Mercurial > repos > iuc > bio_hansel

annotate bio_hansel.xml @ 2:8e46a280c0d5 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 32833cd064153c009ff667f9526515d1aa15d48c
author iuc
date Sat, 05 Oct 2024 11:05:56 +0000
parents ddae7615b431
children
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1
ddae7615b431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
iuc
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1 <tool id="bio_hansel" name="Salmonella Subtyping" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
ddae7615b431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
iuc
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2 <macros>
ddae7615b431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
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3 <import>macros.xml</import>
ddae7615b431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
iuc
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4 </macros>
2
8e46a280c0d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 32833cd064153c009ff667f9526515d1aa15d48c
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5 <xrefs>
8e46a280c0d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 32833cd064153c009ff667f9526515d1aa15d48c
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6 <xref type="bio.tools">Biohansel</xref>
8e46a280c0d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 32833cd064153c009ff667f9526515d1aa15d48c
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7 </xrefs>
1
ddae7615b431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
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8 <expand macro="requirements" />
0
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9 <command detect_errors="exit_code"><![CDATA[
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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10 #if $data_type.type == "paired":
1
ddae7615b431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
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11 #if $data_type.fastq_input1.ext.endswith('.gz'):
ddae7615b431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
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12 gunzip -c '$data_type.fastq_input1' > fast_q_paired_1.fastq &&
ddae7615b431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
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13 gunzip -c '$data_type.fastq_input2' > fast_q_paired_2.fastq &&
ddae7615b431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
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14 #else:
ddae7615b431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
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15 ln -s '$data_type.fastq_input1' fast_q_paired_1.fastq &&
ddae7615b431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
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16 ln -s '$data_type.fastq_input2' fast_q_paired_2.fastq &&
ddae7615b431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
iuc
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17 #end if
0
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18 #elif $data_type.type == "collection":
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ddae7615b431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
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19 #if $data_type.fastq_input1.forward.ext.endswith('.gz'):
ddae7615b431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
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20 gunzip -c '$data_type.fastq_input1.forward' > fast_q_paired_1.fastq &&
ddae7615b431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
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21 gunzip -c '$data_type.fastq_input2.reverse' > fast_q_paired_2.fastq &&
ddae7615b431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
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22 #else:
ddae7615b431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
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23 ln -s '$data_type.fastq_input1.forward' fast_q_paired_1.fastq &&
ddae7615b431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
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24 ln -s '$data_type.fastq_input1.reverse' fast_q_paired_2.fastq &&
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25 #end if
1
ddae7615b431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
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26 #elif $data_type.type == "single":
ddae7615b431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
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27 #if $data_type.fastq_input1.ext.startswith("fastq"):
ddae7615b431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
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28 #if $data_type.fastq_input1.ext.endswith('.gz'):
ddae7615b431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
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29 gunzip -c '$data_type.fastq_input1' > fast_q_single.fastq &&
ddae7615b431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
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30 #else:
ddae7615b431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
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31 ln -s '$data_type.fastq_input1' fast_q_single.fastq &&
ddae7615b431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
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32 #end if
ddae7615b431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
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33 #elif $data_type.fastq_input1.ext.startswith('fasta'):
ddae7615b431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
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34 #if $data_type.fastq_input1.ext.endswith('.gz'):
ddae7615b431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
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35 gunzip -c '$data_type.fastq_input1' > fast_a_single.fasta &&
ddae7615b431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
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36 #else:
ddae7615b431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
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37 ln -s '$data_type.fastq_input1' fast_a_single.fasta &&
ddae7615b431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
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38 #end if
0
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39 #end if
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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40 #end if
1
ddae7615b431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
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41 #if $type_of_scheme.scheme_type == "custom":
ddae7615b431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
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42 #if $type_of_scheme.scheme_input.ext.startswith('fasta'):
ddae7615b431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
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43 #if $type_of_scheme.scheme_input.ext.endswith('.gz'):
ddae7615b431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
iuc
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44 gunzip -c '$type_of_scheme.scheme_input' > custom_scheme.fasta &&
ddae7615b431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
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45 #else:
ddae7615b431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
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46 ln -s '$type_of_scheme.scheme_input' custom_scheme.fasta &&
ddae7615b431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
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47 #end if
ddae7615b431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
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48 #end if
ddae7615b431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
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49 #end if
0
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50 hansel
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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51 -s
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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52 #if $type_of_scheme.scheme_type == "heidelberg":
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53 heidelberg
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54 #elif $type_of_scheme.scheme_type == "enteritidis":
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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55 enteritidis
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56 #elif $type_of_scheme.scheme_type == "custom":
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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57 custom_scheme.fasta
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58 #end if
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59 #if $kmer_min
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60 --min-kmer-freq $kmer_min
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61 #end if
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62 #if $kmer_max
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63 --max-kmer-freq $kmer_max
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64 #end if
1
ddae7615b431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
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65 -vvv -t \${GALAXY_SLOTS:-1} -o 'results.tab' -O 'match_results.tab'
0
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66 #if $data_type.type == "single":
1
ddae7615b431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
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67 #if $data_type.fastq_input1.ext.startswith('fastq'):
0
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68 fast_q_single.fastq
1
ddae7615b431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
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69 #elif $data_type.fastq_input1.ext.startswith('fasta'):
0
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70 fast_a_single.fasta
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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 #else
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73 -p fast_q_paired_1.fastq fast_q_paired_2.fastq
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74 #end if
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75 ]]></command>
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76 <inputs>
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77 <conditional name="data_type">
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78 <param name="type" type="select" label="Specify the read type.">
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79 <option value="single">Single-end Data</option>
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80 <option value="paired">Paired-end Data</option>
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81 <option value="collection">Collection Paired-end Data</option>
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82 </param>
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83 <when value="single">
1
ddae7615b431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
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84 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz,fasta,fasta.gz" label="Single end read file(s)"/>
0
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85 </when>
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86 <when value="paired">
1
ddae7615b431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
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87 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" label="Forward paired-end read file"/>
ddae7615b431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
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88 <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" label="Reverse paired-end read file"/>
0
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89 </when>
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90 <when value="collection">
1
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91 <param name="fastq_input1" type="data_collection" label="Paired-end reads collection" optional="false" format="fastqsanger,fastqsanger.gz,fastq,fastq.gz" collection_type="paired" />
0
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92 </when>
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93 </conditional>
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94 <conditional name="type_of_scheme">
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95 <param name="scheme_type" type="select" label="Specify scheme to use. (Heidelberg is default)">
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96 <option value="heidelberg">Heidelberg scheme</option>
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97 <option value="enteritidis">Enteritidis scheme</option>
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98 <option value="custom">Specify your own custom scheme</option>
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99 </param>
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100 <when value="heidelberg"/>
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101 <when value="enteritidis"/>
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102 <when value="custom">
1
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103 <param name="scheme_input" type="data" format="fasta,fasta.gz" label="Scheme Input"/>
0
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104 </when>
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105 </conditional>
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106 <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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107 <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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108 </inputs>
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109 <outputs>
1
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110 <data format="tabular" name="results" from_work_dir="results.tab" label="${tool.name} on ${on_string}: results.tab"/>
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111 <data format="tabular" name="match_results" from_work_dir="match_results.tab" label="${tool.name} on ${on_string}: match_results.tab"/>
0
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112 </outputs>
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113 <tests>
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114 <test>
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115 <param name="type" value="single"/>
2
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116 <param name="type_of_scheme|scheme_type" value="heidelberg"/>
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117 <param name="fastq_input1" ftype="fasta.gz" value="SRR1002850_SMALL.fasta.gz"/>
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118 <output name="results" ftype="tabular" file="results1.tab" compare="contains"/>
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119 <output name="match_results" ftype="tabular" file="match_results1.tab" compare="contains"/>
0
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120 </test>
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121 <test>
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122 <param name="type" value="paired"/>
2
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123 <param name="type_of_scheme|scheme_type" value="heidelberg"/>
1
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124 <param name="fastq_input1" ftype="fastq.gz" value="SRR5646583_SMALL_1.fastq.gz"/>
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125 <param name="fastq_input2" value="SRR5646583_SMALL_2.fastq.gz"/>
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126 <output name="results" ftype="tabular" file="results2.tab" compare="contains"/>
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127 <output name="match_results" ftype="tabular" file="match_results2.tab" compare="contains"/>
0
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128 </test>
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129 </tests>
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130 <help><![CDATA[
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131 ***********************************************************
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132 bio_hansel - Heidelberg And eNteritidis Snp ELucidation
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133 ***********************************************************
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134
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135 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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136 Subtype *Salmonella* genome assemblies (FASTA files) and/or whole-genome sequencing reads (FASTQ files)!
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137
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138
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139 Usage
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140 =====
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141 1) Enter your FASTA/FASTQ file(s)
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142 2) Select which scheme you would like to use (e.g. heidelberg, enteritidis, or specify your own)
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143 3) Click Execute
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144
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145 For more information visit `https://github.com/phac-nml/bio_hansel`
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146
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147
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148 Example Usage
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149 =============
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150
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151 Analysis of a single FASTA file
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152 -------------------------------
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153
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154 Contents of ``results.tab``:
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155
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156 +------------+------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+----------------------------+---------------------------+---------------------------------+--------------------------+--------------------------------+------------+
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157 | 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 |
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158 +------------+------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+----------------------------+---------------------------+---------------------------------+--------------------------+--------------------------------+------------+
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159 | 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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160 +------------+------------+-------------+------------------------------------------------+---------------------------------------------------------------+-------------------------+-----------------------+----------------------+----------------------------+---------------------------+---------------------------------+--------------------------+--------------------------------+------------+
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161
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162
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163
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164 Contents of ``match_results.tab``:
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165
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166 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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167 | 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 |
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168 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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169 | 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 |
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170 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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171 | 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 |
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172 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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173 | 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 |
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174 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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175 | 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 |
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176 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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177 | 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
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178 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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179 | 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
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180 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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181 | 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
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182 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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183 | 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
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184 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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185 | 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
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186 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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187 | 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
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188 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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189 | 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
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190 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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191 | 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
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192 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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193 | 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
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194 +-----------------------------+---------------------------------------+--------+--------+----------+---------+--------+------+--------+--------+--------+----------+------+--------+-----------------------------------+----------+----------+-----------------+-------------+-------------+--------+------------+------------+
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195
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196 Next 196 lines omitted.
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197
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198
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199
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200 Analysis of a single FASTQ readset
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201 ----------------------------------
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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202
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203 Contents of ``results.tab``:
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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204
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205 +--------+------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+----------------------------+---------------------------+---------------------------------+--------------------------+--------------------------------+------------------------------------------+
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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206 | 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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207 +--------+------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+----------------------------+---------------------------+---------------------------------+--------------------------+--------------------------------+------------------------------------------+
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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208 | 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
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209 +--------+------------+-------------+------------------------------------------------+------------------------------------------+-------------------------+-----------------------+----------------------+----------------------------+---------------------------+---------------------------------+--------------------------+--------------------------------+------------------------------------------+
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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210
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211
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212 Contents of ``match_results.tab``:
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213
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214 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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215 | 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
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216 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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217 | 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
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218 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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219 | 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
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220 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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221 | 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
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222 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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223 | 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
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224 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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225 | 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
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226 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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227 | 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
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228 +-----------------------------------+------+--------+------------------------------------------+------------------+-------------+-----------+-------------+-------------------+------------+
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229
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230 Next 200 lines omitted.
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231
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232 ]]></help>
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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233 <citations>
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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234 <citation type="bibtex">@ARTICLE{a1,
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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235 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
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236 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.},
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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237 url = {https://github.com/phac-nml/bio_hansel}
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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238 }
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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239 }</citation>
726cd66ca2f9 planemo upload for repository https://github.com/phac-nml/bio_hansel commit 4ff4534765d620458c521bcac760cc8e01bc22f1
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240 </citations>
1
ddae7615b431 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hansel commit 80309b6403ad219d7fa3a25288c6339d0b33ed63"
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241 </tool>