annotate macros.xml @ 1:3bdd8fa109b1 draft

"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit a5d038871ff0e1b133039b59183dee795449b383"

<?xml version="1.0"?>
<macros>
    <token name="@TOOL_VERSION@">3.1.3</token>
    <token name="@TOOL_NAME@">ont_fast5_api:</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">ont-fast5-api</requirement>
            <requirement type="package" version="1.10.5">hdf5</requirement>
        </requirements>
    </xml>

    <!-- command -->
    <token name="@BATCHSIZE@"><![CDATA[
--batch_size $batch_size
    ]]></token>
    <token name="@COMPRESSION@"><![CDATA[
#if $compression != 'none'
    --compression '$compression'
#end if
    ]]></token>
    <token name="@INITIALIZE@"><![CDATA[
mkdir -p './data' &&
tar -xf '$input_path' -C './data' &&
    ]]></token>
    <token name="@INPUTPATH@"><![CDATA[
--input_path './data'
    ]]></token>
    <token name="@SAVEPATH@"><![CDATA[
--save_path './results'
    ]]></token>
    <token name="@TARBALL@"><![CDATA[
&& find './results' -type f -name '*.fast5' | tar --transform 's/.*\///g' -cvf './results.fast5.tar' --files-from=/dev/stdin
    ]]></token>
    <token name="@THREADS@"><![CDATA[
--threads \${GALAXY_SLOTS:-4}
    ]]></token>

    <!-- input -->
    <xml name="input" token_argument="--input_path" token_label="multi">
        <param argument="@ARGUMENT@" type="data" format="fast5.tar" label="Select @LABEL@ read input file"/>
    </xml>
    <xml name="batch_size">
        <param argument="--batch_size" type="integer" value="4000" min="1" label="Set batch size" help="Number of single reads to include in each multi read file"/>
    </xml>
    <xml name="compression">
        <param argument="compression" type="select" label="Select output compression type">
            <yield/>
            <option value="vbz_legacy_v0">VBZ legacy v0</option>
            <option value="gzip">GZIP</option>
        </param>
    </xml>

    <!-- output -->
    <xml name="output">
        <data name="out_results" format="fast5.tar" from_work_dir="results.fast5.tar" label="${tool.name} on ${on_string}: Results"/>
    </xml>

   <!-- help -->
    <token name="@WID@"><![CDATA[
*ont_fast5_api* is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format.

- concrete implementation of the FAST5 file schema using the generic h5py library
- plain-english-named methods to interact with and reflect the FAST5 file schema
- tools to convert between multi_read and single_read formats
- tools to compress/decompress raw data in files
    ]]></token>
    <token name="@REFERENCES@"><![CDATA[
More information are available on `github <https://github.com/nanoporetech/ont_fast5_api>`_.
    ]]></token>

    <xml name="citations">
        <citations>
            <citation type="bibtex">
                @online{ont_fast5_api,
                author = {Oxford Nanopore Technologies },
                title = {ont_fast5_api},
                year = 2020,
                url = {https://github.com/nanoporetech/ont_fast5_api},
                urldate = {2020-06-01}
            }</citation>
        </citations>
    </xml>
</macros>