Mercurial > repos > iuc > bio_hansel

annotate bio_hansel.xml @ 0:726cd66ca2f9 draft

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planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
author iuc
date Tue, 03 Oct 2017 10:38:47 -0400
parents
children ddae7615b431
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0
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
1 <tool id="bio_hansel" name="Salmonella Subtyping" version="0.1.0">
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
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2 <requirements>
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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3 <requirement type="package" version="0.1.0">bio_hansel</requirement>
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
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4 <requirement type="package" version="17.2.0">attrs</requirement>
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
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5 </requirements>
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
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6 <command detect_errors="exit_code"><![CDATA[
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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7 ## Preparing file input.
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
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8 #if $data_type.type == "paired":
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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9
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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10 ln -s '$data_type.fastq_input1' fast_q_paired_1.fastq &&
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
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11 ln -s '$data_type.fastq_input2' fast_q_paired_2.fastq &&
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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12
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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13 #elif $data_type.type == "collection":
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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15 ln -s '$data_type.fastq_input1.forward' fast_q_paired_1.fastq &&
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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16 ln -s '$data_type.fastq_input1.reverse' fast_q_paired_2.fastq &&
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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17
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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18 #elif $data_type.type == "single":
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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20 #if $data_type.fastq_input1.is_of_type('fastqsanger') or $data_type.fastq_input1.is_of_type('fastq'):
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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21 ln -s '$data_type.fastq_input1' fast_q_single.fastq &&
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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22 #end if
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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23
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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24 #if $data_type.fastq_input1.is_of_type('fasta'):
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
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25 ln -s '$data_type.fastq_input1' fast_a_single.fasta &&
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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26 #end if
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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27
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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28 #end if
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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29
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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30
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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31 ## Checking for custom scheme.
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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32 #if $type_of_scheme.scheme_type == "custom":
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
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33 #if $type_of_scheme.scheme_input.is_of_type('fasta'):
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
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34 ln -s '$type_of_scheme.scheme_input' custom_scheme.fasta &&
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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35 #end if
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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36 #end if
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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37
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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38 ## Start the actual command here
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
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39 hansel
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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40
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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41
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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42 ## Select the scheme
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
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43 -s
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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44
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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45 #if $type_of_scheme.scheme_type == "heidelberg":
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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46 heidelberg
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
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47 #elif $type_of_scheme.scheme_type == "enteritidis":
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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48 enteritidis
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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49 #elif $type_of_scheme.scheme_type == "custom":
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
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50 custom_scheme.fasta
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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51 #end if
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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52
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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53
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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54 #if $kmer_min
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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55 --min-kmer-freq $kmer_min
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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56 #end if
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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57
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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58 #if $kmer_max
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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59 --max-kmer-freq $kmer_max
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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60 #end if
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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61
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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62 ## Adding more parameters to the command.
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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63 -vvv -t "\${GALAXY_SLOTS:-1}" -o results.tab -O match_results.tab
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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64
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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65
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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66 ## Entering the file inputs.
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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67 #if $data_type.type == "single":
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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68
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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69 #if $data_type.fastq_input1.is_of_type('fastqsanger') or $data_type.fastq_input1.is_of_type('fastq'):
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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70 fast_q_single.fastq
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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71 #end if
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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72
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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73 #if $data_type.fastq_input1.is_of_type('fasta'):
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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74 fast_a_single.fasta
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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75 #end if
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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76
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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77 #else
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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78
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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79 ##use -p to declare using two files.
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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80 -p fast_q_paired_1.fastq fast_q_paired_2.fastq
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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81
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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82 #end if
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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83 ]]></command>
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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84 <inputs>
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
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85 <conditional name="data_type">
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
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86 <param name="type" type="select" label="Specify the read type.">
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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87 <option value="single">Single-end Data</option>
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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88 <option value="paired">Paired-end Data</option>
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
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89 <option value="collection">Collection Paired-end Data</option>
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
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90 </param>
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
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91 <when value="single">
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
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92 <param name="fastq_input1" type="data" format="fastqsanger, fastq, fasta" label="Single end read file(s)"/>
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
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93 </when>
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
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94 <when value="paired">
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
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95 <param name="fastq_input1" type="data" format="fastqsanger, fastq" label="Forward paired-end read file"/>
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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96 <param name="fastq_input2" type="data" format="fastqsanger, fastq" label="Reverse paired-end read file"/>
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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97 </when>
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
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98 <when value="collection">
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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99 <param name="fastq_input1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger, fastq" collection_type="paired" />
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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100 </when>
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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101 </conditional>
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
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102 <conditional name="type_of_scheme">
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103 <param name="scheme_type" type="select" label="Specify scheme to use. (Heidelberg is default)">
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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104 <option value="heidelberg">Heidelberg scheme</option>
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105 <option value="enteritidis">Enteritidis scheme</option>
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106 <option value="custom">Specify your own custom scheme</option>
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107 </param>
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108 <when value="heidelberg"/>
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109 <when value="enteritidis"/>
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110 <when value="custom">
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111 <param name="scheme_input" type="data" format="fasta" label="Scheme Input"/>
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112 </when>
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113 </conditional>
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114 <param name="kmer_min" argument="--min-kmer-freq" optional="True" type="integer" min="0" label="Min k-mer freq/coverage" help="default = 10"/>
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115 <param name="kmer_max" argument="--max-kmer-freq" optional="True" type="integer" min="1" label="Max k-mer freq/coverage" help="default = 200"/>
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116 </inputs>
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117 <outputs>
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118 <data format="tabular" name="results.tab" from_work_dir="results.tab" label="results.tab"/>
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119 <data format="tabular" name="match_results.tab" from_work_dir="match_results.tab" label="match_results.tab"/>
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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120 </outputs>
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121 <tests>
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122 <test>
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123 <param name="type" value="single"/>
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124 <param name="type_of_scheme" value="heidelberg"/>
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125 <param name="fastq_input1" value="SRR1002850_SMALL.fasta"/>
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126 <output name="results.tab">
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127 <assert_contents>
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128 <!-- Verifying that the columns are as expected. -->
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129 <has_text_matching expression="sample\s+scheme\s+subtype\s+all_subtypes\s+tiles_matching_subtype\s+are_subtypes_consistent\s+inconsistent_subtypes\s+n_tiles_matching_all\s+n_tiles_matching_all_total\s+n_tiles_matching_positive\s+n_tiles_matching_positive_total\s+n_tiles_matching_subtype\s+n_tiles_matching_subtype_total\s+file_path"/>
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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130 <!-- Verifying that the output of running the test file is expected. This is done via REGEX because the name and path of the file outputted to results.tab changes each test. -->
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131 <has_text_matching expression="(heidelberg)\s+(2.2.2.2.1.4)\s+(2;)\s+(2.2;)\s+(2.2.2;)\s+(2.2.2.2;)\s+(2.2.2.2.1;)\s+(2.2.2.2.1.4)\s+(1037658-2.2.2.2.1.4;)\s+(2154958-2.2.2.2.1.4;)\s+(3785187-2.2.2.2.1.4)\s+(True)\s+(202)\s+(202)\s+(17)\s+(17)\s+(3)\s+(3)"/>
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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132 </assert_contents>
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133 </output>
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134 <output name="match_results.tab">
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135 <assert_contents>
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136 <!-- This is the last line in the file, this assertion is to make sure that we have the correct number of items. -->
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137 <has_text_matching expression="negative4738855-1.1"/>
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138 </assert_contents>
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139 </output>
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140 </test>
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141 <test>
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142 <param name="type" value="paired"/>
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143 <param name="type_of_scheme" value="heidelberg"/>
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144 <param name="fastq_input1" value="SRR5646583_SMALL_1.fastq"/>
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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145 <param name="fastq_input2" value="SRR5646583_SMALL_2.fastq"/>
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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146 <output name="results.tab">
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147 <assert_contents>
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148 <!-- Verifying that the columns are as expected. -->
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149 <has_text_matching expression="sample\s+scheme\s+subtype\s+all_subtypes\s+tiles_matching_subtype\s+are_subtypes_consistent\s+inconsistent_subtypes\s+n_tiles_matching_all\s+n_tiles_matching_all_total\s+n_tiles_matching_positive\s+n_tiles_matching_positive_total\s+n_tiles_matching_subtype\s+n_tiles_matching_subtype_total\s+file_path"/>
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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150 <!-- Verifying that the output of running the test file is expected. This is done via REGEX because the name and path of the file outputted to results.tab changes each test. -->
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151 <has_text_matching expression="(heidelberg)\s+(2.2.1.1.1.1)\s+(2;)\s+(2.2;)\s+(2.2.1;)\s+(2.2.1.1;)\s+(2.2.1.1.1;)\s+(2.2.1.1.1.1)\s+(1983064-2.2.1.1.1.1;)\s+(4211912-2.2.1.1.1.1)\s+(True)\s+(202)\s+(202)\s+(20)\s+(20)\s+(2)\s+(2)"/>
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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152 </assert_contents>
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153 </output>
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154 </test>
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155 </tests>
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156 <help><![CDATA[
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157 ***********************************************************
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158 bio_hansel - Heidelberg And eNteritidis Snp ELucidation
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159 ***********************************************************
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160
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161 Subtype *Salmonella enterica* subsp. enterica serovar Heidelberg and Enteritidis genomes using *in-silico* 33 bp k-mer SNP subtyping schemes developed by Genevieve Labbe et al.
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162 Subtype *Salmonella* genome assemblies (FASTA files) and/or whole-genome sequencing reads (FASTQ files)!
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163
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164
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165 Usage
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166 =====
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167 1) Enter your FASTA/FASTQ file(s)
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168 2) Select which scheme you would like to use (e.g. heidelberg, enteritidis, or specify your own)
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169 3) Click Execute
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170
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171 For more information visit `https://github.com/phac-nml/bio_hansel`
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172
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173
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174 Example Usage
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175 =============
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176
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177 Analysis of a single FASTA file
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178 -------------------------------
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179
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180 Contents of ``results.tab``:
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181
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182 +------------+------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+----------------------------+---------------------------+---------------------------------+--------------------------+--------------------------------+------------+
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183 | sample | scheme | subtype | all_subtypes | tiles_matching_subtype | are_subtypes_consistent | inconsistent_subtypes | n_tiles_matching_all | n_tiles_matching_all_total | n_tiles_matching_positive | n_tiles_matching_positive_total | n_tiles_matching_subtype | n_tiles_matching_subtype_total | file_path |
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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184 +------------+------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+----------------------------+---------------------------+---------------------------------+--------------------------+--------------------------------+------------+
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185 | file.fasta | heidelberg | 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 | 1037658-2.2.2.2.1.4; 2154958-2.2.2.2.1.4; 3785187-2.2.2.2.1.4 | True | | 202 | 202 | 17 | 17 | 3 | 3 | file.fasta |
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186 +------------+------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+----------------------------+---------------------------+---------------------------------+--------------------------+--------------------------------+------------+
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187
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188
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189
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190 Contents of ``match_results.tab``:
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191
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192 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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193 | tilename | stitle | pident | length | mismatch | gapopen | qstart | qend | sstart | send | evalue | bitscore | qlen | slen | seq | coverage | is_trunc | refposition | subtype | is_pos_tile | sample | file_path | scheme |
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
194 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
195 | 775920-2.2.2.2 | NODE_2_length_512016_cov_46.4737_ID_3 | 100 | 33 | 0 | 0 | 1 | 33 | 474875 | 474907 | 2E-11 | 62.1 | 33 | 512016 | GTTCAGGTGCTACCGAGGATCGTTTTTGGTGCG | 1 | False | 775920 | 2.2.2.2 | True | out | file.fasta | heidelberg |
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
196 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
197 | negative3305400-2.1.1.1 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 276235 | 276267 | 2E-11 | 62.1 | 33 | 427905 | CATCGTGAAGCAGAACAGACGCGCATTCTTGCT | 1 | False | negative3305400 | 2.1.1.1 | False | out | file.fasta | heidelberg |
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
198 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
199 | negative3200083-2.1 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 170918 | 170950 | 2E-11 | 62.1 | 33 | 427905 | ACCCGGTCTACCGCAAAATGGAAAGCGATATGC | 1 | False | negative3200083 | 2.1 | False | out | file.fasta | heidelberg |
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
200 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
201 | negative3204925-2.2.3.1.5 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 175760 | 175792 | 2E-11 | 62.1 | 33 | 427905 | CTCGCTGGCAAGCAGTGCGGGTACTATCGGCGG | 1 | False | negative3204925 | 2.2.3.1.5 | False | out | file.fasta | heidelberg |
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
202 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
203 | negative3230678-2.2.2.1.1.1 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 201513 | 201545 | 2E-11 | 62.1 | 33 | 427905 | AGCGGTGCGCCAAACCACCCGGAATGATGAGTG | 1 | False | negative3230678 | 2.2.2.1.1.1 | False | out | file.fasta | heidelberg |
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
204 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
205 | negative3233869-2.1.1.1.1 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 204704 | 204736 | 2E-11 | 62.1 | 33 | 427905 | CAGCGCTGGTATGTGGCTGCACCATCGTCATTA | 1 | False | negative3233869 | 2.1.1.1.1 | False | out | file.fasta | heidelberg |
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
206 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
207 | negative3254229-2.2.3.1.3 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 225064 | 225096 | 2E-11 | 62.1 | 33 | 427905 | CGCCACCACGCGGTTAGCGTCACGCTGACATTC | 1 | False | negative3254229 | 2.2.3.1.3 | False | out | file.fasta | heidelberg |
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
208 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
209 | negative3257074-2.2.1 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 227909 | 227941 | 2E-11 | 62.1 | 33 | 427905 | CGGCAACCAGACCGACTACGCCGCCAAGCAGAC | 1 | False | negative3257074 | 2.2.1 | False | out | file.fasta | heidelberg |
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
210 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
211 | negative3264474-2.2.2.1.1.1 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 235309 | 235341 | 2E-11 | 62.1 | 33 | 427905 | AATGGCGCCGATCGTCGCCAGATAACCGTTGCC | 1 | False | negative3264474 | 2.2.2.1.1.1 | False | out | file.fasta | heidelberg |
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
212 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
213 | negative3267927-2.2.2.2.2.1 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 238762 | 238794 | 2E-11 | 62.1 | 33 | 427905 | AAAGAGAAATATGATGCCAGGCTGATACATGAC | 1 | False | negative3267927 | 2.2.2.2.2.1 | False | out | file.fasta | heidelberg |
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
214 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
215 | negative3278067-1.1 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 248902 | 248934 | 2E-11 | 62.1 | 33 | 427905 | TGTGAGTAAGTTGCGCGATATTCTGCTGGATTC | 1 | False | negative3278067 | 1.1 | False | out | file.fasta | heidelberg |
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
216 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
217 | negative3299717-2.2.3.1.4 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 270552 | 270584 | 2E-11 | 62.1 | 33 | 427905 | ATGCCGGACAGCAGGCGAAACTCGAACCGGATA | 1 | False | negative3299717 | 2.2.3.1.4 | False | out | file.fasta | heidelberg |
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
218 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
219 | negative3373069-2.2.2.2.1.1 | NODE_3_length_427905_cov_48.1477_ID_5 | 100 | 33 | 0 | 0 | 1 | 33 | 344011 | 344043 | 2E-11 | 62.1 | 33 | 427905 | CTCTCCAGAAGATGAAGCCCGTGATGCGGCGCA | 1 | False | negative3373069 | 2.2.2.2.1.1 | False | out | file.fasta | heidelberg |
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
220 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
221
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
222 Next 196 lines omitted.
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223
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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224
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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225
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
226 Analysis of a single FASTQ readset
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
227 ----------------------------------
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
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228
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
229 Contents of ``results.tab``:
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
230
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
231 +--------+------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+----------------------------+---------------------------+---------------------------------+--------------------------+--------------------------------+------------------------------------------+
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
232 | sample | scheme | subtype | all_subtypes | tiles_matching_subtype | are_subtypes_consistent | inconsistent_subtypes | n_tiles_matching_all | n_tiles_matching_all_total | n_tiles_matching_positive | n_tiles_matching_positive_total | n_tiles_matching_subtype | n_tiles_matching_subtype_total | file_path |
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
233 +--------+------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+----------------------------+---------------------------+---------------------------------+--------------------------+--------------------------------+------------------------------------------+
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
234 | 564 | heidelberg | 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 | forward.fastqsanger; reverse.fastqsanger |
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
235 +--------+------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+----------------------------+---------------------------+---------------------------------+--------------------------+--------------------------------+------------------------------------------+
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
236
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
237
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
238 Contents of ``match_results.tab``:
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
239
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
240 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
241 | seq | freq | sample | file_path | tilename | is_pos_tile | subtype | refposition | is_kmer_freq_okay | scheme |
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
242 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
243 | ACGGTAAAAGAGGACTTGACTGGCGCGATTTGC | 68 | 564 | forward.fastqsanger; reverse.fastqsanger | 21097-2.2.1.1.1 | True | 2.2.1.1.1 | 21097 | True | heidelberg |
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
244 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
245 | AACCGGCGGTATTGGCTGCGGTAAAAGTACCGT | 77 | 564 | forward.fastqsanger; reverse.fastqsanger | 157792-2.2.1.1.1 | True | 2.2.1.1.1 | 157792 | True | heidelberg |
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
246 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
247 | CCGCTGCTTTCTGAAATCGCGCGTCGTTTCAAC | 67 | 564 | forward.fastqsanger; reverse.fastqsanger | 293728-2.2.1.1 | True | 2.2.1.1 | 293728 | True | heidelberg |
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
248 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
249 | GAATAACAGCAAAGTGATCATGATGCCGCTGGA | 91 | 564 | forward.fastqsanger; reverse.fastqsanger | 607438-2.2.1 | True | 2.2.1 | 607438 | True | heidelberg |
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
250 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
251 | CAGTTTTACATCCTGCGAAATGCGCAGCGTCAA | 87 | 564 | forward.fastqsanger; reverse.fastqsanger | 691203-2.2.1.1 | True | 2.2.1.1 | 691203 | True | heidelberg |
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
252 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
253 | CAGGAGAAAGGATGCCAGGGTCAACACGTAAAC | 33 | 564 | forward.fastqsanger; reverse.fastqsanger | 944885-2.2.1.1.1 | True | 2.2.1.1.1 | 944885 | True | heidelberg |
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
254 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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parents:
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255
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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diff changeset
256 Next 200 lines omitted.
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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257
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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parents:
diff changeset
258 ]]></help>
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
259 <citations>
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
diff changeset
260 <citation type="bibtex">@ARTICLE{a1,
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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parents:
diff changeset
261 title = {A robust genotyping scheme for *Salmonella enterica* serovar Heidelberg clones circulating in North America.},
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
iuc
parents:
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262 author = {Geneviève Labbé, James Robertson, Peter Kruczkiewicz, Chad R. Laing, 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, Philip Mabon, Elissa Giang, Lok Kan Lee, Jonathan Moffat, Marisa Rankin, Joanne MacKinnon, Roger Johnson, John H.E. Nash.},
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263 url = {https://github.com/phac-nml/bio_hansel}
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264 }
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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265 }</citation>
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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266 </citations>
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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267 </tool>