# HG changeset patch
# User sebastian-boegel
# Date 1356079575 18000
# Node ID 155b796033b67297b97a9a123b694a2115f5788f
# Parent  913ea6991ee4647dc5c8bfd3a2c8352312686e89
Uploaded

diff -r 913ea6991ee4 -r 155b796033b6 README
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README	Fri Dec 21 03:46:15 2012 -0500
@@ -0,0 +1,62 @@
+=============================================================================
+We developed an in-silico method "seq2HLA", written in python and R, which
+takes standard paired end RNA-Seq sequence reads in fastq format
+as input, uses a bowtie index comprising all HLA alleles and outputs the most
+likely HLA class I and class II genotypes, a p-value for each call, and the
+expression of each class.
+=============================================================================
+Author:
+Sebastian Boegel
+=============================================================================
+
+Tool dependencies:
+
+- bowtie
+- R
+
+=============================================================================
+To implement this script into Galaxy you have to copy the scripts folder in
+your "$GALAXYHOME/tools/" folder and add the path of seq2HLA.xml
+to your "$GALAXYHOME/tool_conf.xml"
+
+Example:
+#  <tool file="rna_seq/mapping_counter.xml" />
+#    <tool file="rna_seq/count_genes_exons_junctions.xml" />
+#    <tool file="rna_seq_auto/get_RNA-seq_data.xml" />
+#  </section>
+  <section name="HLA Typing" id="hla_type">
+    <tool file="seq2HLA/seq2HLA.xml"/>
+  </section>
+#  <section name="RSeQC" id="rseqc">
+#    <tool file="RSeQC/bam2wig.xml" />
+#    <tool file="RSeQC/bam_stat.xml" />
+#    <tool file="RSeQC/clipping_profile.xml" />
+#    <tool file="RSeQC/geneBody_coverage.xml" />
+#    <tool file="RSeQC/infer_experiment.xml" />
+...
+==============================================================================
+The script uses in its subprocesses 4 cores, so you will also have to add a
+setting to your "$GALAXYHOME/universe_wsgi.ini" to configure the queue for that
+script
+
+...
+[galaxy:tool_runners]
+
+#biomart = local:///
+#encode_db1 = local:///
+#hbvar = local:///
+#microbial_import1 = local:///
+ucsc_table_direct1 = local:///
+#ucsc_table_direct_archaea1 = local:///
+#ucsc_table_direct_test1 = local:///
+upload1 = local:///
+bowtie_wrapper = pbs:////-l nodes=1:ppn=4
+bowtie2_wrapper = pbs:////-l nodes=1:ppn=4
+tophat = pbs:////-l nodes=1:ppn=4
+tophat_color = pbs:////-l nodes=1:ppn=4
+cuffdiff = pbs:////-l nodes=1:ppn=4
+cufflinks = pbs:////-l nodes=1:ppn=4
+cuffmerge = pbs:////-l nodes=1:ppn=4
+seqhla = pbs:////-l nodes=1:ppn=6               (this line should be added)
+...
+=============================================================================
diff -r 913ea6991ee4 -r 155b796033b6 seq2HLA.py
--- a/seq2HLA.py	Thu Dec 20 10:37:01 2012 -0500
+++ b/seq2HLA.py	Fri Dec 21 03:46:15 2012 -0500
@@ -54,23 +54,23 @@
 readspergroup={}
 allelesPerLocus={}
 
-def main(runName,readFile1,readFile2,fastaClassI,fastaClassII,bowtiebuildClassI,bowtiebuildClassII,mismatch,trim3,output1,output2,logfile,gzipped):
+def main(runName,readFile1,readFile2,fastaClassI,fastaClassII,bowtiebuildClassI,bowtiebuildClassII,mismatch,trim3,output1,output2,logfile,gzipped,num_threads):
 	log = open(logfile,"w")
 #	mapopt="-a -v"+str(mismatch)
 	mapopt="-a -v"+str(mismatch)
 	#call HLA typing for Class I
-	mainClassI(runName+"-ClassI",readFile1,readFile2,bowtiebuildClassI,fastaClassI,mapopt,trim3,output1,log,gzipped)
+	mainClassI(runName+"-ClassI",readFile1,readFile2,bowtiebuildClassI,fastaClassI,mapopt,trim3,output1,log,gzipped,num_threads)
 	#call HLA typing for Class II
-	mainClassII(runName+"-ClassII",readFile1,readFile2,bowtiebuildClassII,fastaClassII,mapopt,trim3,output2,log,gzipped)
+	mainClassII(runName+"-ClassII",readFile1,readFile2,bowtiebuildClassII,fastaClassII,mapopt,trim3,output2,log,gzipped,num_threads)
 
 #---------------Class I-------------------------------
-def mainClassI(runName,readFile1,readFile2,bowtiebuild,hla1fasta,mapopt,trim3,finaloutput,log,gzipped):
+def mainClassI(runName,readFile1,readFile2,bowtiebuild,hla1fasta,mapopt,trim3,finaloutput,log,gzipped,num_threads):
 	#-------1st iteration-----------------------------------
 	log.write("----------HLA class I------------\n")
 	sam1=runName+"-iteration1.bam"
 	iteration=1
 	log.write("First iteration starts....\nMapping ......\n")
-	mapping(sam1,runName,readFile1,readFile2,bowtiebuild,1,mapopt,trim3,log,gzipped)
+	mapping(sam1,runName,readFile1,readFile2,bowtiebuild,1,mapopt,trim3,log,gzipped,num_threads)
 	medians=[]
 	medians.extend([0,0,0])
 	medianflag=False
@@ -90,7 +90,7 @@
 	sam2=runName+"-iteration2.bam"
 	newReadFile1=runName+"-2nditeration_1.fq"
 	newReadFile2=runName+"-2nditeration_2.fq"
-	mapping(sam2,runName,newReadFile1,newReadFile2,bowtiebuild,2,mapopt,trim3,log,gzipped)
+	mapping(sam2,runName,newReadFile1,newReadFile2,bowtiebuild,2,mapopt,trim3,log,gzipped,num_threads)
 	medianfile=runName+".digitalhaplotype1"
 	for i in range(2,5):
 		medians.append(linecache.getline(medianfile, i).split('\t', 3)[2])
@@ -107,13 +107,13 @@
 	expression("A","B","C",694,694,694,map,runName,readFile1,finaloutput,gzipped)
 
 #--------------Class II----------------------------------------
-def mainClassII(runName,readFile1,readFile2,bowtiebuild,hla2fasta,mapopt,trim3,finaloutput,log,gzipped):
+def mainClassII(runName,readFile1,readFile2,bowtiebuild,hla2fasta,mapopt,trim3,finaloutput,log,gzipped,num_threads):
 	#-------1st iteration----------------------------------------
 	log.write("----------HLA class II------------\n")
 	sam1=runName+"-iteration1.bam"
 	iteration=1
 	log.write("ClassII: first iteration starts....\nMapping ......\n")
-	mapping(sam1,runName,readFile1,readFile2,bowtiebuild,1,mapopt,trim3,log,gzipped)
+	mapping(sam1,runName,readFile1,readFile2,bowtiebuild,1,mapopt,trim3,log,gzipped,num_threads)
 	medians=[]
 	medians.extend([0,0,0])
 	medianflag=False
@@ -132,7 +132,7 @@
 	sam2=runName+"-iteration2.bam"
 	newReadFile1=runName+"-2nditeration_1.fq"
 	newReadFile2=runName+"-2nditeration_2.fq"
-	mapping(sam2,runName,newReadFile1,newReadFile2,bowtiebuild,2,mapopt,trim3,log,gzipped)
+	mapping(sam2,runName,newReadFile1,newReadFile2,bowtiebuild,2,mapopt,trim3,log,gzipped,num_threads)
 	medianfile=runName+".digitalhaplotype1"
 	for i in range(2,5):
 		medians.append(float(linecache.getline(medianfile, i).split('\t', 3)[2])/2.0)
@@ -149,18 +149,18 @@
 	expression("DQA1","DQB1","DRB1",400,421,421,map,runName,readFile1,finaloutput,gzipped)
 
 #performs the bowtie mapping for the 2 iterations using the given parameters
-def mapping(sam,runName,readFile1,readFile2,bowtiebuild,iteration,mapopt,trim3,log,gzipped):
+def mapping(sam,runName,readFile1,readFile2,bowtiebuild,iteration,mapopt,trim3,log,gzipped,num_threads):
 	if iteration==1:
 		if gzipped == "True":
 			sam = sam.rsplit(".",1)[0]
-			cmd1 = "bowtie --threads 4 -3 %s --quiet -S %s --al %s.aligned %s -1 <(zcat %s) -2 <(zcat %s) |  awk -F '\t' '$3 != \"*\"{ print $0 }' | samtools view -bS - | samtools sort - %s" % (trim3,mapopt,runName,bowtiebuild,readFile1,readFile2,sam)
+			cmd1 = "bowtie --threads "+num_threads+" -3 %s --quiet -S %s --al %s.aligned %s -1 <(zcat %s) -2 <(zcat %s) |  awk -F '\t' '$3 != \"*\"{ print $0 }' | samtools view -bS - | samtools sort - %s" % (trim3,mapopt,runName,bowtiebuild,readFile1,readFile2,sam)
 			mappingOutput = execBowtie(cmd1)
 			
 			cmd2 = "samtools index %s.bam" % sam
 			createBAMIndex(cmd2)
 		else:
 			sam = sam.rsplit(".",1)[0]
-			cmd1 = "bowtie --threads 4 -3 %s --quiet -S %s --al %s.aligned %s -1 %s -2 %s |  awk -F '\t' '$3 != \"*\"{ print $0 }' | samtools view -bS - | samtools sort - %s" % (trim3,mapopt,runName,bowtiebuild,readFile1,readFile2,sam)
+			cmd1 = "bowtie --threads "+num_threads+" -3 %s --quiet -S %s --al %s.aligned %s -1 %s -2 %s |  awk -F '\t' '$3 != \"*\"{ print $0 }' | samtools view -bS - | samtools sort - %s" % (trim3,mapopt,runName,bowtiebuild,readFile1,readFile2,sam)
 			mappingOutput = execBowtie(cmd1)
 
 			cmd2 = "samtools index %s.bam" % sam
@@ -169,7 +169,7 @@
 	else:
 		
 		sam = sam.rsplit(".",1)[0]
-		cmd2 = "bowtie --threads 4 -3 %s --quiet -S %s %s -1 %s -2 %s | samtools view -bS - | samtools sort - %s" % (trim3,mapopt,bowtiebuild,readFile1,readFile2,sam)
+		cmd2 = "bowtie --threads "+num_threads+" -3 %s --quiet -S %s %s -1 %s -2 %s | samtools view -bS - | samtools sort - %s" % (trim3,mapopt,bowtiebuild,readFile1,readFile2,sam)
 		mappingOutput = execBowtie(cmd2)
 
 		cmd3 = "samtools index %s.bam" % sam
@@ -766,6 +766,7 @@
 			dest="output2",
 			help="Output file 2")
 	parser.add_option("-g","--log",action="store",dest="logfile",help="Output Log File")
+	parser.add_option("-t","--threads",type="int",dest="num_threads",help="Define amount of threads to use for Bowtie in this script")
 
 
 	(options, args) = parser.parse_args()
@@ -796,6 +797,6 @@
 	else:
 		mismatch=3
 	trim3=str(options.trim3)
-	main(runName,readFile1,readFile2,fastaClassI,fastaClassII,bowtiebuildClassI,bowtiebuildClassII,mismatch,trim3,output1,output2,logfile,gzipped)
+	main(runName,readFile1,readFile2,fastaClassI,fastaClassII,bowtiebuildClassI,bowtiebuildClassII,mismatch,trim3,output1,output2,logfile,gzipped,options.num_threads)
 	sys.stderr = log_stderr
 	log_file.close()
diff -r 913ea6991ee4 -r 155b796033b6 seq2HLA.xml
--- a/seq2HLA.xml	Thu Dec 20 10:37:01 2012 -0500
+++ b/seq2HLA.xml	Fri Dec 21 03:46:15 2012 -0500
@@ -2,6 +2,7 @@
     <description>HLA typing from RNA-Seq sequence read</description>
     <command interpreter="python">
       seq2HLA.py
+      -t $threads
       -z $compressed
       -1 $readFile1
       -2 $readFile2
@@ -13,12 +14,13 @@
       -g $logfile
     </command>
     <inputs>
-      <param name="compressed" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Select if your input files are compressed gzipped fastq files" help="Leave default if you didn't upload the files or don't know"/>
+      <param name="compressed" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Select if your input files are compressed gzipped fastq files" help="Leave default (not checked) if you are unsure"/>
       <param format="fastq,fastqsanger" name="readFile1" type="data" label="Forward FASTQ File" help="FASTQ File with forward reads" />
       <param format="fastq,fastqsanger" name="readFile2" type="data" label="Reverse FASTQ File" help="FASTQ File with reverse reads" />
       <param name="runName" type="text" value="Run1" label="Run Name" help="Name of the Run" />
       <param name="readLength" type="integer" value="50" label="Read Length" help="Length of the input reads" />
       <param name="trim" type="integer" value="0" label="Trim x bases from the low quality 3' end" help="Trim x bases from the low quality 3' end. Default: 0" />
+      <param name="threads" type="integer" value="4" label="Number of threads to use for Bowtie" help="Choose a plausible amount of threads to use for Bowtie in this tool" />
     </inputs>
     <outputs>
       <data format="txt" name="out1" label="${tool.name} on ${on_string}: Output 1" />
@@ -33,6 +35,7 @@
 	<param name="runName" value="Run1"/>
 	<param name="readLength" value="37"/>
 	<param name="trim" value="0"/>
+	<param name="threads" value="4"/>
 	<output name="out1" file="output1.txt"/>
 	<output name="out2" file="output2.txt"/>
 	<output name="logfile" file="log.txt"/>
@@ -51,6 +54,11 @@
 
 .. class:: infomark
 
+**Dependencies**
+
+- bowtie
+- R
+
 **Input**
 
 Input files in FASTQ format
@@ -73,7 +81,7 @@
 
 -----
 
-.. image:: ./static/images/tron_logo.png
+.. image:: http://tron-mainz.de/wp-content/themes/tron/images/page_logo.png
 
 </help>
 </tool>