view aacoverage.xml @ 9:18aad692772a draft default tip

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

<tool id="aacoverage" name="Amino Acid Coverage" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description>Builds an aa census and returns its coverage</description>
    <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 aacoverage '${input_bam.name}' $ref_file $input_genes -o output.csv

    ]]></command>
    <inputs>
        <param name="input_bam" type="data" format="bam" optional="false" label="Bam file" />
        <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" />
        <param name="input_genes" type="data" format="bed" optional="false" label="Gene file" />
    </inputs>
    <outputs>
        <data format="csv" name="output" from_work_dir="output.csv" />
    </outputs>
    <tests>
        <test>
            <param name="input_bam" value="align.bam" />
            <param name="ref_file" value="hxb2_pol.fas" />
            <param name="input_genes" ftype="bed" value="hxb2_pol.bed" />
            <output name="output" >
                <assert_contents>
                    <has_text text="frame: 0" />
                    <has_text text="1,0" />
                    <has_text text="948,1" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

Amino Acid Coverage
===================

Builds an amino acid census and returns its coverage.

**Output**

A file with one entry per line with the AA position and the coverage at the position.

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