<tool id="pairtools_stats" name="Pairtools Stats" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="@PROFILE_VERSION@" 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[
        #if $merge:
            #set $input_file_links = str($input_file).replace(',', ' ')
        #else
            #set $input_file_links = ""
            #for $i, $f in enumerate($input_file):
                #if $f.is_of_type('4dn_pairs.gz') or $f.is_of_type('4dn_pairsam.gz'):
                    ln -s '$f' 'input_file_${i}.gz' &&
                    #set $input_file_links += ' input_file_%d.gz ' % $i
                #else:
                    ln -s '$f' 'input_file_${i}' &&   
                    #set $input_file_links += ' input_file_%d ' % $i
                #end if
            #end for
        #end if

        pairtools stats
            $merge
            $with_chromsizes
            $yaml
            -o '$pairs_output'
            --nproc-in \${GALAXY_SLOTS:-4}
            --nproc-out \${GALAXY_SLOTS:-4}
            $input_file_links
    ]]></command>
    <inputs>
        <param type="data" name="input_file" format="4dn_pairs,4dn_pairsam,4dn_pairs.gz,4dn_pairsam.gz" multiple="true" label="Input pairs or pairsam file" help="Input 4dn pairs or pairsam file"></param>
        <param type="boolean" argument="--merge" truevalue="--merge" falsevalue="" checked="False" label="Merge input stats files" help="If selected, will merge multiple input stats files instead of calculating statistics of .pairs/.pairsam file"></param>
        <param type="boolean" argument="--with-chromsizes" truevalue="--with-chromsizes" falsevalue="" checked="False" label="Store sizes of chromosomes from the header of the pairs file in the stats file"></param>
        <param type="boolean" argument="--yaml" truevalue="--yaml" falsevalue="" checked="False" label="Output stats in yaml format instead of table"></param>
        </inputs>
    <outputs>
        <data name="pairs_output" format="tabular" label="${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" ftype="4dn_pairs" 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" ftype="4dn_pairs" 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>
        <!--Test 05 with compressed input pair file as input and default parameters-->
        <test expect_num_outputs="1">
            <param name="input_file" ftype="4dn_pairs" value="output_parsed_pairs_sam.pairs.gz"/>
            <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. Setting merge to true will
    merge multiple input stats files instead of calculating statistics of .pairs/.pairsam file.

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