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