annotate dedup.xml @ 4:55a53b5e308d draft

planemo upload for repository https://github.com/open2c/pairtools commit 162c595b19e442f40be4c2f5434b20b56ade52d4

<tool id="pairtools_dedup" name="Pairtools dedup" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2" license="MIT">
    <description>Find and remove PCR/optical duplicates</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        pairtools dedup
            '$pairs_path'
            -o '$output_dedup_pairs'
            #if $output_dups:
                --output-dups '$output_dups_pairs'
            #end if
            $mark_dups
            #if $output_stats:
                  --output-stats '$dedup_pairs_stats'
            #end if
            --nproc-in \${GALAXY_SLOTS:-4}
            --nproc-out \${GALAXY_SLOTS:-4}
    ]]></command>
    <inputs>      
        <param name="pairs_path" type="data" format="4dn_pairs,4dn_pairsam" label="Input pairs file" help="Input triu-flipped sorted .pairs or .pairsam file"/>
        <param argument="--mark-dups" type="boolean" truevalue="--mark-dups" falsevalue="" checked="True" label="Duplicate pairs are marked as DD in pair_type and as a duplicate in the SAM entries"/>
        <param argument="--output-dups" type="boolean" truevalue="--output-dups" falsevalue="" checked="False" label="Output file for duplicate pairs"/>
        <param argument="--output-stats" type="boolean" truevalue="--output-stats" falsevalue="" checked="False" label="Output file for duplicate statistics"/>
    </inputs>
    <outputs>
        <data name="output_dedup_pairs" format_source="pairs_path" label="${tool.name} on ${on_string}: Deduplicated Pairs"/>
        <data name="output_dups_pairs" format_source="pairs_path" label="${tool.name} on ${on_string}: Duplicate Pairs">
            <filter>output_dups</filter>
        </data>
        <data name="dedup_pairs_stats" format="tabular" label="${tool.name} on ${on_string}: Deduplicated stats">
            <filter>output_stats</filter>
        </data>
    </outputs>
    <tests>
        <!--Test 01 with default parameters-->
        <test expect_num_outputs="1">
            <param name="pairs_path" value="output_sorted_pairs.pairsam"/>
            <output name="output_dedup_pairs" file="output_dedup_pairs.pairsam" lines_diff="20"/>
        </test>
        <!--Test 02 mark_dups enabled and output_dups-->
        <test expect_num_outputs="2">
            <param name="pairs_path" value="output_sorted_pairs.pairsam"/>
            <param name="mark_dups" value="true"></param>
            <param name="output_dups" value="true"></param>
            <output name="output_dedup_pairs" file="output_dedup_pairs_markdups.pairsam" lines_diff="20"/>
            <output name="output_dups_pairs"  file="output_dups_pairs_markdups.pairsam" lines_diff="20"/>
        </test>
        <!--Test 03 mark_dups and output_stats enabled-->
        <test expect_num_outputs="2">
            <param name="pairs_path" value="output_sorted_pairs.pairsam"/>
            <param name="mark_dups" value="true"></param>
            <param name="output_stats" value="true"></param>
            <output name="output_dedup_pairs" file="output_dedup_pairs_markdups.pairsam" lines_diff="20"/>
            <output name="dedup_pairs_stats"  file="output_dedup_pairs.stats" lines_diff="20"/>
        </test>
    </tests>
    <help><![CDATA[
        **Pairtools dedup**

        Find PCR/optical duplicates in an upper-triangular flipped sorted pairs/pairsam file. Allow for a +/-N bp mismatch at each side of duplicated molecules.
              
    ]]></help>
    <expand macro="citations"/>
    <expand macro="creator"/>
</tool>