Mercurial > repos > nml > abacas
comparison abacas.sh @ 0:a1fdc6925620 draft default tip
"planemo upload for repository https://github.com/phac-nml/abacas commit f6856961094e89e4cad0ee7df6c2a49bf005e4bf"
| author | nml |
|---|---|
| date | Thu, 21 Nov 2019 12:53:20 -0500 |
| parents | |
| children |
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| -1:000000000000 | 0:a1fdc6925620 |
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| 1 #!/bin/bash | |
| 2 | |
| 3 #wrapper for abacas | |
| 4 ##our arguments will come in as an array | |
| 5 | |
| 6 args=("$@") | |
| 7 | |
| 8 #to keep things readable assign vars | |
| 9 input_ref="${args[0]}" | |
| 10 input_query="${args[1]}" | |
| 11 ordered_contigs="${args[2]}" | |
| 12 use_bin="${args[3]}" | |
| 13 non="${args[4]}" | |
| 14 append_bin="${args[5]}" | |
| 15 out_bin="${args[6]}" | |
| 16 out_crunch="${args[7]}" | |
| 17 out_gaps="${args[8]}" | |
| 18 out_fasta="${args[9]}" | |
| 19 out_tab="${args[10]}" | |
| 20 out_unused="${args[11]}" | |
| 21 out_multi="${args[12]}" | |
| 22 out_binmulti="${args[13]}" | |
| 23 out_nonpseudo="${args[14]}" | |
| 24 | |
| 25 ##ok lets do up the optional tags.....I have four thus far | |
| 26 ##generate ordered multifasta file | |
| 27 | |
| 28 if [ "$ordered_contigs" == "yes" ]; then | |
| 29 options="-m" | |
| 30 fi | |
| 31 | |
| 32 if [ "$use_bin" == "yes" ]; then | |
| 33 options="$options -b" | |
| 34 fi | |
| 35 | |
| 36 if [ "$non" == "yes" ]; then | |
| 37 options="$options -N" | |
| 38 fi | |
| 39 | |
| 40 if [ "$append_bin" == "yes" ]; then | |
| 41 options="$options -a" | |
| 42 fi | |
| 43 | |
| 44 options="$options -o ab_out" | |
| 45 | |
| 46 script_path="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd)" | |
| 47 | |
| 48 #run abacas | |
| 49 eval "perl $script_path/abacas.1.1.pl $options -r $input_ref -q $input_query -p nucmer" | |
| 50 echo "perl $script_path/abacas.1.1.pl $options -r $input_ref -q $input_query -p nucmer" | |
| 51 #ok now we have to remove the nucmer files to cleanup a bit... | |
| 52 rm nucmer.delta | |
| 53 rm nucmer.filtered.delta | |
| 54 rm nucmer.tiling | |
| 55 | |
| 56 #name the datafiles properly | |
| 57 mv ab_out.bin "$out_bin" | |
| 58 if [ "$ordered_contigs" == "yes" ]; then | |
| 59 mv ab_out.contigs.fas "$out_multi" | |
| 60 fi | |
| 61 | |
| 62 if [ "$use_bin" == "yes" ]; then | |
| 63 mv ab_out.contigsInbin.fas "$out_binmulti" | |
| 64 fi | |
| 65 | |
| 66 mv ab_out.crunch "$out_crunch" | |
| 67 mv ab_out.fasta "$out_fasta" | |
| 68 mv ab_out.gaps "$out_gaps" | |
| 69 | |
| 70 if [ "$non" == "yes" ]; then | |
| 71 mv ab_out.NoNs.fasta "$out_nonpseudo" | |
| 72 fi | |
| 73 | |
| 74 mv ab_out.tab "$out_tab" | |
| 75 mv unused_contigs.out "$out_unused" | |
| 76 | |
| 77 #end script for now |