annotate poretools_extract.xml @ 2:08064da7b7fb draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit 506782d1e671505617ff539e6811fcdcc2c02cd5

<tool id="poretools_extract" name="Extract reads" version="@VERSION@.0" profile="@PROFILE@">
    <description>in FASTA or FASTQ format from nanopore files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements" />
    <command detect_errors="aggressive">
    <![CDATA[
        poretools $output_format --type $type --min-length $min_length --max-length $max_length
        $quality
        #if $group:
            --group '$group'
        #end if
        #if $start:
            --start '$start'
        #end if
        #if $end:
            --end '$end'
        #end if
        '$input' > '$output'
    ]]>
    </command>
    <inputs>
        <param name="input" type="data" format="h5,fast5.tar,fast5.tar.gz,fast5.tar.bz2" label="Input fast5 or archive of fast5 files" />
        <param name="output_format" type="select" label="Output format">
            <option value="fastq">FASTQ</option>
            <option value="fasta">FASTA</option>
        </param>
        <expand macro="length_options" />
        <param argument="--type" type="select" label="FASTQ Type">
            <option value="all">All</option>
            <option value="fwd">Forward</option>
            <option value="rev">Reverse</option>
            <option value="2D">2D</option>
            <option value="fwd,rev">Forward and reverse</option>
            <option value="best">Best</option>
        </param>
        <param name="quality" type="select" label="Filter by complement events">
            <option value="">Do not filter</option>
            <option value="--high-quality">Only report reads with more</option>
            <option value="--normal-quality">Only report reads with fewer</option>
        </param>
        <param argument="--group" type="integer" optional="True" label="Base calling group serial number to extract" />
        <param argument="--start" type="integer" optional="True" label="Start timestamp" />
        <param argument="--end" type="integer" optional="True" label="End timestamp" />
    </inputs>
    <outputs>
        <data name="output" format="fastq">
            <change_format>
                <when input="output_format" value="fasta" format="fasta" />
            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <expand macro="test_input" />
            <param name="output_format" value="fastq" />
            <output name="output" file="poretools-extract-out1.fastq" ftype="fastq" />
        </test>
        <test>
            <expand macro="test_input" />
            <param name="output_format" value="fasta" />
            <output name="output" file="poretools-extract-out1.fasta" ftype="fasta" />
        </test>
    </tests>
    <help>
        Extract sequences from fast5 files generated by the Oxford Nanopore sequencing technology.
    </help>
    <expand macro="citations" />
</tool>