Mercurial > repos > iuc > data_manager_clair3_models
diff data_manager/install_clair3_models.xml @ 0:11e42265a9b0 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_clair3_models commit 2672414472cc968c736dc7d42f5a119ff8c16c62
author | iuc |
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date | Thu, 20 Feb 2025 17:57:11 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/install_clair3_models.xml Thu Feb 20 17:57:11 2025 +0000 @@ -0,0 +1,102 @@ +<tool id="data_manager_clair3_models" name="Clair3 model downloader" version="0.0.1" tool_type="manage_data" profile="23.2"> + <requirements> + <requirement type="package" version="3.12">python</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + ## this code looks up the existing table and uses it to build a list of known models + ## because models are uniquely identified by their name, downloading duplicate models + ## would be an error, so it is useful to know which models we already have + ## + ## $__app__.tool_data_tables is a dictionary where the keys are data table names and the values + ## are TabularToolDataTable objects (from lib/galaxy/tools/data/__init__.py) + ## + ## the get_fields() method on the TabularToolDataTable returns a list of lists, with one list + ## per line of the tool data table, so row[0] is the first field (i.e. the value column) + ## + + #set $data_table = $__app__.tool_data_tables.get("clair3_models") + #if $data_table is not None and len($data_table.get_fields()) > 0: + #set $known_models = ','.join([ row[0] for row in $data_table.get_fields() ]) + #set $sha256_sums = ','.join([ row[1] for row in $data_table.get_fields() ]) + #else + #set $known_models = None + #set $sha256_sums = None + #end if + + python '$__tool_directory__/model_fetcher.py' + '${output_file}' + #if $known_models is not None + --known_models '$known_models' + --sha256_sums '$sha256_sums' + #end if + #if $model_selection.source == 'latest' + --download_latest + #elif $model_selection.source == 'chosen' + --download_models '$model_selection.model_list' + #end if + ]]></command> + <inputs> + <conditional name="model_selection"> + <param name="source" label="Select the source of the list of models to download" type="select"> + <option value="latest">Latest models from Rerio page</option> + <option value="chosen">User provided list of models</option> + </param> + <when value="latest"> + </when> + <when value="chosen"> + <param name="model_list" type="text" label="List of models to download" help="A comma separated list of model to download, e.g. 'r1041_e82_400bps_sup_v430,r1041_e82_400bps_hac_v430'"> + <validator type="regex" message="Invalid model list. Format is a comma separated list of model names (e.g. 'r1041_e82_400bps_sup_v430,r1041_e82_400bps_hac_v430')">^[a-z_0-9,]+$</validator> + </param> + </when> + </conditional> + </inputs> + <outputs> + <data name="output_file" format="data_manager_json" label="Data Manager Output (JSON)" /> + </outputs> + <tests> + <test> <!-- test1 --> + <conditional name="model_selection"> + <param name="source" value="chosen"/> + <param name="model_list" value="r1041_e82_400bps_sup_v500,r1041_e82_400bps_hac_v500" /> + </conditional> + <output name="output_file"> + <assert_contents> + <!-- the text 'r1041_e82_400bps_sup_v500' is only there if the test is run for the first time (i.e. empty test-data/clair3_models.loc) so need to look for something else --> + <has_text text='clair3_models' /> + </assert_contents> + </output> + </test> + <test> <!-- test2 --> + <conditional name="model_selection"> + <param name="source" value="latest"/> + </conditional> + <output name="output_file"> + <assert_contents> + <!-- because we don't know what the names of the latest models are we can only test to see if the data table output is created --> + <has_text text='data_tables' /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + Clair3_ is a variant caller for long read data developed at the University of Hong Kong. This tool makes use of models trained to match particular + sequencing technologies and basecallers. Oxford Nanopore provides a set of models for Clair3 on their Rerio_ page. These tools are designed for + "research release" under the terms of the "Oxford Nanopore Technologies, Ltd. Public License Version 1.0" license_. This data manager allows + downloading model files from the Rerio page and installing them on a Galaxy server. + + .. _Clair3: https://github.com/HKU-BAL/Clair3 + .. _Rerio: https://github.com/nanoporetech/rerio + .. _license: https://github.com/nanoporetech/rerio/blob/master/LICENCE.txt + ]]> + </help> + <citations> + <citation type="doi">10.1101/2021.12.29.474431v2</citation> + <citation type="bibtex"><![CDATA[@misc{ONT2024, + title = {Rerio}, + author = {Oxford Nanopore Technologies}, + year = 2024, + howpublished = {\url{https://github.com/nanoporetech/rerio}}, + commit = {c0c8ce6} + }]]></citation> + </citations> +</tool>