<tool id="gedlab-khmer-do-partition" name="Sequence partition all-in-one" version="@WRAPPER_VERSION@-4">
    <description>Load, partition, and annotate FAST[AQ] sequences</description>
    <macros>
        <token name="@BINARY@">do-partition.py</token>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version" />
    <command><![CDATA[
set -xu &&
#for $num, $input in enumerate($inputs)
ln -s ${input} sequence-${num} &&
#end for
mkdir -p output && cd output &&
@BINARY@
@TABLEPARAMS@
@THREADS@
output
../sequence-*
&&
mv output.info $information
]]>
    </command>
    <inputs>
        <expand macro="input_sequences_filenames" />
        <expand macro="tableinputs" />
    </inputs>
    <outputs>
        <data name="information" format="txt" label="${tool.name} summary." />
        <collection name="annotated_sequence_files" type="list">
            <discover_datasets pattern="__name__" directory="output" />
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="inputs" value="random-20-a.fa"/>
            <output_collection name="annotated_sequence_files" type="list">
                <element name="sequence-0.part" file="random-20-a.fa.part" />
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
Load in a set of sequences, partition them, merge the partitions, and
annotate the original sequences files with the partition information.

This script combines the functionality of `load-graph.py`,
`partition-graph.py`, `merge-partitions.py`, and
`annotate-partitions.py` into one script. This is convenient
but should probably not be used for large data sets, because
`do-partition.py` doesn't provide save/resume functionality.
]]>
    </help>
    <citations>
        <expand macro="software-citation" />
        <expand macro="graph-citation" />
    </citations>
</tool>