice")
+
+## symlink for .fasta/q (extension required)
+## command line built with -r option
+identifier = ""
+for i in range(0,len(input_dat)):
+ tmp_input_fasta = os.path.join(tmp_dir, 'input'+str(i)+'.'+input_ext[i])
+ identifier += 'input'+str(i)+'_'
+ os.symlink(input_dat[i], tmp_input_fasta)
+ command_line.append("-r")
+ command_line.append(tmp_input_fasta)
+
+## command line (end)
+opath=tmp_dir+"/results"
+nocontext = ""
+nosnp = ""
+if output_contex_value == "yes":
+ command_line.extend(["-k", kmer_value,
+ "-c", smallc_value, "-C", bigc_value,
+ "--counts", counts_value, "--output-context",
+ "-o", opath, "-s"])
+else:
+ command_line.extend(["-k", kmer_value,
+ "-c", smallc_value, "-C", bigc_value,
+ "--counts", counts_value,
+ "-o", opath, "-s"])
+
+## running kissplice
+p=subprocess.Popen(command_line,
+ stdout=subprocess.PIPE,stderr=subprocess.PIPE)
+stdoutput = p.communicate()
+
+## outputs
+output_f1=sys.argv[1]
+out1=open(output_f1, 'w' )
+out1.write(stdoutput[0])
+out1.close()
+
+output_type0=sys.argv[2]
+output_type1=sys.argv[3]
+output_type2=sys.argv[4]
+output_type3=sys.argv[5]
+output_type4=sys.argv[6]
+
+result_type0 = opath+"/"+"results_"+identifier+"k"+kmer_value+"_coherents_type_0.fa"
+result_type1 = opath+"/"+"results_"+identifier+"k"+kmer_value+"_coherents_type_1.fa"
+result_type2 = opath+"/"+"results_"+identifier+"k"+kmer_value+"_coherents_type_2.fa"
+result_type3 = opath+"/"+"results_"+identifier+"k"+kmer_value+"_coherents_type_3.fa"
+result_type4 = opath+"/"+"results_"+identifier+"k"+kmer_value+"_coherents_type_4.fa"
+
+shutil.move(result_type0, output_type0)
+shutil.move(result_type1, output_type1)
+shutil.move(result_type2, output_type2)
+shutil.move(result_type3, output_type3)
+shutil.move(result_type4, output_type4)
+
+## cleaning
+shutil.rmtree(tmp_dir)
diff -r 000000000000 -r 131c36a303ee tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Fri Jun 05 11:40:36 2015 -0400
@@ -0,0 +1,6 @@
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