view compress_fast5.xml @ 0:0fbeff566070 draft default tip

"planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/ont_fast5_api commit 9fb27995131a4106053eb85d687857d2cbd2a5c6"

<?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 '$compression'
## optional
@THREADS@

## create tarball
@TARBALL@
    ]]></command>
    <inputs>
        <expand macro="input"/>
        <param argument="compression" type="select" label="Select output compression type">
            <option value="gzip" selected="true">GZIP</option>
            <option value="vbz_legacy_v0">VBZ legacy v0</option>
            <option value="vbz">VBZ</option>
        </param>
    </inputs>
    <outputs>
        <data name="out_results" format="fast5.tar" from_work_dir="results.fast5.tar" label="${tool.name} on ${on_string}: Results">
            <change_format>
                <when input="compression" value="gzip" format="fast5.tar.gz"/>
                <when input="compression" value="vbz_legacy_v0" format="fast5.tar.bz2"/>
                <when input="compression" value="vbz" format="fast5.tar.bz2"/>
            </change_format>
        </data>
    </outputs>
    <tests>
        <!-- #1 default -->
        <test expect_num_outputs="1">
            <param name="input_path" value="multi.fast5.tar"/>
            <param name="compression" value="vbz"/>
            <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>