Mercurial > repos > galaxy-australia > alphafold2
diff alphafold.xml @ 16:f9eb041c518c draft
planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
author | galaxy-australia |
---|---|
date | Mon, 03 Apr 2023 01:00:42 +0000 |
parents | a58f7eb0df2c |
children | 5b85006245f3 |
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--- a/alphafold.xml Fri Mar 10 02:48:07 2023 +0000 +++ b/alphafold.xml Mon Apr 03 01:00:42 2023 +0000 @@ -2,7 +2,8 @@ <description> - AI-guided 3D structural prediction of proteins</description> <macros> <token name="@TOOL_VERSION@">2.3.1</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@TOOL_MINOR_VERSION@">2.3</token> + <token name="@VERSION_SUFFIX@">2</token> <import>macro_output.xml</import> <import>macro_test_output.xml</import> </macros> @@ -24,8 +25,11 @@ ## in planemo's gx_venv_n/bin/activate script. AlphaFold outputs will be copied ## from the test-data directory instead of running the tool. -## $ALPHAFOLD_DB variable should point to the location of the AlphaFold -## databases - defaults to /data +## $ALPHAFOLD_DB variable should point to the location containing the versioned +## AlphaFold databases - defaults to /data +## that is the directory should contain a subdir / symlink named identical as +## the value of the TOOL_MINOR_VERSION token which contains the AF reference data +## for the corresponding version ## Read FASTA input ----------------------------------------------------------- #if $fasta_or_text.input_mode == 'history': @@ -34,7 +38,7 @@ echo '$fasta_or_text.fasta_text' > input.fasta #end if -&& python3 '$__tool_directory__/validate_fasta.py' input.fasta +&& python3 '$__tool_directory__/scripts/validate_fasta.py' input.fasta --min_length \${ALPHAFOLD_AA_LENGTH_MIN:-0} --max_length \${ALPHAFOLD_AA_LENGTH_MAX:-0} #if $model_preset == 'multimer': @@ -51,26 +55,26 @@ #if os.environ.get('PLANEMO_TESTING'): ## Run in testing mode (mocks a successful AlphaFold run by copying outputs) && echo "Creating dummy outputs for model_preset=$model_preset..." - && bash '$__tool_directory__/mock_alphafold.sh' $model_preset + && bash '$__tool_directory__/scripts/mock_alphafold.sh' $model_preset #else: ## Run AlphaFold && python /app/alphafold/run_alphafold.py --fasta_paths alphafold.fasta --output_dir output - --data_dir \${ALPHAFOLD_DB:-/data} + --data_dir \${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/ --model_preset=$model_preset ## Set reference database paths - --uniref90_database_path \${ALPHAFOLD_DB:-/data}/uniref90/uniref90.fasta - --mgnify_database_path \${ALPHAFOLD_DB:-/data}/mgnify/mgy_clusters_2022_05.fa - --template_mmcif_dir \${ALPHAFOLD_DB:-/data}/pdb_mmcif/mmcif_files - --obsolete_pdbs_path \${ALPHAFOLD_DB:-/data}/pdb_mmcif/obsolete.dat + --uniref90_database_path \${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/uniref90/uniref90.fasta + --mgnify_database_path \${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/mgnify/mgy_clusters_2022_05.fa + --template_mmcif_dir \${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/pdb_mmcif/mmcif_files + --obsolete_pdbs_path \${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/pdb_mmcif/obsolete.dat #if $dbs == 'full': - --bfd_database_path \${ALPHAFOLD_DB:-/data}/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt - --uniref30_database_path \${ALPHAFOLD_DB:-/data}/uniref30/UniRef30_2021_03 + --bfd_database_path \${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt + --uniref30_database_path \${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/uniref30/UniRef30_2021_03 #else --db_preset=reduced_dbs - --small_bfd_database_path \${ALPHAFOLD_DB:-/data}/small_bfd/bfd-first_non_consensus_sequences.fasta + --small_bfd_database_path \${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/small_bfd/bfd-first_non_consensus_sequences.fasta #end if #if $max_template_date: @@ -82,16 +86,16 @@ --use_gpu_relax=\${ALPHAFOLD_USE_GPU:-True} ## introduced in v2.1.2 #if $model_preset == 'multimer': - --pdb_seqres_database_path=\${ALPHAFOLD_DB:-/data}/pdb_seqres/pdb_seqres.txt - --uniprot_database_path=\${ALPHAFOLD_DB:-/data}/uniprot/uniprot.fasta + --pdb_seqres_database_path=\${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/pdb_seqres/pdb_seqres.txt + --uniprot_database_path=\${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/uniprot/uniprot.fasta --num_multimer_predictions_per_model=1 ## introduced in v2.2.0 #else - --pdb70_database_path \${ALPHAFOLD_DB:-/data}/pdb70/pdb70 + --pdb70_database_path \${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/pdb70/pdb70 #end if #end if ## Generate additional outputs ------------------------------------------------ -&& python3 '$__tool_directory__/outputs.py' output/alphafold +&& python3 '$__tool_directory__/scripts/outputs.py' output/alphafold $outputs.plddts $outputs.model_pkls $outputs.pae_csv