Mercurial > repos > galaxy-australia > alphafold2

comparison alphafold.xml @ 10:072c324f20fc draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c8f9b460b5c5f2ef0344719d38f6be9d1a3da573
author galaxy-australia
date Fri, 16 Sep 2022 02:19:37 +0000
parents 3bd420ec162d
children c0e71cb2bd1b
comparison
equal deleted inserted replaced
9:3bd420ec162d 10:072c324f20fc
1 <tool id="alphafold" name="Alphafold 2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> 1 <tool id="alphafold" name="Alphafold 2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
2 <description> - AI-guided 3D structural prediction of proteins</description> 2 <description> - AI-guided 3D structural prediction of proteins</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">2.1.2</token> 4 <token name="@TOOL_VERSION@">2.1.2</token>
5 <token name="@VERSION_SUFFIX@">2</token> 5 <token name="@VERSION_SUFFIX@">3</token>
6 </macros> 6 </macros>
7 <edam_topics> 7 <edam_topics>
8 <edam_topic>topic_0082</edam_topic> 8 <edam_topic>topic_0082</edam_topic>
9 </edam_topics> 9 </edam_topics>
10 <edam_operations> 10 <edam_operations>
45 ## run alphafold ------------------------- 45 ## run alphafold -------------------------
46 python /app/alphafold/run_alphafold.py 46 python /app/alphafold/run_alphafold.py
47 --fasta_paths alphafold.fasta 47 --fasta_paths alphafold.fasta
48 --output_dir output 48 --output_dir output
49 --data_dir \${ALPHAFOLD_DB:-/data} 49 --data_dir \${ALPHAFOLD_DB:-/data}
50 --uniref90_database_path \${ALPHAFOLD_DB:-/data}/uniref90/uniref90.fasta
51 --mgnify_database_path \${ALPHAFOLD_DB:-/data}/mgnify/mgy_clusters_2018_12.fa
52 --template_mmcif_dir \${ALPHAFOLD_DB:-/data}/pdb_mmcif/mmcif_files
53 --obsolete_pdbs_path \${ALPHAFOLD_DB:-/data}/pdb_mmcif/obsolete.dat
54 --max_template_date=\$DATE 50 --max_template_date=\$DATE
55 --bfd_database_path \${ALPHAFOLD_DB:-/data}/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt 51
52 ## Set reference data explicitly
53 --uniref90_database_path \${ALPHAFOLD_DB:-/data}/uniref90/uniref90.fasta
54 --mgnify_database_path \${ALPHAFOLD_DB:-/data}/mgnify/mgy_clusters_2018_12.fa
55 --template_mmcif_dir \${ALPHAFOLD_DB:-/data}/pdb_mmcif/mmcif_files
56 --obsolete_pdbs_path \${ALPHAFOLD_DB:-/data}/pdb_mmcif/obsolete.dat
57 #if $dbs == 'full':
58 --bfd_database_path \${ALPHAFOLD_DB:-/data}/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt
56 --uniclust30_database_path \${ALPHAFOLD_DB:-/data}/uniclust30/uniclust30_2018_08/uniclust30_2018_08 59 --uniclust30_database_path \${ALPHAFOLD_DB:-/data}/uniclust30/uniclust30_2018_08/uniclust30_2018_08
60 #else
61 --db_preset=reduced_dbs
62 --small_bfd_database_path \${ALPHAFOLD_DB:-/data}/small_bfd/bfd-first_non_consensus_sequences.fasta
63 #end if
57 64
58 ## Param introduced in AlphaFold v2.1.2: 65 ## Param introduced in AlphaFold v2.1.2:
59 --use_gpu_relax=\${ALPHAFOLD_USE_GPU:-True} 66 --use_gpu_relax=\${ALPHAFOLD_USE_GPU:-True}
60 67
61 #if $multimer: 68 #if $multimer:
98 </when> 105 </when>
99 <when value="textbox"> 106 <when value="textbox">
100 <param name="fasta_text" type="text" area="true" value="" label="Paste sequence" help="Paste single protein sequence into the textbox. If you wish to fold multiple proteins, submit individual jobs for each protein. If you wish to run AlphaFold multimer, please supply multiple sequences in FASTA format." /> 107 <param name="fasta_text" type="text" area="true" value="" label="Paste sequence" help="Paste single protein sequence into the textbox. If you wish to fold multiple proteins, submit individual jobs for each protein. If you wish to run AlphaFold multimer, please supply multiple sequences in FASTA format." />
101 </when> 108 </when>
102 </conditional> 109 </conditional>
110
111 <param
112 name="dbs"
113 type="select"
114 display="radio"
115 label="Select database"
116 help="The reduced database allows significantly faster run time in
117 exchange for a small loss in accuracy."
118 >
119 <option value="reduced" selected="true">Reduced database</option>
120 <option value="full">Full database</option>
121 </param>
103 122
104 <param 123 <param
105 name="multimer" 124 name="multimer"
106 type="boolean" 125 type="boolean"
107 checked="false" 126 checked="false"