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annotate krocus.xml @ 0:d3ccbecf8f7f draft

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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/krocus commit 15e535fd467e72874790ae7efd039237709b11ba-dirty
author thanhlv
date Thu, 07 Feb 2019 12:02:43 -0500
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d3ccbecf8f7f planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/krocus commit 15e535fd467e72874790ae7efd039237709b11ba-dirty
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1 <tool id="krocus" name="krocus" version="@VERSION@">
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2 <description>Multi-locus sequence typing (MLST) from uncorrected long reads</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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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[
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9 krocus
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10 --output_file detected_mlst.tsv
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11 #if str($opt_args.filtered_reads_file) != ""
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12 --filtered_reads_file $opt_args.filtered_reads_file
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13 #end if
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14 --max_gap $opt_args.max_gap
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15 --min_kmers_for_onex_pass $opt_args.min_kmers_for_onex_pass
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16 --margin $opt_args.margin
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17 --min_block_size $opt_args.min_block_size
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18 --min_fasta_hits $opt_args.min_fasta_hits
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19 --min_kmers_for_onex_pass $opt_args.min_kmers_for_onex_pass
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20 --max_kmers $opt_args.max_kmers
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21 --print_interval $opt_args.print_interval
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22 --kmer $opt_args.kmer
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23
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24 #if $opt_args.divisible_by_3
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25 --divisible_by_3
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26 #end if
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27
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28 #if $opt_args.verbose
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29 --verbose
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30 #end if
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31
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32 '$krocus_mlst_databases.fields.path' '$fastq'
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33 ]]></command>
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34
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35 <inputs>
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36 <param name="fastq" type="data" format="fastqsanger,fastqsanger.gz" label="Select fastq dataset" help="Specify dataset with single read"/>
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37 <param label="Select a database" name="krocus_mlst_databases" type="select">
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38 <options from_data_table="krocus_mlst_databases">
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39 <validator message="No database is available" type="no_options" />
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40 </options>
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41 </param>
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42 <section name="opt_args" title="Optional Arguments">
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43 <param argument="--filtered_reads_file" type="text" value="" optional="True" label="Filename to save matching reads to" help="Default: None" />
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44 <param argument="--max_gap" type="integer" value="4" label="Maximum gap for blocks to be contigous, measured in
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45 multiples of the k-mer size" help="Default:4" />
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46 <param argument="--margin" type="integer" value="10" label="Flanking region around a block to use for mapping" help="Default:10" />
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47 <param argument="--min_block_size" type="integer" value="150" label="Minimum block size in bases" help="Default:150" />
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48 <param argument="--min_fasta_hits" type="integer" value="10" label="Minimum No. of kmers matching a read" help="Default:10" />
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49 <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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50 <param argument="--max_kmers" type="integer" value="10" label="Dont count kmers occuring more than this many times" help="Default:10" />
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51 <param argument="--print_interval" type="integer" value="10" label="Print ST every this number of reads" help="(Default:500)" />
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52 <param argument="--kmer" type="integer" value="10" label="k-mer size" help="(Default:11)" />
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53 <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)" />
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54 <param argument="--target_st" type="integer" value="" optional="True" label="For performance testing print time to find given ST" help="(Default:None)" />
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55 <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="false" label="Turn on debugging" help="(Default:No)" />
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56 </section>
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57 </inputs>
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58
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59 <outputs>
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60 <data name="output_file" format="tabular" label="${tool.name} on ${on_string}: Output" from_work_dir="detected_mlst.tsv"/>
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61 </outputs>
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62
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63 <tests>
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64 <test>
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65 <param name="fastq" value="pacbio.fastq.gz" ftype="fastqsanger" />
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66 <param name="krocus_mlst_databases" value="mlst_db"/>
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67 <output name="output_file" ftype="tabular" file="mlst_output_pacbio.tsv" compare="contains" />
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68 </test>
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69 </tests>
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70
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71 <help><![CDATA[
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72 usage: krocus [options] allele_directory input.fastq
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73
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74 multi-locus sequence typing (MLST) from uncorrected long reads
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75
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76 Documentation can be found at `<https://github.com/andrewjpage/krocus>`_.
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77 ]]></help>
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78 <expand macro="citations" />
d3ccbecf8f7f planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/krocus commit 15e535fd467e72874790ae7efd039237709b11ba-dirty
thanhlv
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79 </tool>