Mercurial > repos > nml > biohansel
annotate biohansel.xml @ 6:ba6a0af656a6 draft
planemo upload for repository https://github.com/phac-nml/biohansel commit 27adc5d715e9adc4b037586cccf1244cf031a7af
author | nml |
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date | Wed, 20 Mar 2019 13:44:02 -0400 |
parents | c0b8de7aa02e |
children | 3360158bb0c5 |
rev | line source |
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6
ba6a0af656a6
planemo upload for repository https://github.com/phac-nml/biohansel commit 27adc5d715e9adc4b037586cccf1244cf031a7af
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1 <tool id="biohansel" name="biohansel" version="2.1.5"> |
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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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c6e29bb1ab31
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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c6e29bb1ab31
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
nml
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32 #elif $fastq_dump_match |
ba6a0af656a6
planemo upload for repository https://github.com/phac-nml/biohansel commit 27adc5d715e9adc4b037586cccf1244cf031a7af
nml
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33 #return $fastq_dump_match.group(1) |
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c6e29bb1ab31
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) |
c6e29bb1ab31
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' |
c6e29bb1ab31
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)) |
c6e29bb1ab31
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 |
c6e29bb1ab31
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 |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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74 ## Checking for custom scheme. |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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75 #if $type_of_scheme.scheme_type == "custom": |
c6e29bb1ab31
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' '$type_of_scheme.scheme_input.name' && |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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78 #end if |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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79 #end if |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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80 |
c6e29bb1ab31
planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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81 #def get_subtype_metadata_filename($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) |
c6e29bb1ab31
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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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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115 #if $type_of_scheme.scheme_type == "custom": |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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116 '$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 $subtype_metadata_filename |
4
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planemo upload for repository https://github.com/phac-nml/biohansel commit 369308400b3da271319e5ca89245bde68ece87de
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121 --scheme-metadata '$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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parents:
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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"> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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192 <param name="scheme_type" type="select" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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193 label="SNP Subtyping Scheme" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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194 help="Select the SNP subtyping scheme you wish to subtype with"> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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195 <option value="heidelberg">Salmonella Heidelberg subtyping scheme</option> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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196 <option value="enteritidis">Salmonella Enteritidis subtyping scheme</option> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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197 <option value="custom">Specify your own custom scheme</option> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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198 </param> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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199 <when value="heidelberg"/> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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200 <when value="enteritidis"/> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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201 <when value="custom"> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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202 <param name="scheme_input" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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203 type="data" format="fasta" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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204 label="Your biohansel SNP Subtyping Scheme"/> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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205 </when> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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206 </conditional> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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207 <param name="subtype_metadata" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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208 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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209 optional="true" |
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210 label="Scheme Subtype Metadata Table [Optional]" |
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211 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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212 /> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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213 <!-- K-mer frequencies. --> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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214 <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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215 <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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216 argument="--min-kmer-freq" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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217 optional="true" |
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218 min="0" value="8" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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219 label="Min k-mer frequency/coverage" |
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220 help="default = 8"/> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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221 <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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222 argument="--max-kmer-freq" |
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223 optional="true" |
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224 min="1" value="1000" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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225 label="Max k-mer frequency/coverage" |
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226 help="default = 1000"/> |
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227 </section> |
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228 <!-- Quality Checking Parameters --> |
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229 <section name="qc_vals" title="Quality Checking Thresholds" expanded="False"> |
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230 <param name="low_cov_depth_freq" type="integer" |
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231 argument="--low-cov-depth-freq" |
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232 value="20" min="0" |
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233 optional="true" |
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234 label="QC: Frequency below this coverage are considered low coverage" |
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235 help="default = 20"/> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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236 <param name="min_ambiguous_tiles" type="integer" |
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237 argument="--min-ambiguous-tiles" |
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238 optional="true" |
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239 value="3" min="0" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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240 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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241 help="default = 3"/> |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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242 <param name="max_missing_tiles" type="float" |
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243 argument="--max-missing-tiles" |
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244 optional="true" |
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245 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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246 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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247 <param name="max_intermediate_tiles" type="float" |
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248 argument="--max-intermediate-tiles" |
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249 optional="true" |
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250 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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251 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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252 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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253 <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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254 argument="--low-cov-warning" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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255 optional="true" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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256 value="20" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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257 label="QC: Overall tile coverage below this value will trigger a low coverage warning" |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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258 help="default = 20"/> |
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259 </section> |
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260 <section name="dev_args" title="Developer Options" expanded="False"> |
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261 <param name="use_json" |
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262 type="boolean" |
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263 checked="false" |
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264 truevalue="--json" |
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265 falsevalue="" |
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266 label="Output JSON results" |
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267 help="Use this option of you need json representations of analysis' details"/> |
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268 </section> |
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269 </inputs> |
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270 <outputs> |
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271 <data format="tabular" name="results.tab" from_work_dir="results.tab" label="results.tab"/> |
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272 <data format="tabular" name="match_results.tab" from_work_dir="match_results.tab" label="match_results.tab"/> |
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273 <data format="tabular" name="tech_results.tab" from_work_dir="tech_results.tab" label="tech_results.tab"/> |
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274 <data format="json" name="results.json" from_work_dir="results.tab.json" label="results.json"> |
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275 <filter>dev_args['use_json']</filter> |
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276 </data> |
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277 <data format="json" name="match_results.json" from_work_dir="match_results.tab.json" label="match_results.json"> |
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278 <filter>dev_args['use_json']</filter> |
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279 </data> |
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280 <data format="json" name="tech_results.json" from_work_dir="tech_results.tab.json" label="tech_results.json"> |
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281 <filter>dev_args['use_json']</filter> |
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282 </data> |
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283 </outputs> |
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284 <tests> |
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285 <test> |
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286 <conditional name="input"> |
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287 <param name="type" value="fasta"/> |
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288 <param name="fasta" value="SRR1002850_SMALL.fasta"/> |
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289 </conditional> |
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290 <param name="type_of_scheme" value="heidelberg"/> |
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291 <output name="results.tab" |
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292 value="SRR1002850_SMALL.fasta-results.tab" |
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293 ftype="tabular" |
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294 compare="sim_size" |
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295 delta="1000"> |
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296 </output> |
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297 <output name="match_results.tab" |
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298 value="SRR1002850_SMALL.fasta-match_results.tab" |
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299 ftype="tabular" |
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300 compare="sim_size" |
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301 delta="16000"> |
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302 </output> |
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303 <output name="tech_results.tab" |
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304 value="SRR1002850_SMALL.fasta-tech_results.tab" |
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305 ftype="tabular" |
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306 lines_diff="0"> |
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307 </output> |
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308 </test> |
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309 <test> |
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310 <conditional name="input"> |
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311 <param name="type" value="paired"/> |
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312 <param name="forward" value="SRR5646583_SMALL_1.fastq"/> |
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313 <param name="reverse" value="SRR5646583_SMALL_2.fastq"/> |
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314 </conditional> |
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315 <param name="type_of_scheme" value="heidelberg"/> |
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316 <output name="tech_results.tab" |
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317 value="SRR5646583_SMALL-tech_results.tab" |
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318 ftype="tabular" |
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319 lines_diff="0"> |
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320 </output> |
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321 <output name="results.tab" |
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322 value="SRR5646583_SMALL-results.tab" |
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323 ftype="tabular" |
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324 compare="sim_size" |
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325 delta="1000"> |
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326 </output> |
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327 <output name="match_results.tab" |
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328 value="SRR5646583_SMALL-match_results.tab" |
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329 ftype="tabular" |
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330 compare="sim_size" |
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331 delta="16000"> |
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332 </output> |
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333 </test> |
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334 </tests> |
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335 <help><![CDATA[ |
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336 Subtype microbial whole-genome sequencing (WGS) data using single-nucleotide polymorphism (SNP) targeting k-mer subtyping schemes. |
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337 |
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338 **Usage** |
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339 |
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340 1) Select the sequence data you wish to subtype (FASTAs or FASTQs) |
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341 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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342 3) [Optional] Select your subtype metadata information table to include subtype metadata along with your subtype results |
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343 4) Click ``Execute`` |
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344 |
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345 For more information, visit `the biohansel project page <https://github.com/phac-nml/biohansel>`_. |
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346 |
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347 |
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348 **Example analysis results of a single FASTA file** |
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349 |
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350 Contents of ``results.tab``: |
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351 |
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352 +------------------+------------+----------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+------------------------+-----------+------------+ |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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353 | 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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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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354 +------------------+------------+----------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+------------------------+-----------+------------+ |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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355 | 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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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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356 +------------------+------------+----------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+------------------------+-----------+------------+ |
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357 |
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358 |
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359 Contents of ``match_results.tab``: |
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360 |
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361 +---------------------------+-----------------------------------+------------+---------------------------------------+-------------+-------------+-------------+-------------+------------------+------------------------+------------+----------------+-----------+------------+ |
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362 | 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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363 +---------------------------+-----------------------------------+------------+---------------------------------------+-------------+-------------+-------------+-------------+------------------+------------------------+------------+----------------+-----------+------------+ |
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364 | 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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365 +---------------------------+-----------------------------------+------------+---------------------------------------+-------------+-------------+-------------+-------------+------------------+------------------------+------------+----------------+-----------+------------+ |
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366 | 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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367 +---------------------------+-----------------------------------+------------+---------------------------------------+-------------+-------------+-------------+-------------+------------------+------------------------+------------+----------------+-----------+------------+ |
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368 |
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369 *Next 201 lines omitted.* |
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370 |
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371 |
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372 |
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373 **Example analysis results of a single FASTQ readset** |
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374 |
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375 |
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376 Contents of ``results.tab``: |
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377 |
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378 +------------------+------------+----------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+----------------------------------------------------------+-------------------+-----------+------------+ |
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379 | 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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380 +------------------+------------+----------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+----------------------------------------------------------+-------------------+-----------+------------+ |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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381 | 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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382 +------------------+------------+----------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+-------------------------------+---------------------------+------------------------------------+--------------------------+-----------------------------------+----------------------------------------------------------+-------------------+-----------+------------+ |
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383 |
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384 Contents of ``match_results.tab``: |
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385 |
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386 +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+ |
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387 | tilename | seq | freq | refposition | subtype | is_pos_tile | is_kmer_freq_okay | sample | scheme | scheme_version | qc_status | qc_message | |
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388 +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+ |
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389 | negative4642573-1.2 | TACCAGGAAGTGCTGGAAGAGTTTAACGAACAT | 62 | 4642573 | 1.2 | False | True | SRR5646583_SMALL | heidelberg | 0.5.0 | PASS | | |
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390 +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+ |
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391 | 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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392 +---------------------+-----------------------------------+------+-------------+-----------+-------------+-------------------+------------------+------------+----------------+-----------+------------+ |
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393 |
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394 *Next 202 lines omitted.* |
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395 |
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396 |
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397 **Example Subtype Metadata** |
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398 |
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399 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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400 |
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401 |
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402 +-------------+-------+--------+------------------+ |
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planemo upload for repository https://github.com/phac-nml/biohansel commit 854e6b30be03b1402efd45d0a7925cce15c3af0c
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403 | subtype | clade | source | disease_symptoms | |
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404 +-------------+-------+--------+------------------+ |
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405 | 1 | I | geese | death | |
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406 +-------------+-------+--------+------------------+ |
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407 | 1.1 | I | moose | burns | |
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408 +-------------+-------+--------+------------------+ |
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409 | 2.2.1.1.1 | II | mouse | boils | |
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410 +-------------+-------+--------+------------------+ |
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411 | 2.2.2.2.1.4 | IIa | house | rash | |
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412 +-------------+-------+--------+------------------+ |
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413 |
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414 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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415 |
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416 |
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417 Galaxy wrapper written by Matthew Gopez and Peter Kruczkiewicz at the Public Health Agency of Canada, National Microbiology Laboratory. |
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418 |
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419 ]]></help> |
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420 <citations> |
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421 <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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422 title = {A robust genotyping scheme for Salmonella enterica serovar Heidelberg clones circulating in North America}, |
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423 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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424 url = {https://github.com/phac-nml/bio_hansel} |
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425 } |
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426 }</citation> |
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427 </citations> |
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428 </tool> |