<tool id="ivar_filtervariants" name="ivar filtervariants" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
    <description>Filter variants across replicates or multiple samples aligned using the same reference</description>
        <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="xrefs"/>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="exit_code"><![CDATA[
        #for $counter, $input in enumerate($inputs):
            ln -s '$input' ./var_${counter}.tsv &&
        #end for
        ivar filtervariants 
        -p filtered.tsv
        #for $counter, $input in enumerate($inputs)
            ./var_${counter}.tsv
        #end for
    ]]></command>
    <inputs>
        <param name="inputs" type="data" format="tabular" multiple="true" label="Variant tsv files for each replicate"/>
    </inputs>
    <outputs>
        <data name="output_filtered" format="tabular" label="${tool.name} on ${on_string}" from_work_dir="filtered.tsv"/>
    </outputs>
    <tests>
        <test>
            <param name="inputs" value="zika/Z52_a.tsv,zika/Z52_b.tsv" ftype="tabular"/>
            <output name="output_filtered" file="zika/Z52.tsv" ftype="tabular" lines_diff="10"/>
        </test>
    </tests>
    <help><![CDATA[
        iVar can be used to get an intersection of variants(in .tsv files) called
        from any number of replicates or from different samples using the same
        reference sequence. This intersection will filter out any iSNVs that do not
        occur in a minimum fraction of the files supplied. This parameter can be
        changed using the -t flag which range from 0 to 1 (default). Fields that are
        different across replicates(fields apart from REGION, POS, REF, ALT,
        REF_CODON, REF_AA, ALT_CODON, ALT_AA) will have the filename added as a
        suffix. If there are a large number of files to be filtered, the -f flag can
        be used to supply a text file with one sample/replicate variant .tsv file
        per line.
        
        Documentation can be found at `<https://andersen-lab.github.io/ivar/html/manualpage.html>`_.
    ]]></help>
<expand macro="citations" />
</tool>