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