view tiptoft.xml @ 0:7987b0437fe1 draft default tip

"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/tiptoft commit fae924375dd50aec403ad6bf632f2a8ffeac3863-dirty"

<tool id="tiptoft" name="tiptoft" version="@VERSION@">
    <description>Plasmid replicon and incompatibility group prediction from uncorrected long reads</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="exit_code"><![CDATA[
        tiptoft
        #if str($opt_input.plasmid_data) != ""
            --plasmid_data '$plasmid_data'
        #end if
        --kmer $opt_input.kmer
        #if str($opt_output.filtered_reads_file) != ""
        --filtered_reads_file $opt_output.filtered_reads_file
        #end if
        #if str($opt_output.output_file) != ""
        --output_file $opt_output.output_file
        #end if
         #if $opt_adv.no_hc_compression
        --no_hc_compression
        #end if
        #if $opt_adv.no_gene_filter
        --no_gene_filter
        #end if
        --max_gap $opt_adv.max_gap
        --max_kmer_count $opt_adv.max_kmer_count
        --margin $opt_adv.margin
        --min_block_size $opt_adv.min_block_size
        --min_fasta_hits $opt_adv.min_fasta_hits
        --min_perc_coverage $opt_adv.min_perc_coverage
        --min_kmers_for_onex_pass $opt_adv.min_kmers_for_onex_pass
        '$fastq' > '$output'
    ]]></command>
    
    <inputs>
       <param name="fastq" type="data" format="fastqsanger,fastqsanger.gz" label="Select fastq dataset" help="Specify dataset with single reads"/>
        
        <section name="opt_input" title="Optional Input">
        <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"/>
        <param argument="--kmer" type="integer" value="13" label="K-mer size" help="Default: 13"/>
        </section>

        <section name="opt_output" title="Optional Output">
        <param argument="--filtered_reads_file" type="text" value="" label="Filename to save matching reads to" help="Default: None" />
        <param argument="--output_file" type="text" value="" label="Output file" help="Default: None" />
        </section>

        <section name="opt_adv" title="Optional Advanced Input Arguments">
        <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" />
        <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" />
        <param argument="--max_gap" type="integer" value="3" label="Maximum gap for blocks to be contigous, measured in
                        multiples of the k-mer size" help="Default:3" />
        <param argument="--max_kmer_count" type="integer" value="10" label="Exclude k-mers which occur more than this number of
                        times in a sequence" help="Default:10" />
        <param argument="--margin" type="integer" value="10" label="Flanking region around a block to use for mapping" help="Default:10" />
        <param argument="--min_block_size" type="integer" value="50" label="Minimum block size in bases" help="Default:10" />
        <param argument="--min_fasta_hits" type="integer" value="8" label="Minimum No. of kmers matching a read" help="Default:8" />
        <param argument="--min_perc_coverage" type="integer" value="8" label="Minimum percentage coverage of typing sequence to
                        report" help="Default:85" />
        <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" />
        </section>
    </inputs>

    <outputs>
        <data name="output" format="tabular" label="${tool.name} on ${on_string} report file" />
    </outputs>

    <tests>
        <test>
             <param name="fastq" value="query_gz.fastq" ftype="fastqsanger"/>
             <param name="plasmid_data" value="plasmid.fa" ftype="fasta"/>
             <output name="output" file="expected_outputfile" ftype="tabular" />
        </test>
    </tests>
    <help><![CDATA[
    usage: tiptoft [options] input.fastq

    Plasmid replicon and incompatibility group prediction from uncorrected long
    reads

    Documentation can be found at `<https://github.com/andrewjpage/tiptoft>`_.

    ]]></help>
    <citations>
        <citation type="bibtex">
@UNPUBLISHED{Page2018,
    author = {Page, Andrew},
    title = {tiptoft: Predict plasmids from uncorrected long read data},
    year = {2018},
    url = {https://github.com/andrewjpage/tiptoft},
}
        </citation>
    </citations>
</tool>