Mercurial > repos > eugen > bs_seq_test_1
changeset 12:1d29aebf96ae draft
Deleted selected files
author | eugen |
---|---|
date | Wed, 15 Aug 2012 08:52:40 -0400 |
parents | 7ad77d2e23d0 |
children | ee3bd6ad3958 |
files | bismark_meth_caller.sh bismark_wrapper.sh |
diffstat | 2 files changed, 0 insertions(+), 149 deletions(-) [+] |
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--- a/bismark_meth_caller.sh Wed Aug 15 08:27:03 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,35 +0,0 @@ -#!/bin/bash -# -# Galaxy wrapper for Bismark Methylation Caller -# - -set -e - -#get parameters - -until [ $# -eq 0 ] -do - case $1 in - input=*) - input=${1#input=} - ;; - method=*) - method=${1#method=} - ;; - output=*) - output=${1#output=} - ;; - tempdir=*) - tempdir=${1#tempdir=} - ;; - esac - shift -done -(grep ^@ $input; grep -v ^@ $input | sort -k3,3 -k1,1) > $tempdir"bismark_sam_sorted.sam" -methylation_extractor -$method -o $output $tempdir"bismark_sam_sorted.sam" 2>&1 > /dev/null - - - - - -
--- a/bismark_wrapper.sh Wed Aug 15 08:27:03 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,114 +0,0 @@ -#!/bin/bash -# -# Galaxy wrapper for Bismark -# - -set -e - -export PATH="/home/galaxy/dependencies/bismark:$PATH" -export PATH="/home/galaxy/dependencies/diverse:$PATH" - -#get parameters - -until [ $# -eq 0 ] -do - case $1 in - ref=*) - ref=${1#ref=} - ;; - library=*) - library=${1#library=} - ;; - fullparam=*) - fullparam=${1#fullparam=} - ;; - mate1=*) - mate1=${1#mate1=} - ;; - mate2=*) - mate2=${1#mate2=} - ;; - qual=*) - qual=${1#qual=} - ;; - seedmms=*) - seedmms="--seedmms ${1#seedmms=}" - ;; - seedlen=*) - seedlen="--seedlen ${1#seedlen=}" - ;; - maqerr=*) - maqerr="--maqerr ${1#maqerr=}" - ;; - directional=*) - directional=${1#directional=} - ;; - header=*) - header=${1#header=} - ;; - minins=*) - minins="--minins ${1#minins=}" - ;; - maxins=*) - maxins="--maxins ${1#maxins=}" - ;; - mapped=*) - mapped=${1#mapped=} - ;; - summary=*) - summary=${1#summary=} - ;; - tempdir=*) - tempdir=${1#tempdir=} - ;; - esac - shift -done - - -if [ "$library" == "single" ] -then - if [ "$fullparam" == 'false' ] - then - bismark --output_dir $tempdir --temp_dir $tempdir --quiet $ref $mate1 2>&1 > /dev/null - else - bismark --output_dir $tempdir --temp_dir $tempdir --quiet $qual $seedmms $seedlen $maqerr $directional $header $ref $mate1 2>&1 > /dev/null - fi -else - if [ "$fullparam" == 'false' ] - then - bismark --output_dir $tempdir --temp_dir $tempdir --quiet $ref -1 $mate1 -2 $mate2 2>&1 > /dev/null - else - bismark --output_dir $tempdir --temp_dir $tempdir --quiet $qual $seedmms $seedlen $maqerr $directional $header $minins $maxins $ref -1 $mate1 -2 $mate2 2>&1 > /dev/null - fi -fi - - -#call bismark. output in temp-directory (files_path) - - -#parse the filename of the input -> same as output -IFS="/" -set - $mate1 -outfile=${*:$#:1} - -#sort the mapped reads by chromosome -#sort -k 3,3 -k 4,4n "$tempdir/${outfile}_bismark_pe.sam" > "$tempdir/${outfile}_bismark_pe_sorted.sam" - -#copy resultfiles back into galaxy -#cp "$tempdir/${outfile}_bismark_sorted.sam" "$mapped" -if [ "$library" == "single" ] -then - cp "$tempdir/${outfile}_bismark.sam" "$mapped" - cp "$tempdir/${outfile}_Bismark_mapping_report.txt" "$summary" -else - cp "$tempdir/${outfile}_bismark_pe.sam" "$mapped" - cp "$tempdir/${outfile}_Bismark_paired-end_mapping_report.txt" "$summary" -fi - - - - - - -