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"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/tiptoft commit fae924375dd50aec403ad6bf632f2a8ffeac3863-dirty"
author thanhlv
date Fri, 10 Jan 2020 14:17:18 +0000
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7987b0437fe1 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/tiptoft commit fae924375dd50aec403ad6bf632f2a8ffeac3863-dirty"
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1 <tool id="tiptoft" name="tiptoft" version="@VERSION@">
7987b0437fe1 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/tiptoft commit fae924375dd50aec403ad6bf632f2a8ffeac3863-dirty"
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2 <description>Plasmid replicon and incompatibility group prediction from uncorrected long reads</description>
7987b0437fe1 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/tiptoft commit fae924375dd50aec403ad6bf632f2a8ffeac3863-dirty"
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3 <macros>
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4 <import>macros.xml</import>
7987b0437fe1 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/tiptoft commit fae924375dd50aec403ad6bf632f2a8ffeac3863-dirty"
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5 </macros>
7987b0437fe1 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/tiptoft commit fae924375dd50aec403ad6bf632f2a8ffeac3863-dirty"
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6 <expand macro="requirements" />
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7 <expand macro="version_command" />
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8 <command detect_errors="exit_code"><![CDATA[
7987b0437fe1 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/tiptoft commit fae924375dd50aec403ad6bf632f2a8ffeac3863-dirty"
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9 tiptoft
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10 #if str($opt_input.plasmid_data) != ""
7987b0437fe1 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/tiptoft commit fae924375dd50aec403ad6bf632f2a8ffeac3863-dirty"
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11 --plasmid_data '$plasmid_data'
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12 #end if
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13 --kmer $opt_input.kmer
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14 #if str($opt_output.filtered_reads_file) != ""
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15 --filtered_reads_file $opt_output.filtered_reads_file
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16 #end if
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17 #if str($opt_output.output_file) != ""
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18 --output_file $opt_output.output_file
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19 #end if
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20 #if $opt_adv.no_hc_compression
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21 --no_hc_compression
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22 #end if
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23 #if $opt_adv.no_gene_filter
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24 --no_gene_filter
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25 #end if
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26 --max_gap $opt_adv.max_gap
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27 --max_kmer_count $opt_adv.max_kmer_count
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28 --margin $opt_adv.margin
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29 --min_block_size $opt_adv.min_block_size
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30 --min_fasta_hits $opt_adv.min_fasta_hits
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31 --min_perc_coverage $opt_adv.min_perc_coverage
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32 --min_kmers_for_onex_pass $opt_adv.min_kmers_for_onex_pass
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33 '$fastq' > '$output'
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34 ]]></command>
7987b0437fe1 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/tiptoft commit fae924375dd50aec403ad6bf632f2a8ffeac3863-dirty"
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35
7987b0437fe1 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/tiptoft commit fae924375dd50aec403ad6bf632f2a8ffeac3863-dirty"
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36 <inputs>
7987b0437fe1 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/tiptoft commit fae924375dd50aec403ad6bf632f2a8ffeac3863-dirty"
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37 <param name="fastq" type="data" format="fastqsanger,fastqsanger.gz" label="Select fastq dataset" help="Specify dataset with single reads"/>
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38
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39 <section name="opt_input" title="Optional Input">
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40 <param name="plasmid_data" argument="--plasmid_data" type="data" format="fasta" label="Plasmid database" help="A fasta file containing plasmid data. Defaults to bundled database"/>
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41 <param argument="--kmer" type="integer" value="13" label="K-mer size" help="Default: 13"/>
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42 </section>
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43
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44 <section name="opt_output" title="Optional Output">
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45 <param argument="--filtered_reads_file" type="text" value="" label="Filename to save matching reads to" help="Default: None" />
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46 <param argument="--output_file" type="text" value="" label="Output file" help="Default: None" />
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47 </section>
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48
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49 <section name="opt_adv" title="Optional Advanced Input Arguments">
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50 <param argument="--no_hc_compression" type="boolean" truevalue="--no_hc_compression" falsevalue="" checked="false" label="Turn off homoploymer compression of k-mers" help="Default:No" />
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51 <param argument="--no_gene_filter" type="boolean" truevalue="--no_gene_filter" falsevalue="" checked="false" label="Dont filter out lower coverage genes from same group" help="Default:No" />
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52 <param argument="--max_gap" type="integer" value="3" label="Maximum gap for blocks to be contigous, measured in
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53 multiples of the k-mer size" help="Default:3" />
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54 <param argument="--max_kmer_count" type="integer" value="10" label="Exclude k-mers which occur more than this number of
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55 times in a sequence" help="Default:10" />
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56 <param argument="--margin" type="integer" value="10" label="Flanking region around a block to use for mapping" help="Default:10" />
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57 <param argument="--min_block_size" type="integer" value="50" label="Minimum block size in bases" help="Default:10" />
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58 <param argument="--min_fasta_hits" type="integer" value="8" label="Minimum No. of kmers matching a read" help="Default:8" />
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59 <param argument="--min_perc_coverage" type="integer" value="8" label="Minimum percentage coverage of typing sequence to
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60 report" help="Default:85" />
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61 <param argument="--min_kmers_for_onex_pass" type="integer" value="5" label="Minimum No. of kmers matching a read in 1st pass" help="Default:5" />
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62 </section>
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63 </inputs>
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64
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65 <outputs>
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66 <data name="output" format="tabular" label="${tool.name} on ${on_string} report file" />
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67 </outputs>
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68
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69 <tests>
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70 <test>
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71 <param name="fastq" value="query_gz.fastq" ftype="fastqsanger"/>
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72 <param name="plasmid_data" value="plasmid.fa" ftype="fasta"/>
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73 <output name="output" file="expected_outputfile" ftype="tabular" />
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74 </test>
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75 </tests>
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76 <help><![CDATA[
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77 usage: tiptoft [options] input.fastq
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78
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79 Plasmid replicon and incompatibility group prediction from uncorrected long
7987b0437fe1 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/tiptoft commit fae924375dd50aec403ad6bf632f2a8ffeac3863-dirty"
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80 reads
7987b0437fe1 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/tiptoft commit fae924375dd50aec403ad6bf632f2a8ffeac3863-dirty"
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81
7987b0437fe1 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/tiptoft commit fae924375dd50aec403ad6bf632f2a8ffeac3863-dirty"
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82 Documentation can be found at `<https://github.com/andrewjpage/tiptoft>`_.
7987b0437fe1 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/tiptoft commit fae924375dd50aec403ad6bf632f2a8ffeac3863-dirty"
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83
7987b0437fe1 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/tiptoft commit fae924375dd50aec403ad6bf632f2a8ffeac3863-dirty"
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84 ]]></help>
7987b0437fe1 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/tiptoft commit fae924375dd50aec403ad6bf632f2a8ffeac3863-dirty"
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85 <citations>
7987b0437fe1 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/tiptoft commit fae924375dd50aec403ad6bf632f2a8ffeac3863-dirty"
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86 <citation type="bibtex">
7987b0437fe1 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/tiptoft commit fae924375dd50aec403ad6bf632f2a8ffeac3863-dirty"
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87 @UNPUBLISHED{Page2018,
7987b0437fe1 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/tiptoft commit fae924375dd50aec403ad6bf632f2a8ffeac3863-dirty"
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88 author = {Page, Andrew},
7987b0437fe1 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/tiptoft commit fae924375dd50aec403ad6bf632f2a8ffeac3863-dirty"
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89 title = {tiptoft: Predict plasmids from uncorrected long read data},
7987b0437fe1 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/tiptoft commit fae924375dd50aec403ad6bf632f2a8ffeac3863-dirty"
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90 year = {2018},
7987b0437fe1 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/tiptoft commit fae924375dd50aec403ad6bf632f2a8ffeac3863-dirty"
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91 url = {https://github.com/andrewjpage/tiptoft},
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92 }
7987b0437fe1 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/tiptoft commit fae924375dd50aec403ad6bf632f2a8ffeac3863-dirty"
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93 </citation>
7987b0437fe1 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/tiptoft commit fae924375dd50aec403ad6bf632f2a8ffeac3863-dirty"
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94 </citations>
7987b0437fe1 "planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/tiptoft commit fae924375dd50aec403ad6bf632f2a8ffeac3863-dirty"
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95 </tool>