# HG changeset patch
# User ntino-krampis
# Date 1359657695 18000
# Node ID beaf42837914648feb7826b1b40c7a303cb65dab
viral cloud resource galaxy tool definitions initial commit
diff -r 000000000000 -r beaf42837914 viral_assembly_annotation/VIGOR.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/viral_assembly_annotation/VIGOR.py Thu Jan 31 13:41:35 2013 -0500
@@ -0,0 +1,42 @@
+#!/usr/bin/env python
+
+"""
+Runs VIGOR3 on given input fasta file.
+"""
+
+import os, sys, subprocess, tempfile, shutil
+
+def __main__():
+ # Parse the command line options
+ (inputFasta,outputALN,outputCDS,outputFS,outputPEP,outputRPT,outputSTATS,outputTBL) = sys.argv[1:]
+
+ # Set up output variables
+ outputDir = "/usr/local/VIGOR/tools/vigor/test"
+ outputName = "output"
+ outputLog = "%s/%s_log.txt" % (outputDir,outputName)
+ vigorOutputALN = "%s/%s.aln" % (outputDir,outputName)
+ vigorOutputCDS = "%s/%s.cds" % (outputDir,outputName)
+ vigorOutputFS = "%s/%s.fs" % (outputDir,outputName)
+ vigorOutputPEP = "%s/%s.pep" % (outputDir,outputName)
+ vigorOutputRPT = "%s/%s.rpt" % (outputDir,outputName)
+ vigorOutputSTATS = "%s/%s.stats" % (outputDir,outputName)
+ vigorOutputTBL = "%s/%s.tbl" % (outputDir,outputName)
+
+ # Create empty output log file (cannot be created by VIGOR command alone).
+ os.system("sudo touch %s" % outputLog)
+ os.system("sudo chmod 777 %s" % outputLog)
+
+ # Run command
+ command = "/usr/local/VIGOR/tools/vigor/prod3/VIGOR3.pl -A -i %s -O %s/%s > %s" % (inputFasta,outputDir,outputName,outputLog)
+ os.system("sudo %s" % command)
+ os.system("sudo chmod 777 %s/%s.*" % (outputDir,outputName))
+ os.system("sudo cp %s %s" % (vigorOutputALN,outputALN))
+ os.system("sudo cp %s %s" % (vigorOutputCDS,outputCDS))
+ os.system("sudo cp %s %s" % (vigorOutputFS,outputFS))
+ os.system("sudo cp %s %s" % (vigorOutputPEP,outputPEP))
+ os.system("sudo cp %s %s" % (vigorOutputRPT,outputRPT))
+ os.system("sudo cp %s %s" % (vigorOutputSTATS,outputSTATS))
+ os.system("sudo cp %s %s" % (vigorOutputTBL,outputTBL))
+
+if __name__=="__main__":
+ __main__()
diff -r 000000000000 -r beaf42837914 viral_assembly_annotation/VIGOR.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/viral_assembly_annotation/VIGOR.xml Thu Jan 31 13:41:35 2013 -0500
@@ -0,0 +1,24 @@
+
+ Run VIGOR
+
+ VIGOR.py $input $outputALN $outputCDS $outputFS $outputPEP $outputRPT $outputSTATS $outputTBL
+
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+
+
+**What it does**
+
+This tool runs VIGOR on the input set of fasta sequences.
+
+
diff -r 000000000000 -r beaf42837914 viral_assembly_annotation/viral_assembly.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/viral_assembly_annotation/viral_assembly.py Thu Jan 31 13:41:35 2013 -0500
@@ -0,0 +1,38 @@
+#!/usr/bin/env python
+
+"""
+Takes input from viral_assembly.xml and sends it to vir-assembly-pipeline.sh.
+"""
+
+import os, sys, subprocess, tempfile, shutil
+
+def __prepare_input__(draftFilename,finalFilename,finalDir):
+ result = "%s/%s" % (finalDir,finalFilename)
+
+ if draftFilename == "None":
+ os.system("sudo touch %s" % result)
+ else:
+ os.system("sudo cp %s %s" % (draftFilename,result))
+
+ return result
+
+def __main__():
+ # Parse the command line options
+ (input_454,input_Sanger,input_Solexa,input_Solexa_tp,database,outputFasta) = sys.argv[1:]
+
+ # Copy the input files to the VHTNGS location. If an input file was not given, create an empty dummy file as a replacement.
+ inputDir = "/usr/local/VHTNGS"
+
+ input_454_ready = __prepare_input__(input_454,"input_454.sff",inputDir)
+ input_Sanger_ready = __prepare_input__(input_Sanger,"input_Sanger.fasta",inputDir)
+ input_Solexa_ready = __prepare_input__(input_Solexa,"input_Solexa.fastq",inputDir)
+ input_Solexa_tp_ready = __prepare_input__(input_Solexa_tp,"input_Solexa.fastq.trimpoints",inputDir)
+
+ command = "/usr/local/VHTNGS/vir-assembly-pipeline.sh %s %s %s %s %s" % (input_454_ready,input_Sanger_ready,input_Solexa_ready,input_Solexa_tp_ready,database)
+ virAssemblyOutput = "/usr/local/VHTNGS/project/mapping/sample_hybrid_edited_refs_consensus.fasta"
+ os.system("sudo %s" % command)
+ os.system("sudo chmod 777 %s" % virAssemblyOutput)
+ os.system("sudo cp %s %s" % (virAssemblyOutput,outputFasta))
+
+if __name__=="__main__":
+ __main__()
diff -r 000000000000 -r beaf42837914 viral_assembly_annotation/viral_assembly.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/viral_assembly_annotation/viral_assembly.xml Thu Jan 31 13:41:35 2013 -0500
@@ -0,0 +1,38 @@
+
+ Run Viral assembly
+
+ viral_assembly.py $input_454 $input_Sanger $input_Solexa $input_Solexa_tp $database $output_Fasta
+
+
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+
+
+**What it does**
+
+This tool uses vir-assembly-pipeline.sh to run viral assembly and consensus sequence generation on the input sequence data.
+
+