<tool id="seqwish" name="seqwish" version="@TOOL_VERSION@" >
    <description>Alignment to variation graph inducer</description>
    <macros>
        <token name="@TOOL_VERSION@">0.7.2</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">seqwish</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
seqwish
-p '$paf_alns'
-s ${ ' '.join(["'%s'" % x for x in $seqs]) }
--gfa='$out_gfa'
#if $m:
    -m '$m'
#end if
--threads=\${GALAXY_SLOTS:-1}
#if str($r):
    -r $r
#end if
#if str($k):
    -k $k
#end if
#if str($B):
    -B $B
#end if
    ]]></command>
    <inputs>
        <param argument="--paf-alns" type="data" format="paf" label="Induce the graph from these PAF formatted alignments" />
        <param argument="--seqs" type="data" format="fasta,fasta.gz,fastq,fastq.gz" multiple="true" label="The sequences used to generate the alignments" />
        <param argument="-m" type="data" optional="true" format="txt,tabular" label="Subset the input alignments"
            help="" />
        <param argument="-r" type="integer" min="1" optional="true" label="Limit copies of a given input base"
            help="Limit transitive closure to include no more than N copies of a given input base" />
        <param argument="-k" type="integer" min="1" optional="true" label="Filter exact matches below this length"
            help="This can smooth the graph locally and prevent the formation of complex local graph topologies from forming due to differential alignments." />
        <param argument="-B" type="integer" min="1" optional="true" label="Number of bp to use for transitive closure batch"
            help="" />
    </inputs>

    <outputs>
        <data name="out_gfa" format="gfa1" label="${tool.name} on ${on_string}" />
    </outputs>

    <tests>
        <test>
            <param name="seqs" value="A-3105.fa.gz" />
            <param name="paf_alns" value="A-3105.paf.gz" />
            <output name="out_gfa" md5="f82bea6331f62e86cce543c36fb4c1f6" />
        </test>
        <test>
            <param name="seqs" value="A-3105.fa.gz" />
            <param name="paf_alns" value="A-3105.paf.gz" />
            <param name="r" value="3000" />
            <param name="k" value="1" />
            <param name="B" value="1000000" />
            <output name="out_gfa" md5="f82bea6331f62e86cce543c36fb4c1f6" />
        </test>
    </tests>
    <help><![CDATA[
These **seq**uences **wish** they were squished into a graph.

seqwish implements a lossless conversion from pairwise alignments between sequences to a variation graph encoding the sequences
and their alignments. As input we typically take all-versus-all alignments, but the exact structure of the alignment set may
be defined in an application specific way. This algorithm uses a series of disk-backed sorts and passes over the alignment
and sequence inputs to allow the graph to be constructed from very large inputs that are commonly encountered when working with
large numbers of noisy input sequences. Memory usage during construction and traversal is limited by the use of sorted
disk-backed arrays and succinct rank/select dictionaries to record a queryable version of the graph.
    ]]></help>
    <citations>
    </citations>
</tool>