<tool id="nanopolish_index" name="Nanopolish::index" version="0.8.5">

    <description>Index FASTQ reads in FAST5 file</description>

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    <requirements>
        <requirement type="package" version="0.8.5">nanopolish</requirement>
    </requirements>

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    <version_command>nanopolish --version | perl -wnE'print "$1\n" for /^nanopolish version (.+)$/mg'</version_command>

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    <command detect_errors="aggressive">
    <![CDATA[

    perl $__tool_directory__/nanopolish_index.pl

        --reads $input_reads
        --fast5 $input_fast5
        --out   $out_index

    ]]>
    </command>

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    <inputs>

        <param name="input_reads" type="data" format="fasta,fastq" label="Input reads (FASTA/Q)" />
        <param name="input_fast5" type="data" format="fast5.tar" label="Input reads (FAST5)" />

    </inputs>

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    <outputs>

        <data name="out_index" format="tar" label="${tool.name} on ${on_string}" />

    </outputs>

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    <tests>
        <test>
            <param name="input_reads" value="called.fa" ftype="fasta" />
            <param name="input_fast5" value="test.fast5.tar.gz" ftype="fast5.tar.gz" />
            <output name="out_index" file="index.tar" compare="sim_size" delta="100"/>
        </test>
    </tests>

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    <help>
    <![CDATA[

**Description**

Nanopolish is a software package for signal-level analysis of Oxford Nanopore
sequencing data. Nanopolish can calculate an improved consensus sequence for a
draft genome assembly, detect base modifications, call SNPs and indels with
respect to a reference genome and more.

The Galaxy wrapper has modified nanopolish to take a gzip tarball of FAST5 reads
as input, such as can be produced by `poretools combine`, and always outputs a
single FASTQ file.

This is the `index` module.

    ]]>
    </help>

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    <citations>
    </citations>

</tool>