| Previous changeset 9:3bd420ec162d (2022-09-13) Next changeset 11:81d1ef460bb3 (2022-09-16) |
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Commit message:
planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c8f9b460b5c5f2ef0344719d38f6be9d1a3da573 |
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modified:
alphafold.xml |
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| diff -r 3bd420ec162d -r 072c324f20fc alphafold.xml --- a/alphafold.xml Tue Sep 13 22:04:12 2022 +0000 +++ b/alphafold.xml Fri Sep 16 02:19:37 2022 +0000 |
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| @@ -2,7 +2,7 @@ <description> - AI-guided 3D structural prediction of proteins</description> <macros> <token name="@TOOL_VERSION@">2.1.2</token> - <token name="@VERSION_SUFFIX@">2</token> + <token name="@VERSION_SUFFIX@">3</token> </macros> <edam_topics> <edam_topic>topic_0082</edam_topic> @@ -47,13 +47,20 @@ --fasta_paths alphafold.fasta --output_dir output --data_dir \${ALPHAFOLD_DB:-/data} ---uniref90_database_path \${ALPHAFOLD_DB:-/data}/uniref90/uniref90.fasta ---mgnify_database_path \${ALPHAFOLD_DB:-/data}/mgnify/mgy_clusters_2018_12.fa ---template_mmcif_dir \${ALPHAFOLD_DB:-/data}/pdb_mmcif/mmcif_files ---obsolete_pdbs_path \${ALPHAFOLD_DB:-/data}/pdb_mmcif/obsolete.dat --max_template_date=\$DATE ---bfd_database_path \${ALPHAFOLD_DB:-/data}/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt + +## Set reference data explicitly +--uniref90_database_path \${ALPHAFOLD_DB:-/data}/uniref90/uniref90.fasta +--mgnify_database_path \${ALPHAFOLD_DB:-/data}/mgnify/mgy_clusters_2018_12.fa +--template_mmcif_dir \${ALPHAFOLD_DB:-/data}/pdb_mmcif/mmcif_files +--obsolete_pdbs_path \${ALPHAFOLD_DB:-/data}/pdb_mmcif/obsolete.dat +#if $dbs == 'full': +--bfd_database_path \${ALPHAFOLD_DB:-/data}/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt --uniclust30_database_path \${ALPHAFOLD_DB:-/data}/uniclust30/uniclust30_2018_08/uniclust30_2018_08 +#else +--db_preset=reduced_dbs +--small_bfd_database_path \${ALPHAFOLD_DB:-/data}/small_bfd/bfd-first_non_consensus_sequences.fasta +#end if ## Param introduced in AlphaFold v2.1.2: --use_gpu_relax=\${ALPHAFOLD_USE_GPU:-True} @@ -102,6 +109,18 @@ </conditional> <param + name="dbs" + type="select" + display="radio" + label="Select database" + help="The reduced database allows significantly faster run time in + exchange for a small loss in accuracy." + > + <option value="reduced" selected="true">Reduced database</option> + <option value="full">Full database</option> + </param> + + <param name="multimer" type="boolean" checked="false" |