Mercurial > repos > galaxy-australia > dorado
changeset 1:fc5b6491cf78 draft
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 04:51:23 +0000 |
| parents | 63d8ecfcfab1 |
| children | 99c9427219d3 |
| files | README.md dorado.xml macros.xml test-data/dorado_models.loc tool-data/dorado_models.loc.sample |
| diffstat | 5 files changed, 126 insertions(+), 126 deletions(-) [+] |
line wrap: on
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--- a/README.md Fri Jun 28 03:39:11 2024 +0000 +++ b/README.md Mon Jul 22 04:51:23 2024 +0000 @@ -25,8 +25,8 @@ Because models can be added and removed, models are listed **per container** in the loc file. -Here's some code to **append** the models from the container with hash -`1c65eb070a9fc1d88710c4dc09b06541f96fdd28` to the loc file. +Here's some code to update the loc file with models from the container with hash +`1c65eb070a9fc1d88710c4dc09b06541f96fdd28`. ```bash export DORADO_HASH="1c65eb070a9fc1d88710c4dc09b06541f96fdd28" @@ -34,7 +34,7 @@ apptainer exec "docker://nanoporetech/dorado:sha${DORADO_HASH}" \ ls /models | \ awk -v hash="${DORADO_HASH}" '{print hash "_" $0 "\t" hash "\t" $0 "\t/models/" $0}' \ - >> tool-data/dorado_models.loc.sample + > tool-data/dorado_models.loc.sample ``` The loc file doesn't have a header, so you can keep it sorted.
--- a/dorado.xml Fri Jun 28 03:39:11 2024 +0000 +++ b/dorado.xml Mon Jul 22 04:51:23 2024 +0000 @@ -1,4 +1,4 @@ -<tool id="dorado" name="Dorado" version="@VERSION@+galaxy0" python_template_version="3.5" profile="21.05"> +<tool id="dorado" name="Dorado" version="@VERSION@+galaxy0" python_template_version="3.5" profile="24.1"> <description>basecaller for raw Oxford Nanopore data</description> <macros> <import>macros.xml</import> @@ -28,9 +28,7 @@ ]]></command> <inputs> - <!-- FIXME: add pod5 datatype to Galaxy and change here. - https://github.com/galaxyproject/galaxy/pull/18419 --> - <param name="pod5_file" type="data" format="binary" label="Raw pod5 file" help="Only pod5 is supported. You can convert fast5 to pod5 with the fast5 to pod5 tool."/> + <param name="pod5_file" type="data" format="pod5" label="Raw pod5 file" help="Only pod5 is supported. You can convert fast5 to pod5 with the fast5 to pod5 tool."/> <param name="model" type="select" label="Basecalling model. See the Help section for info on model names."> <options from_data_table="dorado_models"> <!-- only allow models that shipped in this container --> @@ -134,7 +132,7 @@ </output> <output name="out_tsv" ftype="tsv"> <assert_contents> - <has_size size="1103e241-dd7f-43bc-ae19-9a3c6326ad83"/> + <has_text text="1103e241-dd7f-43bc-ae19-9a3c6326ad83"/> <has_text text="SQK-RBK114-96_barcode04"/> </assert_contents> </output>
--- a/macros.xml Fri Jun 28 03:39:11 2024 +0000 +++ b/macros.xml Mon Jul 22 04:51:23 2024 +0000 @@ -1,7 +1,7 @@ <macros> <!-- UPDATING: pull the latest container and check the version. Update both tokens. You MUST also update the model list. See README.md for more. --> - <token name="@VERSION@">0.7.1+80da5f5</token> - <token name="@CONTAINER_HASH@">1c65eb070a9fc1d88710c4dc09b06541f96fdd28</token> + <token name="@VERSION@">0.7.2+9ac85c6</token> + <token name="@CONTAINER_HASH@">58b978562389bd0f1842601fb83cdf1eb2920218</token> <xml name="requirements"> <requirements> <container type="docker">nanoporetech/dorado:sha@CONTAINER_HASH@</container>
--- a/test-data/dorado_models.loc Fri Jun 28 03:39:11 2024 +0000 +++ b/test-data/dorado_models.loc Mon Jul 22 04:51:23 2024 +0000 @@ -1,58 +1,59 @@ -1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_260bps_fast@v4.1.0 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r10.4.1_e8.2_260bps_fast@v4.1.0 /models/dna_r10.4.1_e8.2_260bps_fast@v4.1.0 -1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_260bps_fast@v4.1.0_5mCG_5hmCG@v2 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r10.4.1_e8.2_260bps_fast@v4.1.0_5mCG_5hmCG@v2 /models/dna_r10.4.1_e8.2_260bps_fast@v4.1.0_5mCG_5hmCG@v2 -1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_260bps_hac@v4.1.0 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r10.4.1_e8.2_260bps_hac@v4.1.0 /models/dna_r10.4.1_e8.2_260bps_hac@v4.1.0 -1c65eb070a9fc1d88710c4dc09b06541f96fdd28_dna_r10.4.1_e8.2_260bps_hac@v4.1.0_5mCG_5hmCG@v2 1c65eb070a9fc1d88710c4dc09b06541f96fdd28 dna_r10.4.1_e8.2_260bps_hac@v4.1.0_5mCG_5hmCG@v2 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