| Previous changeset 33:22fabe161cf3 (2016-12-15) Next changeset 35:744e5e2e3556 (2016-12-16) |
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Commit message:
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modified:
shm_csr.xml wrapper.sh |
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| diff -r 22fabe161cf3 -r 96c1276ceefe shm_csr.xml --- a/shm_csr.xml Thu Dec 15 09:44:17 2016 -0500 +++ b/shm_csr.xml Fri Dec 16 09:53:09 2016 -0500 |
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| @@ -1,7 +1,7 @@ <tool id="shm_csr" name="SHM & CSR pipeline" version="1.0"> <description></description> <command interpreter="bash"> - wrapper.sh $in_file custom $out_file $out_file.files_path ${in_file.name} "-" $functionality $unique $naive_output_cond.naive_output $naive_output_ca $naive_output_cg $naive_output_cm $naive_output_ce $naive_output_all $filter_uniques $class_filter_cond.class_filter $empty_region_filter $fast + wrapper.sh $in_file custom $out_file $out_file.files_path "${in_file.name}" "-" $functionality $unique $naive_output_cond.naive_output $naive_output_ca $naive_output_cg $naive_output_cm $naive_output_ce $naive_output_all $filter_uniques $class_filter_cond.class_filter $empty_region_filter $fast </command> <inputs> <param name="in_file" type="data" label="IMGT zip file to be analysed" /> |
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| diff -r 22fabe161cf3 -r 96c1276ceefe wrapper.sh --- a/wrapper.sh Thu Dec 15 09:44:17 2016 -0500 +++ b/wrapper.sh Fri Dec 16 09:53:09 2016 -0500 |
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| @@ -6,7 +6,7 @@ log=$3 #becomes the main html page at the end outdir=$4 output="$outdir/index.html" #copied to $log location at the end -title=$5 +title="$5" include_fr1=$6 functionality=$7 unique=$8 @@ -37,8 +37,8 @@ elif [[ "$type" == *"XZ compressed data"* ]] ; then echo "ZX archive" echo "tar -xJf $input -C $PWD/files/" - mkdir -p $PWD/files/$title - tar -xJf $input -C $PWD/files/$title + mkdir -p "$PWD/files/$title" + tar -xJf $input -C "$PWD/files/$title" fi cat `find $PWD/files/ -name "1_*"` > $PWD/summary.txt @@ -439,7 +439,7 @@ mkdir $outdir/baseline/IGG if [[ $(wc -l < $outdir/new_IMGT_IGG/1_Summary.txt) -gt "1" ]]; then cd $outdir/baseline/IGG - bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGG.txz "cg" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGG.pdf" "Sequence.ID" "$outdir/baseline_IGG.txt" + bash $dir/baseline/wrapper.sh 1 1 1 1 0 0 "25:26:38:55:65:104:-" $outdir/new_IMGT_IGG.txz "IGG" "$dir/baseline/IMGTVHreferencedataset20161215.fa" "$outdir/baseline_IGG.pdf" "Sequence.ID" "$outdir/baseline_IGG.txt" else echo "No IGG sequences" > "$outdir/baseline_IGG.txt" fi |