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comparison dorado_pod5_convert.xml @ 1:28928576e1ea draft

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planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/main/tools/dorado commit c42b6e3fd2cf6d26e231645a9e8a2986503279e2
author galaxy-australia
date Mon, 22 Jul 2024 04:51:13 +0000
parents 18a8d140ec6f
children 1145758d2f0b
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0:18a8d140ec6f 1:28928576e1ea
1 <tool id="dorado_pod5_convert" name="fast5 to pod5" version="@VERSION@+galaxy0" python_template_version="3.5" profile="21.05"> 1 <tool id="dorado_pod5_convert" name="fast5 to pod5" version="@VERSION@+galaxy0" python_template_version="3.5" profile="24.1">
2 <description>converter for raw Oxford Nanopore data</description> 2 <description>converter for raw Oxford Nanopore data</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="xrefs"/> 6 <expand macro="xrefs"/>
25 </command> 25 </command>
26 <inputs> 26 <inputs>
27 <param name="fast5_in" type="data" format="fast5.tar" label="Oxford Nanopore raw data in fast5 format in a tar archive."/> 27 <param name="fast5_in" type="data" format="fast5.tar" label="Oxford Nanopore raw data in fast5 format in a tar archive."/>
28 </inputs> 28 </inputs>
29 <outputs> 29 <outputs>
30 <!-- FIXME: add pod5 datatype to Galaxy and change here. 30 <data format="pod5" name="pod5_out" label="${on_string} converted to pod5 from fast5" from_work_dir="output.pod5"/>
31 https://github.com/galaxyproject/galaxy/pull/18419 -->
32 <data format="binary" name="pod5_out" label="${on_string} converted to pod5 from fast5" from_work_dir="output.pod5"/>
33 </outputs> 31 </outputs>
34 <tests> 32 <tests>
35 <test expect_num_outputs="1"> 33 <test expect_num_outputs="1">
36 <param name="fast5_in" ftype="fast5.tar" value="FAL00375_473bf0ed_0.ten_reads.0_0.fast5.tar"/> 34 <param name="fast5_in" ftype="fast5.tar" value="FAL00375_473bf0ed_0.ten_reads.0_0.fast5.tar"/>
37 <output name="pod5_out" ftype="binary"> 35 <output name="pod5_out" ftype="pod5">
38 <assert_contents> 36 <assert_contents>
39 <has_size value="519736" delta="50000"/> 37 <has_size value="519736" delta="50000"/>
40 </assert_contents> 38 </assert_contents>
41 </output> 39 </output>
42 </test> 40 </test>
43 <test expect_num_outputs="1"> 41 <test expect_num_outputs="1">
44 <param name="fast5_in" ftype="fast5.tar.gz" value="reads_in_directories.tar.gz"/> 42 <param name="fast5_in" ftype="fast5.tar.gz" value="reads_in_directories.tar.gz"/>
45 <output name="pod5_out" ftype="binary"> 43 <output name="pod5_out" ftype="pod5">
46 <assert_contents> 44 <assert_contents>
47 <has_size value="950136" delta="90000"/> 45 <has_size value="950136" delta="90000"/>
48 </assert_contents> 46 </assert_contents>
49 </output> 47 </output>
50 </test> 48 </test>