annotate compress_fast5.xml @ 1:52da1e2c82d3 draft

"planemo upload for repository https://github.com/nanoporetech/ont_fast5_api/ commit 2df36b6d30fd69ea532a4fd42daf4741363074f3"

<?xml version="1.0"?>
<tool id="ont_fast5_api_compress_fast5" name="@TOOL_NAME@ Compress" version="@TOOL_VERSION@+galaxy0" profile="18.01">
    <description>multi read file(s)</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <version_command><![CDATA[compress_fast5 -v]]></version_command>
    <command detect_errors="exit_code"><![CDATA[
## initialize
@INITIALIZE@

## run
compress_fast5
--recursive
## required
@INPUTPATH@
@SAVEPATH@
@COMPRESSION@
## optional
@THREADS@

## create tarball
@TARBALL@
    ]]></command>
    <inputs>
        <expand macro="input"/>
        <expand macro="compression">
            <option value="vbz" selected="true">VBZ</option>
        </expand>
    </inputs>
    <outputs>
        <expand macro="output"/>
    </outputs>
    <tests>
        <!-- #1 default -->
        <test expect_num_outputs="1">
            <param name="input_path" value="multi.fast5.tar"/>
            <output name="out_results">
                <assert_contents>
                    <has_size value="40960"/>
                </assert_contents>
            </output>
        </test>
        <!-- #2 -->
        <test expect_num_outputs="1">
            <param name="input_path" value="multi.fast5.tar"/>
            <param name="compression" value="vbz_legacy_v0"/>
            <output name="out_results">
                <assert_contents>
                    <has_size value="40960"/>
                </assert_contents>
            </output>
        </test>
        <!-- #3 -->
        <test expect_num_outputs="1">
            <param name="input_path" value="multi.fast5.tar"/>
            <param name="compression" value="gzip"/>
            <output name="out_results">
                <assert_contents>
                    <has_size value="40960"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
.. class:: infomark

**What it does**

@WID@

*compress_fast5* copies and converts raw data between vbz and gzip compression formats.

**Input**

Multi read file(s) in FAST5 format that are stored in a flat TAR.

**Output**

Multi read FAST5 file(s) containing compressed reads that are stored in a flat TAR. Further detail of HDF5 data management strategies can be found `here <https://support.hdfgroup.org/HDF5/doc/Advanced/FileSpaceManagement/FileSpaceManagement.pdf>`_.

.. class:: infomark

**References**

@REFERENCES@
    ]]></help>
    <expand macro="citations"/>
</tool>