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--- | ||
auto_tool_repositories: | ||
name_template: "{{ tool_id }}" | ||
description_template: "{{ tool_name }} from the dorado suite" | ||
categories: | ||
- Sequence Analysis | ||
description: Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. | ||
exclude: | ||
- tool_test_output.html | ||
- tool_test_output.json | ||
homepage_url: https://github.com/nanoporetech/dorado | ||
long_description: > | ||
Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. | ||
name: dorado | ||
owner: galaxy-australia | ||
remote_repository_url: https://github.com/usegalaxy-au/tools-au/tree/main/tools/dorado | ||
suite: | ||
name: suite_dorado | ||
description: > | ||
Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. | ||
long_description: > | ||
Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. | ||
type: unrestricted |
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<tool id="dorado_pod5_convert" name="fast5 to pod5" description="converter for raw Oxford Nanopore data" version="@VERSION@+galaxy0" python_template_version="3.5" profile="21.05"> | ||
<macros> | ||
<import>macros.xml</import> | ||
</macros> | ||
<expand macro="xrefs"/> | ||
<expand macro="requirements"/> | ||
<command><![CDATA[ | ||
ln -s '$fast5_in' ./input.fast5 && | ||
pod5 convert fast5 input.fast5 --output output.pod5 | ||
]]> | ||
</command> | ||
<inputs> | ||
<param name="fast5_in" type="data" format="fast5" label="Oxford Nanopore raw data in fast5 format"/> | ||
</inputs> | ||
<outputs> | ||
<data format="fast5" name="pod5_out" label="Oxford Nanopore raw data in in pod5 format" from_work_dir="output.pod5"/> | ||
</outputs> | ||
<tests> | ||
<test expect_num_outputs="1"> | ||
<param name="fast5_in" value="FAL00375_473bf0ed_0.ten_reads.0_0.fast5"/> | ||
<output name="pod5_out" file="convert.test1.pod5"/> | ||
</test> | ||
</tests> | ||
<help><![CDATA[ | ||
Convert fast5 to `pod5 <https://github.com/nanoporetech/pod5-file-format>`__ for basecalling with Dorado. | ||
]]></help> | ||
</tool> |
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