annotate single_to_multi_fast5.xml @ 1:ea77d69db382 draft

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

<?xml version="1.0"?>
<tool id="ont_fast5_api_single_to_multi_fast5" name="@TOOL_NAME@ Single to multi" version="@TOOL_VERSION@+galaxy0" profile="18.01">
    <description>read file(s)</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <version_command><![CDATA[single_to_multi -v]]></version_command>
    <command detect_errors="exit_code"><![CDATA[
## initialize
@INITIALIZE@

## run
single_to_multi_fast5
--recursive
## required
@INPUTPATH@
@SAVEPATH@
## optional
@COMPRESSION@
@BATCHSIZE@
@THREADS@

## create tarball
@TARBALL@
    ]]></command>
    <inputs>
        <expand macro="input" label="single"/>
        <expand macro="batch_size"/>
        <expand macro="compression">
            <option value="none" selected="true">None</option>
            <option value="vbz">VBZ</option>
        </expand>
    </inputs>
    <outputs>
        <expand macro="output"/>
    </outputs>
    <tests>
        <!-- #1 default -->
        <test expect_num_outputs="1">
            <param name="input_path" value="single.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="single.fast5.tar"/>
            <param name="batch_size" value="3"/>
            <param name="compression" value="vbz"/>
            <output name="out_results">
                <assert_contents>
                    <has_size value="51200"/>
                </assert_contents>
            </output>
        </test>
        <!-- #3 -->
        <test expect_num_outputs="1">
            <param name="input_path" value="single.fast5.tar"/>
            <param name="compression" value="vbz_legacy_v0"/>
            <output name="out_results">
                <assert_contents>
                    <has_size value="40960"/>
                </assert_contents>
            </output>
        </test>
        <!-- #4 -->
        <test expect_num_outputs="1">
            <param name="input_path" value="single.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@

*single_to_multi_fast5* converts single read FAST5 files into multi read FAST5 file(s).

**Input**

Single read files in FAST5 format that are stored in a flat TAR.

**Output**

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

.. class:: infomark

**References**

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