changeset 58:e7de191375e6 draft

Uploaded

--- a/README.rst	Mon Jan 05 04:55:17 2015 -0500
+++ b/README.rst	Thu Jan 08 06:18:04 2015 -0500
@@ -5,7 +5,7 @@
 
 The typical workflow is as follows:
 * paired-end amplicon sequencing
-* merge pairs by overlapping them
+* merge pairs (so only overlapping pairs are included)
 * map the single read fastq with BWA
 * perform variant calling with FALCO
 * create (html) report of the results
@@ -18,15 +18,6 @@
 Input of the caller is a BAM file, output VCF
 
 
-History
-
-============== ================================================================
-Date            Changes
--------------- ----------------------------------------------------------------
-December 2014    * first release in Test Tool Shed
-============== ================================================================
-
-
 Bug Reports & other questions
 =============================
 

--- a/falco-call.sh	Mon Jan 05 04:55:17 2015 -0500
+++ b/falco-call.sh	Thu Jan 08 06:18:04 2015 -0500
@@ -4,12 +4,10 @@
 echo "Started FALCO calling"
 
 ## ----------
-## Variables setup
+## Variables setup ($1 contains the bash config file path)
 ## ----------
 source $1
 
-bam_base=`echo $bam_name | sed 's#.bam$##' - ` 
-
 ## ----------
 ## make sure all is ok
 ## ----------
@@ -22,20 +20,24 @@
 ## ----------
 ## set params
 ## ----------
-if [[ $filter_file != 'None' && $filter_file != '' ]] # Galaxy default somehow is "None"
+if [[ $filter_file != 'None' && $filter_file != '' ]] # Galaxy default is "None" for some reason
 then 
 	FILTER_PARAM=" --filter "$filter_file
 else
 	FILTER_PARAM=""
 fi
 
-if [[ $manifest_file != 'None' && $manifest_file != 'None' ]] # Galaxy default is "None"
+if [[ $manifest_file != 'None' && $manifest_file != 'None' ]] # Galaxy default is "None" for some reason
 then 
 	MANIFEST_PARAM=" --manifest "$manifest_file
 else
 	MANIFEST_PARAM=""
 fi
 
+## name of file in galaxy not always set so will use a user-set job_name instead
+#bam_base=`echo $bam_name | sed 's#.bam$##' - ` 
+bam_base=$job_name
+
 ## ----------
 ## Status / debug
 ## ----------
@@ -62,11 +64,11 @@
 ## ----------
 ## running analysis
 ## ----------
-echo "Starting variant calling"
+echo "[INFO] Starting variant calling"
 CALL_STRING="$TOOLDIR/falco/bin/falco --bam $bam_file --output $bam_base --ref $REF_FILE $FILTER_PARAM $MANIFEST_PARAM"
 echo "[INFO] "$CALL_STRING
 perl $CALL_STRING
-echo "...done with variant calling"
+echo "[INFO] done with variant calling"
 
 
 ## ----------
@@ -113,4 +115,4 @@
 
 ## ----------
 echo "END falco sh"
-exit 0
\ No newline at end of file
+exit 0

--- a/falco-call.xml	Mon Jan 05 04:55:17 2015 -0500
+++ b/falco-call.xml	Thu Jan 08 06:18:04 2015 -0500
@@ -67,6 +67,7 @@
       html_out=$html_output
       vcf_out=$vcf_output
       out_path=${html_output.files_path}
+      job_name=$jobName
       ## reference source
       REF_SOURCE="${genomeSource.refGenomeSource}"
       #if $genomeSource.refGenomeSource == "history":