<tool id="hal_halpctid" name="halPctId" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>calculates % identity by sampling bases</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/> 
    <expand macro="stdio"/>
    <command detect_errors="aggressive"><![CDATA[
        set -o pipefail; ## Sets the pipeline’s exit code to halPctId’s on failure.
        halPctId
            --numSamples $numSamples
            --seed $seed
            ## Pipes output to replace commas with tabs. Output is mostly numerical, and Genome names contain no commas, as this would invalidate the HAL Newick tree.
            '$input_hal' '$refGenome' | sed $'s/, */\t/g' > '$out_file' 
    ]]></command>
    <inputs>
        <expand macro="input_hal"/>
        <expand macro="params_refGenome"/>
        <expand macro="params_numSamples"/>
        <expand macro="params_seed"/>
    </inputs>
    <outputs>
        <data name="out_file" format="tabular" label="${tool.name} on ${on_string}: ${refGenome}"/>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input_hal" value="halTest.hal"/>
            <param name="refGenome" value="Genome_1"/>
            <param name="seed" value="100"/>
            <output name="out_file" ftype="tabular">
                <assert_contents>
                    <has_line line="Genome&#009;IdenticalSites&#009;AlignedSites&#009;PercentIdentity"/>
                    <has_line line="Genome_1&#009;856475&#009;856475&#009;100"/>
                    <has_line line="Genome_2&#009;374132&#009;374132&#009;100"/>
                    <has_n_lines n="4"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <param name="input_hal" value="halTest.hal"/>
            <param name="refGenome" value="Genome_1"/>
            <param name="numSamples" value="1000"/>
            <param name="seed" value="100"/>
            <output name="out_file" ftype="tabular">
                <assert_contents>
                    <has_line line="Genome&#009;IdenticalSites&#009;AlignedSites&#009;PercentIdentity"/>
                    <has_line line="Genome_1&#009;839&#009;839&#009;100"/>
                    <has_line line="Genome_2&#009;339&#009;339&#009;100"/>
                    <has_n_lines n="4"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
halPctId computes percent identity (% ID) for a reference genome in a HAL alignment by randomly sampling bases.
It takes a HAL file and a reference genome name as input and outputs a table summarizing the result.
A random seed can be set for reproducibility.
    ]]></help>
    <expand macro="citation"/>
    <expand macro="creator"/>
</tool>