annotate poretools_qualpos.xml @ 1:4fe6b96aff72 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit d50758dbe64462ba3cdcb7f1df0bcc57a310deab"

<?xml version="1.0"?>
<tool id="poretools_qualpos" name="Generate box-whisker" version="@VERSION@.1">
    <description>plot of quality score distribution over positions in nanopore reads</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="aggressive">
    <![CDATA[
@MPLBACKEND@
poretools qualpos '$input' --saveas qualpos.$extension --min-length $min_length --max-length $max_length --bin-width $bin_width $theme_bw && mv qualpos.$extension '$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" />
        <expand macro="plot_options">
            <option value="pdf">PDF</option>
            <option value="svg">SVG</option>
        </expand>
        <param name="theme_bw" argument="--theme-bw" type="boolean" truevalue="--theme-bw" falsevalue="" label="Use a monochrome color " />
        <expand macro="length_options" />
        <param name="bin_width" argument="--bin-width" type="integer" value="1000" label="The width of bins" />
    </inputs>
    <outputs>
        <expand macro="image_output">
            <when input="extension" value="svg" format="svg" />
        </expand>
    </outputs>
    <tests>
        <test>
            <expand macro="test_input" />
            <param name="extension" value="png" />
            <output name="output" file="poretools-qualpos-out1.png" ftype="png" compare="sim_size" />
        </test>
        <test>
            <expand macro="test_input" />
            <param name="extension" value="pdf" />
            <output name="output" file="poretools-qualpos-out1.pdf" ftype="pdf" lines_diff="36" />
        </test>
    </tests>
    <help>
        Produce a box-whisker plot of quality score distribution over positions in nanopore reads
    </help>
    <expand macro="citations" />
</tool>