annotate complexity_bam.xml @ 9:18aad692772a draft default tip

planemo upload for repository https://github.com/phac-nml/quasitools commit 5a9e4c9a582828654893166caf20576f5e0c418e

<tool id="complexity_bam" name="Complexity BAM" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[

        ln -s $input_bam '${input_bam.name}' &&
        ln -s $input_bam.metadata.bam_index '${input_bam.name}.bai' &&

        quasitools complexity bam '$ref_file' '${input_bam.name}'  $k -f '$filter_size' -o output.csv

    ]]></command>
    <inputs>
        <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" />
        <param name="input_bam" type="data" format="bam" optional="false" label="BAM file" />
        <param name="k" type="integer" label="k-mer size" value="0" min="0" />
        <param name="filter_size" type="integer" label="Filter size" value="0" min="0" />
    </inputs>
    <outputs>
        <data format="csv" name="output" from_work_dir="output.csv" />
    </outputs>
   <tests>
        <test>
            <param name="ref_file" value="generated.fasta" />
            <param name="input_bam" value="generated.bam" />
	    <param name="k" value="200" />
	    <param name="filter_size" value="0" />
            <output name="output" >
                <assert_contents>
                    <has_text text="Position" />
                    <has_text text="0" />
                </assert_contents>
            </output>
        </test>
    </tests>
   
    <help><![CDATA[
Quasispecies Complexity
=======================

Calculates various quasispecies complexity measures on next generation sequenced data from a BAM file and it's corresponding reference file.

The measures of complexity are taken from the following work:
Gregori, Josep, et al. "Viral quasispecies complexity measures." Virology 493 (2016): 227-237.


]]></help>
    <expand macro="citations" />
</tool>