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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/krocus commit b6dad2eecb7ef9234ec878a36242edffed4c1241
author iuc
date Tue, 12 Mar 2024 10:45:51 +0000
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1 <tool id="krocus" name="krocus" version="@VERSION@">
2 <description>Multi-locus sequence typing (MLST) from uncorrected long reads</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <xrefs>
7 <xref type="bio.tools">krocus</xref>
8 </xrefs>
9 <expand macro="requirements" />
10 <expand macro="version_command" />
11 <command detect_errors="exit_code"><![CDATA[
12 krocus
13 --output_file detected_mlst.tsv
14 #if $opt_args.filtered_reads
15 --filtered_reads_file filtered_reads.fq
16 #end if
17 --max_gap $opt_args.max_gap
18 --min_kmers_for_onex_pass $opt_args.min_kmers_for_onex_pass
19 --margin $opt_args.margin
20 --min_block_size $opt_args.min_block_size
21 --min_fasta_hits $opt_args.min_fasta_hits
22 --min_kmers_for_onex_pass $opt_args.min_kmers_for_onex_pass
23 --max_kmers $opt_args.max_kmers
24 --print_interval $opt_args.print_interval
25 --kmer $opt_args.kmer
26 $opt_args.divisible_by_3
27 $opt_args.verbose
28 '$krocus_mlst_databases.fields.path' '$fastq'
29 ]]>
30 </command>
31 <inputs>
32 <param name="fastq" type="data" format="fastqsanger,fastqsanger.gz" label="Select fastq dataset" help="Specify dataset with single read"/>
33 <param label="Select a database" name="krocus_mlst_databases" type="select">
34 <options from_data_table="krocus_mlst_databases">
35 <validator message="No database is available" type="no_options" />
36 </options>
37 </param>
38 <section name="opt_args" title="Optional Arguments">
39 <param name="filtered_reads" type="boolean" truevalue="true" falsevalue="" checked="false" label="Save filtered reads ?"/>
40 <param argument="--max_gap" type="integer" min="1" value="4" label="Maximum gap for blocks to be contigous, measured in
41 multiples of the k-mer size" help="Default:4" />
42 <param argument="--margin" type="integer" min="1" value="10" label="Flanking region around a block to use for mapping" help="Default:10" />
43 <param argument="--min_block_size" type="integer" min="1" value="150" label="Minimum block size in bases" help="Default:150" />
44 <param argument="--min_fasta_hits" type="integer" min="1" value="10" label="Minimum No. of kmers matching a read" help="Default:10" />
45 <param argument="--min_kmers_for_onex_pass" type="integer" min="2" value="5" label="Minimum No. of kmers matching a read in 1st pass" help="Default:5" />
46 <param argument="--max_kmers" type="integer" min="1" value="10" label="Dont count kmers occuring more than this many times" help="Default:10" />
47 <param argument="--print_interval" type="integer" min="1" value="10" label="Print ST every this number of reads" help="(Default:500)" />
48 <param argument="--kmer" type="integer" min="2" value="10" label="k-mer size" help="(Default:11)" />
49 <param argument="--divisible_by_3" type="boolean" truevalue="--divisible_by_3" falsevalue="" checked="false" label="Genes which are not divisible by 3 are excluded" help="(Default:No)" />
50 <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="false" label="Turn on debugging" help="(Default:No)" />
51 </section>
52 </inputs>
53
54 <outputs>
55 <data name="output_file" format="tabular" label="${tool.name} on ${on_string}: Output" from_work_dir="detected_mlst.tsv"/>
56 <data name="filtered_reads" format="fastq" label="${tool.name} on ${on_string}: Filtered reads" from_work_dir="filtered_reads.fq">
57 <filter>opt_args['filtered_reads'] is True</filter>
58 </data>
59 </outputs>
60
61 <tests>
62 <test expect_num_outputs="1">
63 <param name="fastq" value="pacbio.fastq.gz" ftype="fastqsanger" />
64 <param name="krocus_mlst_databases" value="mlst_db"/>
65 <output name="output_file" ftype="tabular" file="mlst_output_pacbio.tsv" compare="sim_size" />
66 </test>
67 <test expect_num_outputs="2">
68 <param name="fastq" value="pacbio.fastq.gz" ftype="fastqsanger" />
69 <param name="filtered_reads" value="True" />
70 <param name="krocus_mlst_databases" value="mlst_db"/>
71 <output name="filtered_reads" ftype="fastq" file="filtered_reads.fq" compare="sim_size" />
72 </test>
73 </tests>
74
75 <help><![CDATA[
76 Multi-locus sequence typing (MLST) from uncorrected long reads
77
78 Krocus can predict a sequence type directly from uncorrected long reads, and
79 which was designed to consume read data as it is produced, providing results
80 in minutes. It is the only tool which can do this from uncorrected long
81 reads. We tested Krocus on over 600 samples sequenced with using long read
82 sequencing technologies from PacBio and Oxford Nanopore. It provides
83 sequence types on average within 90 seconds, with a sensitivity of 94% and
84 specificity of 97%, directly from uncorrected raw sequence reads.
85
86 Documentation can be found at `<https://github.com/andrewjpage/krocus>`_.
87 ]]>
88 </help>
89 <expand macro="citations"/>
90 </tool>