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comparison dorado_pod5_convert.xml @ 0:18a8d140ec6f draft

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planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/main/tools/dorado commit 0e768f088307f927787041b98504c594c6bcbe0f
author galaxy-australia
date Fri, 28 Jun 2024 03:38:39 +0000
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children 28928576e1ea
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-1:000000000000 0:18a8d140ec6f
1 <tool id="dorado_pod5_convert" name="fast5 to pod5" version="@VERSION@+galaxy0" python_template_version="3.5" profile="21.05">
2 <description>converter for raw Oxford Nanopore data</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="xrefs"/>
7 <expand macro="requirements"/>
8 <command><![CDATA[
9
10 mkdir input_fast5
11
12 &&
13
14 tar -xf '$fast5_in' -C input_fast5
15
16 &&
17
18 pod5 convert fast5
19 --threads \${GALAXY_SLOTS:-4}
20 --recursive
21 --output output.pod5
22 input_fast5
23
24 ]]>
25 </command>
26 <inputs>
27 <param name="fast5_in" type="data" format="fast5.tar" label="Oxford Nanopore raw data in fast5 format in a tar archive."/>
28 </inputs>
29 <outputs>
30 <!-- FIXME: add pod5 datatype to Galaxy and change here.
31 https://github.com/galaxyproject/galaxy/pull/18419 -->
32 <data format="binary" name="pod5_out" label="${on_string} converted to pod5 from fast5" from_work_dir="output.pod5"/>
33 </outputs>
34 <tests>
35 <test expect_num_outputs="1">
36 <param name="fast5_in" ftype="fast5.tar" value="FAL00375_473bf0ed_0.ten_reads.0_0.fast5.tar"/>
37 <output name="pod5_out" ftype="binary">
38 <assert_contents>
39 <has_size value="519736" delta="50000"/>
40 </assert_contents>
41 </output>
42 </test>
43 <test expect_num_outputs="1">
44 <param name="fast5_in" ftype="fast5.tar.gz" value="reads_in_directories.tar.gz"/>
45 <output name="pod5_out" ftype="binary">
46 <assert_contents>
47 <has_size value="950136" delta="90000"/>
48 </assert_contents>
49 </output>
50 </test>
51 </tests>
52 <help><![CDATA[
53 Convert fast5 to `pod5 <https://github.com/nanoporetech/pod5-file-format>`__ for basecalling with Dorado.
54
55 Combine all your fast5 files into a single tar archive, and optionally
56 compress the archive with Gzip, Bzip2 or XZ, before uploading it to
57 Galaxy.
58
59 ]]></help>
60 </tool>