Mercurial > repos > nml > biohansel
annotate biohansel.xml @ 7:3360158bb0c5 draft
planemo upload for repository https://github.com/phac-nml/biohansel commit e3553c3c89db60cd285a401bc1c06fdd32665dd2
author | nml |
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date | Mon, 13 May 2019 09:42:08 -0400 |
parents | ba6a0af656a6 |
children | 4fa9d5e748d4 |
rev | line source |
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7
3360158bb0c5
planemo upload for repository https://github.com/phac-nml/biohansel commit e3553c3c89db60cd285a401bc1c06fdd32665dd2
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1 <tool id="biohansel" name="biohansel" version="2.1.6"> |
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c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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2 <description>SNP subtyping of genome sequence reads or assemblies</description> |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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3 <requirements> |
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c0b8de7aa02e
planemo upload for repository https://github.com/phac-nml/biohansel commit 99ec8e4342829bdceefd80c20b286204b563189a
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4 <requirement type="package" version="2.1.1">bio_hansel</requirement> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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5 </requirements> |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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6 <command detect_errors="exit_code"> |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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7 <![CDATA[ |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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8 |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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9 #import re |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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10 |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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11 ## Illumina FASTQ naming regular expression (https://github.com/phac-nml/biohansel/issues/38) |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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12 #set global $ILLUMINA_REGEX = $re.compile(r'^([\w\-\_]+)_S\d+_L\d{3}_R(\d)_001\.fastq(\.gz)?$') |
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ba6a0af656a6
planemo upload for repository https://github.com/phac-nml/biohansel commit 27adc5d715e9adc4b037586cccf1244cf031a7af
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13 #set global $FASTQ_DUMP_REGEX = $re.compile(r'^(\w+|\d+):((forward|reverse)(_\d+)?)') |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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14 |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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15 #def is_gzipped_fastq($data_input) |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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16 ## Is FASTQ data param gzipped type? i.e. either 'fastq.gz' or 'fastqsanger.gz'? |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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17 #return $data_input.is_of_type('fastqsanger.gz') or $data_input.is_of_type('fastq.gz') |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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18 #end def |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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19 |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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20 #def get_fastq_ext($data_input) |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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21 ## Get file extension for FASTQ data param |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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22 #return '.fastq.gz' if $is_gzipped_fastq($data_input) else '.fastq' |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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23 #end def |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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24 |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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25 #def base_sample_name($name) |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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26 ## Get the base sample name and append 1/2 depending on if forward/reverse read |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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27 #set $illumina_match = $ILLUMINA_REGEX.match($name) |
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planemo upload for repository https://github.com/phac-nml/biohansel commit b0060acc515bac2a79f60bb3c9d1f3243a5769f3
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28 #set $fastq_dump_match = $FASTQ_DUMP_REGEX.match($name) |
1f8eccf9d15d
planemo upload for repository https://github.com/phac-nml/biohansel commit b0060acc515bac2a79f60bb3c9d1f3243a5769f3
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29 |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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30 #if $illumina_match |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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31 #return $illumina_match.group(1) |
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ba6a0af656a6
planemo upload for repository https://github.com/phac-nml/biohansel commit 27adc5d715e9adc4b037586cccf1244cf031a7af
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32 #elif $fastq_dump_match |
ba6a0af656a6
planemo upload for repository https://github.com/phac-nml/biohansel commit 27adc5d715e9adc4b037586cccf1244cf031a7af
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33 #return $fastq_dump_match.group(1) |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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34 #elif $re.search(r'_R(1|2)', $name): |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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35 #return $re.sub(r'(.+)_R(1|2)([^\.]*)(\..+)', r'\1\3', $name) |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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36 #elif $re.match(r'.+_\d\.', $name): |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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37 #return $re.sub(r'(.+)_(\d)(\..+)', r'\1', $name) |
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planemo upload for repository https://github.com/phac-nml/biohansel commit b0060acc515bac2a79f60bb3c9d1f3243a5769f3
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38 #else |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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39 #return $name |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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40 #end if |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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41 #end def |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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42 |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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43 #def get_paired_fastq_filename($data_input, $name=None, $is_forward=True) |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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44 ## Get paired FASTQ filename for a data param with appropriate file extension |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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45 ## with '_1' or '_2' appended if forward or reverse reads, respectively. |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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46 #set $name = $name if $name is not None else $data_input.name |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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47 #set $name = $base_sample_name($name) |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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48 #set $postfix = '1' if $is_forward else '2' |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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49 #set $ending = '_{}{}'.format($postfix, $get_fastq_ext($data_input)) |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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50 #return '"{}"'.format($name) if $ending in $name else '"{}{}"'.format($name, $ending) |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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51 #end def |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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52 |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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53 ## Create symlinks from Galaxy *.dat to <sample_name>(.fasta|.fastq|.fastq.gz) |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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54 #if $input.type == 'fasta' |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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55 #set $input_files = '"{}"'.format($input.fasta.name) |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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56 ln -s "$input.fasta" $input_files && |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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57 #elif $input.type == 'paired' |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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58 #set $forward_filename = $get_paired_fastq_filename($input.forward) |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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59 #set $reverse_filename = $get_paired_fastq_filename($input.reverse, is_forward=False) |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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60 #set $input_files = '{} {}'.format($forward_filename, $reverse_filename) |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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61 ln -s "$input.forward" $forward_filename && |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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62 ln -s "$input.reverse" $reverse_filename && |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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63 #elif $input.type == 'single' |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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64 #set $input_files = '"{}"'.format($input.single.name) |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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65 ln -s "$input.single" $input_files && |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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66 #elif $input.type == 'paired_collection' |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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67 #set $forward_filename = $get_paired_fastq_filename($input.paired_collection.forward) |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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68 #set $reverse_filename = $get_paired_fastq_filename($input.paired_collection.reverse, is_forward=False) |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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69 #set $input_files = '{} {}'.format($forward_filename, $reverse_filename) |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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70 ln -s "$input.paired_collection.forward" $forward_filename && |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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71 ln -s "$input.paired_collection.reverse" $reverse_filename && |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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72 #end if |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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73 |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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74 ## Checking for custom scheme. |
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planemo upload for repository https://github.com/phac-nml/biohansel commit e3553c3c89db60cd285a401bc1c06fdd32665dd2
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75 #if $type_of_scheme.scheme_check == "custom": |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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76 #if $type_of_scheme.scheme_input.is_of_type('fasta'): |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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77 ln -s '$type_of_scheme.scheme_input' '$type_of_scheme.scheme_input.name' && |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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78 #end if |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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79 #end if |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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80 |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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81 #def get_subtype_metadata_filename($data_input) |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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82 ## Ensure that the subtype metadata table file has the proper extension - .tab or .csv |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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83 #set $filename = $data_input.name |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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84 #if $data_input.is_of_type('tabular') |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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|
85 #return '{}.tab'.format($filename) |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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|
86 #elif $data_input.is_of_type('csv') |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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87 #return '{}.csv'.format($filename) |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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88 #else |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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89 #return None |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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90 #end if |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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91 #end def |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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92 |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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93 ## Symlink to subtype metadata table if it is specified |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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94 #if $subtype_metadata |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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95 #set global $subtype_metadata_filename = $get_subtype_metadata_filename($subtype_metadata) |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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96 #if $subtype_metadata_filename |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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97 ln -s '$subtype_metadata' '$subtype_metadata_filename' && |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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98 #end if |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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99 #else |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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100 #set global $subtype_metadata_filename = None |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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101 #end if |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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102 |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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103 ################################# |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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104 ## biohansel command starts here: |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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105 ################################# |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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106 hansel |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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107 -vvv |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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108 -t "\${GALAXY_SLOTS:-1}" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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109 -o results.tab |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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110 -O match_results.tab |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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111 -S tech_results.tab |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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112 $dev_args.use_json |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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113 $input_files |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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114 --scheme |
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115 #if $type_of_scheme.scheme_check == "custom": |
0
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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116 '$type_of_scheme.scheme_input.name' |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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117 #else: |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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118 $type_of_scheme.scheme_type |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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119 #end if |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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120 #if $subtype_metadata_filename |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 369308400b3da271319e5ca89245bde68ece87de
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121 --scheme-metadata '$subtype_metadata_filename' |
0
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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122 #end if |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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123 #if $kmer_vals.kmer_min |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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124 --min-kmer-freq $kmer_vals.kmer_min |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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125 #end if |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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126 #if $kmer_vals.kmer_max |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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127 --max-kmer-freq $kmer_vals.kmer_max |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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128 #end if |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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129 #if $qc_vals.low_cov_depth_freq |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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130 --low-cov-depth-freq $qc_vals.low_cov_depth_freq |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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131 #end if |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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132 #if $qc_vals.max_missing_tiles |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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133 --max-missing-tiles $qc_vals.max_missing_tiles |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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134 #end if |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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135 #if $qc_vals.min_ambiguous_tiles |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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136 --min-ambiguous-tiles $qc_vals.min_ambiguous_tiles |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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137 #end if |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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138 #if $qc_vals.max_intermediate_tiles |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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139 --max-intermediate-tiles $qc_vals.max_intermediate_tiles |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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140 #end if |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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141 #if $qc_vals.low_coverage_warning |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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142 --low-cov-warning $qc_vals.low_coverage_warning |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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143 #end if |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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144 ]]> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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145 </command> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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146 <inputs> |
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147 <conditional name="input"> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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148 <param name="type" type="select" label="Sequence Data Type"> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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149 <option value="fasta">Contigs (FASTA)</option> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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150 <option value="paired">Paired-end reads (FASTQ)</option> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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151 <option value="single">Single-end reads (FASTQ)</option> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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152 <option value="paired_collection">Paired-end reads collection (FASTQ)</option> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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153 </param> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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154 <when value="fasta"> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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155 <param name="fasta" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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156 type="data" format="fasta" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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157 optional="false" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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158 label="Contigs (FASTA)" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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|
159 /> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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160 </when> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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161 <when value="paired"> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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162 <param name="forward" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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163 type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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164 optional="false" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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165 label="Forward reads (FASTQ)" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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166 help="Must have ASCII encoded quality scores" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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|
167 /> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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168 <param name="reverse" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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169 type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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170 optional="false" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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171 label="Reverse reads (FASTQ)" |
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172 help="File format must match the Forward FASTQ file" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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173 /> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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174 </when> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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175 <when value="single"> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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176 <param name="single" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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177 type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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178 optional="false" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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179 label="Single-end reads (FASTQ)" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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180 /> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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181 </when> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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182 <when value="paired_collection"> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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183 <param name="paired_collection" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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184 type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,txt" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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185 collection_type="paired" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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186 optional="false" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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187 label="Paired-end reads collection (FASTQ)" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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188 /> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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189 </when> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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190 </conditional> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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191 <conditional name="type_of_scheme"> |
7
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planemo upload for repository https://github.com/phac-nml/biohansel commit e3553c3c89db60cd285a401bc1c06fdd32665dd2
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192 <param name="scheme_check" type="select" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit e3553c3c89db60cd285a401bc1c06fdd32665dd2
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193 label="Subtyping Schemes" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit e3553c3c89db60cd285a401bc1c06fdd32665dd2
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194 help="Use included scheme or custom"> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit e3553c3c89db60cd285a401bc1c06fdd32665dd2
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195 <option value="standard">Included Biohansel Schemes</option> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit e3553c3c89db60cd285a401bc1c06fdd32665dd2
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196 <option value="custom">Select User Custom Scheme</option> |
0
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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197 </param> |
7
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planemo upload for repository https://github.com/phac-nml/biohansel commit e3553c3c89db60cd285a401bc1c06fdd32665dd2
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198 <when value="standard"> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit e3553c3c89db60cd285a401bc1c06fdd32665dd2
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199 <param name="scheme_type" type="select" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit e3553c3c89db60cd285a401bc1c06fdd32665dd2
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200 label="Included SNP Subtyping Scheme"> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit e3553c3c89db60cd285a401bc1c06fdd32665dd2
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201 <option value="heidelberg">Salmonella Heidelberg subtyping scheme</option> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit e3553c3c89db60cd285a401bc1c06fdd32665dd2
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202 <option value="enteritidis">Salmonella Enteritidis subtyping scheme</option> |
3360158bb0c5
planemo upload for repository https://github.com/phac-nml/biohansel commit e3553c3c89db60cd285a401bc1c06fdd32665dd2
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203 </param> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit e3553c3c89db60cd285a401bc1c06fdd32665dd2
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204 </when> |
0
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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205 <when value="custom"> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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206 <param name="scheme_input" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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207 type="data" format="fasta" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit e3553c3c89db60cd285a401bc1c06fdd32665dd2
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208 label="Your Custom Biohansel SNP Subtyping Scheme"/> |
0
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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209 </when> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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210 </conditional> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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211 <param name="subtype_metadata" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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212 type="data" format="tabular,csv" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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213 optional="true" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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214 label="Scheme Subtype Metadata Table [Optional]" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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215 help="CSV or tab-delimited format only. Must contain a 'subtype' column." |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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216 /> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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217 <!-- K-mer frequencies. --> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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218 <section name="kmer_vals" title="K-mer Frequency Thresholds" expanded="False"> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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219 <param name="kmer_min" type="integer" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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220 argument="--min-kmer-freq" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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221 optional="true" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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222 min="0" value="8" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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223 label="Min k-mer frequency/coverage" |
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224 help="default = 8"/> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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225 <param name="kmer_max" type="integer" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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226 argument="--max-kmer-freq" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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227 optional="true" |
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228 min="1" value="1000" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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229 label="Max k-mer frequency/coverage" |
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230 help="default = 1000"/> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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231 </section> |
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232 <!-- Quality Checking Parameters --> |
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233 <section name="qc_vals" title="Quality Checking Thresholds" expanded="False"> |
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234 <param name="low_cov_depth_freq" type="integer" |
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235 argument="--low-cov-depth-freq" |
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236 value="20" min="0" |
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237 optional="true" |
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238 label="QC: Frequency below this coverage are considered low coverage" |
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239 help="default = 20"/> |
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240 <param name="min_ambiguous_tiles" type="integer" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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241 argument="--min-ambiguous-tiles" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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242 optional="true" |
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243 value="3" min="0" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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244 label="QC: Min number of tiles missing for Ambiguous Result" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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245 help="default = 3"/> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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246 <param name="max_missing_tiles" type="float" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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247 argument="--max-missing-tiles" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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248 optional="true" |
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249 value="0.05" min="0" max="1" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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250 label="QC: Decimal Proportion of max allowed missing tiles" help="default = 0.05, valid values {0.0 - 1.0}"/> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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251 <param name="max_intermediate_tiles" type="float" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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252 argument="--max-intermediate-tiles" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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253 optional="true" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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254 value="0.05" min="0" max="1" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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255 label="QC: Decimal Proportion of max allowed missing tiles for an intermediate subtype" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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256 help="default = 0.05, valid values {0.0 - 1.0}"/> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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257 <param name="low_coverage_warning" type="integer" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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258 argument="--low-cov-warning" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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259 optional="true" |
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260 value="20" |
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261 label="QC: Overall tile coverage below this value will trigger a low coverage warning" |
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262 help="default = 20"/> |
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263 </section> |
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264 <section name="dev_args" title="Developer Options" expanded="False"> |
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265 <param name="use_json" |
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266 type="boolean" |
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267 checked="false" |
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268 truevalue="--json" |
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269 falsevalue="" |
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270 label="Output JSON results" |
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271 help="Use this option of you need json representations of analysis' details"/> |
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272 </section> |
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273 </inputs> |
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274 <outputs> |
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275 <data format="tabular" name="results.tab" from_work_dir="results.tab" label="results.tab"/> |
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276 <data format="tabular" name="match_results.tab" from_work_dir="match_results.tab" label="match_results.tab"/> |
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277 <data format="tabular" name="tech_results.tab" from_work_dir="tech_results.tab" label="tech_results.tab"/> |
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278 <data format="json" name="results.json" from_work_dir="results.tab.json" label="results.json"> |
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279 <filter>dev_args['use_json']</filter> |
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280 </data> |
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281 <data format="json" name="match_results.json" from_work_dir="match_results.tab.json" label="match_results.json"> |
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282 <filter>dev_args['use_json']</filter> |
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283 </data> |
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284 <data format="json" name="tech_results.json" from_work_dir="tech_results.tab.json" label="tech_results.json"> |
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285 <filter>dev_args['use_json']</filter> |
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286 </data> |
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287 </outputs> |
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288 <tests> |
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289 <test> |
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290 <conditional name="input"> |
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291 <param name="type" value="fasta"/> |
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292 <param name="fasta" value="SRR1002850_SMALL.fasta"/> |
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293 </conditional> |
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294 <param name="type_of_scheme" value="heidelberg"/> |
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295 <output name="results.tab" |
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296 value="SRR1002850_SMALL.fasta-results.tab" |
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297 ftype="tabular" |
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298 compare="sim_size" |
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299 delta="1000"> |
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300 </output> |
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301 <output name="match_results.tab" |
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302 value="SRR1002850_SMALL.fasta-match_results.tab" |
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303 ftype="tabular" |
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304 compare="sim_size" |
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305 delta="16000"> |
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306 </output> |
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307 <output name="tech_results.tab" |
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308 value="SRR1002850_SMALL.fasta-tech_results.tab" |
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309 ftype="tabular" |
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310 lines_diff="0"> |
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311 </output> |
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312 </test> |
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313 <test> |
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314 <conditional name="input"> |
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315 <param name="type" value="paired"/> |
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316 <param name="forward" value="SRR5646583_SMALL_1.fastq"/> |
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317 <param name="reverse" value="SRR5646583_SMALL_2.fastq"/> |
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318 </conditional> |
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319 <param name="type_of_scheme" value="heidelberg"/> |
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320 <output name="tech_results.tab" |
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321 value="SRR5646583_SMALL-tech_results.tab" |
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322 ftype="tabular" |
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323 lines_diff="0"> |
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324 </output> |
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325 <output name="results.tab" |
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326 value="SRR5646583_SMALL-results.tab" |
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327 ftype="tabular" |
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328 compare="sim_size" |
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329 delta="1000"> |
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330 </output> |
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331 <output name="match_results.tab" |
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332 value="SRR5646583_SMALL-match_results.tab" |
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333 ftype="tabular" |
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334 compare="sim_size" |
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335 delta="16000"> |
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336 </output> |
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337 </test> |
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338 </tests> |
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339 <help><![CDATA[ |
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340 Subtype microbial whole-genome sequencing (WGS) data using single-nucleotide polymorphism (SNP) targeting k-mer subtyping schemes. |
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341 |
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342 **Usage** |
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343 |
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344 1) Select the sequence data you wish to subtype (FASTAs or FASTQs) |
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345 2) Select subtyping scheme (e.g. *Salmonella enterica* serovar Heidelberg subtyping scheme, *Salmonella enterica* serovar Enteritidis subtyping scheme, or your own custom `biohansel` compatible subtyping scheme) |
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346 3) [Optional] Select your subtype metadata information table to include subtype metadata along with your subtype results |
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347 4) Click ``Execute`` |
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348 |
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349 For more information, visit `the biohansel project page <https://github.com/phac-nml/biohansel>`_. |
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350 |
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351 |
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352 **Example analysis results of a single FASTA file** |
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353 |
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354 Contents of ``results.tab``: |
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355 |
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356 +------------------+------------+----------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+------------------------+-----------+------------+ |
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357 | sample | scheme | scheme_version | subtype | all_subtypes | tiles_matching_subtype | are_subtypes_consistent | inconsistent_subtypes | n_tiles_matching_all | n_tiles_matching_all_expected | n_tiles_matching_positive | n_tiles_matching_positive_expected | n_tiles_matching_subtype | n_tiles_matching_subtype_expected | file_path | qc_status | qc_message | |
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358 +------------------+------------+----------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+------------------------+-----------+------------+ |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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359 | SRR1002850_SMALL | heidelberg | 0.5.0 | 2.2.2.2.1.4 | 2; 2.2; 2.2.2; 2.2.2.2; 2.2.2.2.1; 2.2.2.2.1.4 | 2154958-2.2.2.2.1.4; 1037658-2.2.2.2.1.4; 3785187-2.2.2.2.1.4 | True | | 202 | 202 | 17 | 17 | 3 | 3 | SRR1002850_SMALL.fasta | PASS | | |
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360 +------------------+------------+----------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+------------------------+-----------+------------+ |
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361 |
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362 |
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363 Contents of ``match_results.tab``: |
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364 |
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365 +---------------------------+-----------------------------------+------------+---------------------------------------+-------------+-------------+-------------+-------------+------------------+------------------------+------------+----------------+-----------+------------+ |
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366 | tilename | seq | is_revcomp | contig_id | match_index | refposition | subtype | is_pos_tile | sample | file_path | scheme | scheme_version | qc_status | qc_message | |
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367 +---------------------------+-----------------------------------+------------+---------------------------------------+-------------+-------------+-------------+-------------+------------------+------------------------+------------+----------------+-----------+------------+ |
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368 | 2154958-2.2.2.2.1.4 | GGCGCGCCACGGTTACTCCCCGGTGGTCAGCCG | True | NODE_1_length_726282_cov_40.4705_ID_1 | 13732 | 2154958 | 2.2.2.2.1.4 | True | SRR1002850_SMALL | SRR1002850_SMALL.fasta | heidelberg | 0.5.0 | PASS | | |
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369 +---------------------------+-----------------------------------+------------+---------------------------------------+-------------+-------------+-------------+-------------+------------------+------------------------+------------+----------------+-----------+------------+ |
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370 | negative2131791-2.2.3.1.3 | GCTGGGCGAAATGATGCAGTTCACCACTTGCTC | True | NODE_1_length_726282_cov_40.4705_ID_1 | 36900 | 2131791 | 2.2.3.1.3 | False | SRR1002850_SMALL | SRR1002850_SMALL.fasta | heidelberg | 0.5.0 | PASS | | |
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371 +---------------------------+-----------------------------------+------------+---------------------------------------+-------------+-------------+-------------+-------------+------------------+------------------------+------------+----------------+-----------+------------+ |
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372 |
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373 *Next 201 lines omitted.* |
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374 |
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375 |
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376 |
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377 **Example analysis results of a single FASTQ readset** |
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378 |
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379 |
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380 Contents of ``results.tab``: |
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381 |
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382 +------------------+------------+----------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+----------------------------------------------------------+-------------------+-----------+------------+ |
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383 | sample | scheme | scheme_version | subtype | all_subtypes | tiles_matching_subtype | are_subtypes_consistent | inconsistent_subtypes | n_tiles_matching_all | n_tiles_matching_all_expected | n_tiles_matching_positive | n_tiles_matching_positive_expected | n_tiles_matching_subtype | n_tiles_matching_subtype_expected | file_path | avg_tile_coverage | qc_status | qc_message | |
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384 +------------------+------------+----------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+----------------------------------------------------------+-------------------+-----------+------------+ |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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385 | SRR5646583_SMALL | heidelberg | 0.5.0 | 2.2.1.1.1.1 | 2; 2.2; 2.2.1; 2.2.1.1; 2.2.1.1.1; 2.2.1.1.1.1 | 1983064-2.2.1.1.1.1; 4211912-2.2.1.1.1.1 | True | | 202 | 202 | 20 | 20 | 2 | 2 | ['SRR5646583_SMALL_1.fastq', 'SRR5646583_SMALL_2.fastq'] | 42.631 | PASS | | |
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386 +------------------+------------+----------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+----------------------------------------------------------+-------------------+-----------+------------+ |
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387 |
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388 Contents of ``match_results.tab``: |
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389 |
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390 +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+ |
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391 | tilename | seq | freq | refposition | subtype | is_pos_tile | is_kmer_freq_okay | sample | scheme | scheme_version | qc_status | qc_message | |
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392 +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+ |
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393 | negative4642573-1.2 | TACCAGGAAGTGCTGGAAGAGTTTAACGAACAT | 62 | 4642573 | 1.2 | False | True | SRR5646583_SMALL | heidelberg | 0.5.0 | PASS | | |
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394 +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+ |
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395 | 21097-2.2.1.1.1 | GCAAATCGCGCCAGTCAAGTCCTCTTTTACCGT | 42 | 21097 | 2.2.1.1.1 | True | True | SRR5646583_SMALL | heidelberg | 0.5.0 | PASS | | |
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396 +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+ |
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397 |
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398 *Next 202 lines omitted.* |
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399 |
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400 |
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401 **Example Subtype Metadata** |
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402 |
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403 A column with name `subtype` must exist and should have subtype designations that would appear in your biohansel results. There are no requirements for the number of columns or contents of those columns in the table - they can contain whatever you want. |
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404 |
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405 |
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406 +-------------+-------+--------+------------------+ |
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407 | subtype | clade | source | disease_symptoms | |
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408 +-------------+-------+--------+------------------+ |
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409 | 1 | I | geese | death | |
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410 +-------------+-------+--------+------------------+ |
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411 | 1.1 | I | moose | burns | |
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412 +-------------+-------+--------+------------------+ |
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413 | 2.2.1.1.1 | II | mouse | boils | |
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414 +-------------+-------+--------+------------------+ |
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415 | 2.2.2.2.1.4 | IIa | house | rash | |
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416 +-------------+-------+--------+------------------+ |
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417 |
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418 The `biohansel` results table will be joined with the subtype metadata table on the `subtype` field so if there are subtype metadata for your `biohansel` results, it will show up in the final output table. For example, if you have a sample that produces a result with subtype "1", there will also be columns "clade", "source" and "disease_symptoms" with "I", "geese" and "death", respectively. |
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419 |
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420 |
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421 Galaxy wrapper written by Matthew Gopez and Peter Kruczkiewicz at the Public Health Agency of Canada, National Microbiology Laboratory. |
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422 |
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423 ]]></help> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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424 <citations> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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425 <citation type="bibtex">@ARTICLE{a1, |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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426 title = {A robust genotyping scheme for Salmonella enterica serovar Heidelberg clones circulating in North America}, |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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427 author = {Geneviève Labbé, James Robertson, Peter Kruczkiewicz, Marisa Rankin, Matthew Gopez, Chad R. Laing, Philip Mabon, Kim Ziebell, Aleisha R. Reimer, Lorelee Tschetter, Gary Van Domselaar, Sadjia Bekal, Kimberley A. MacDonald, Linda Hoang, Linda Chui, Danielle Daignault, Durda Slavic, Frank Pollari, E. Jane Parmley, Elissa Giang, Lok Kan Lee, Jonathan Moffat, Joanne MacKinnon, Roger Johnson, John H.E. Nash}, |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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428 url = {https://github.com/phac-nml/bio_hansel} |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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429 } |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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430 }</citation> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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431 </citations> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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432 </tool> |