<tool id="pairtools_stats" name="Pairtools Stats" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2" license="MIT">
    <description>Calculates pairs statistics for input pairs and pairsam files.</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        pairtools stats
            $merge
            $with_chromsizes
            $yaml
            -o '$pairs_output'
            --nproc-in \${GALAXY_SLOTS:-4}
            --nproc-out \${GALAXY_SLOTS:-4}
            #if $input_file:
                ${str($input_file).replace(',', ' ')}
            #end if
    ]]></command>
    <inputs>
        <param type="data" name="input_file" format="4dn_pairs,4dn_pairsam" multiple="true" label="Input pairs or pairsam file" help="Input 4dn pairs or pairsam file"></param>
        <param type="boolean" argument="--merge" truevalue="--merge" falsevalue="" checked="False" label="Merge input stats files" help="If selected, will merge multiple input stats files instead of calculating statistics of .pairs/.pairsam file"></param>
        <param type="boolean" argument="--with-chromsizes" truevalue="--with-chromsizes" falsevalue="" checked="False" label="Store sizes of chromosomes from the header of the pairs file in the stats file"></param>
        <param type="boolean" argument="--yaml" truevalue="--yaml" falsevalue="" checked="False" label="Output stats in yaml format instead of table"></param>
        </inputs>
    <outputs>
        <data name="pairs_output" format="tabular" label="${tool.name} on ${on_string}"/>
    </outputs>
    <tests>
        <!--Test 01 with pair file as input and default parameters-->
        <test expect_num_outputs="1">
            <param name="input_file" value="output_parsed_pairs_sam.pairs"/>
            <param name="merge" value="false"/>
            <param name="with_chromsizes" value="false"/>
            <param name="yaml" value="false"/>
            <output name="pairs_output" ftype="tabular" file="pairs_output.stats"/>
        </test>
        <!--Test 02 with multipe input pair files as input and default parameters-->
        <test expect_num_outputs="1">
            <param name="input_file" value="pairs_output.stats,pairs_output2.stats"/>
            <param name="merge" value="true"/>
            <param name="with_chromsizes" value="false"/>
            <param name="yaml" value="false"/>
            <output name="pairs_output" ftype="tabular" file="pairs_output_merged.stats" lines_diff="40"/>
        </test>
        <!--Test 03 with pair files as input with additional chromsizes in output-->
        <test expect_num_outputs="1">
            <param name="input_file" value="output_parsed_pairs_sam.pairs"/>
            <param name="merge" value="false"/>
            <param name="with_chromsizes" value="true"/>
            <param name="yaml" value="false"/>
            <output name="pairs_output" ftype="tabular" file="pairs_output_with_chromsize.stats"/>
        </test>
         <!--Test 04 with pair files as input and yaml output format-->
        <test expect_num_outputs="1">
            <param name="input_file" value="output_parsed_pairs_sam.pairs"/>
            <param name="merge" value="false"/>
            <param name="with_chromsizes" value="false"/>
            <param name="yaml" value="true"/>
            <output name="pairs_output" ftype="tabular" file="pairs_output_yaml.stats"/>
        </test>
    </tests>
    <help><![CDATA[

    Calculate pairs statistics.
    
    By default, uses 4dn pairs or 4dn pairsam file to calculate statistics.

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