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comparison alphafold.xml @ 16:f9eb041c518c draft

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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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15:a58f7eb0df2c 16:f9eb041c518c
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@">2.3.1</token> 4 <token name="@TOOL_VERSION@">2.3.1</token>
5 <token name="@VERSION_SUFFIX@">1</token> 5 <token name="@TOOL_MINOR_VERSION@">2.3</token>
6 <token name="@VERSION_SUFFIX@">2</token>
6 <import>macro_output.xml</import> 7 <import>macro_output.xml</import>
7 <import>macro_test_output.xml</import> 8 <import>macro_test_output.xml</import>
8 </macros> 9 </macros>
9 <edam_topics> 10 <edam_topics>
10 <edam_topic>topic_0082</edam_topic> 11 <edam_topic>topic_0082</edam_topic>
22 23
23 ## Developers: to test with mock alphafold run, set `export PLANEMO_TESTING=1` 24 ## Developers: to test with mock alphafold run, set `export PLANEMO_TESTING=1`
24 ## in planemo's gx_venv_n/bin/activate script. AlphaFold outputs will be copied 25 ## in planemo's gx_venv_n/bin/activate script. AlphaFold outputs will be copied
25 ## from the test-data directory instead of running the tool. 26 ## from the test-data directory instead of running the tool.
26 27
27 ## $ALPHAFOLD_DB variable should point to the location of the AlphaFold 28 ## $ALPHAFOLD_DB variable should point to the location containing the versioned
28 ## databases - defaults to /data 29 ## AlphaFold databases - defaults to /data
30 ## that is the directory should contain a subdir / symlink named identical as
31 ## the value of the TOOL_MINOR_VERSION token which contains the AF reference data
32 ## for the corresponding version
29 33
30 ## Read FASTA input ----------------------------------------------------------- 34 ## Read FASTA input -----------------------------------------------------------
31 #if $fasta_or_text.input_mode == 'history': 35 #if $fasta_or_text.input_mode == 'history':
32 cp '$fasta_or_text.fasta_file' input.fasta 36 cp '$fasta_or_text.fasta_file' input.fasta
33 #elif $fasta_or_text.input_mode == 'textbox': 37 #elif $fasta_or_text.input_mode == 'textbox':
34 echo '$fasta_or_text.fasta_text' > input.fasta 38 echo '$fasta_or_text.fasta_text' > input.fasta
35 #end if 39 #end if
36 40
37 && python3 '$__tool_directory__/validate_fasta.py' input.fasta 41 && python3 '$__tool_directory__/scripts/validate_fasta.py' input.fasta
38 --min_length \${ALPHAFOLD_AA_LENGTH_MIN:-0} 42 --min_length \${ALPHAFOLD_AA_LENGTH_MIN:-0}
39 --max_length \${ALPHAFOLD_AA_LENGTH_MAX:-0} 43 --max_length \${ALPHAFOLD_AA_LENGTH_MAX:-0}
40 #if $model_preset == 'multimer': 44 #if $model_preset == 'multimer':
41 --multimer 45 --multimer
42 #end if 46 #end if
49 53
50 ## Run AlphaFold ------------------------------------------------------------- 54 ## Run AlphaFold -------------------------------------------------------------
51 #if os.environ.get('PLANEMO_TESTING'): 55 #if os.environ.get('PLANEMO_TESTING'):
52 ## Run in testing mode (mocks a successful AlphaFold run by copying outputs) 56 ## Run in testing mode (mocks a successful AlphaFold run by copying outputs)
53 && echo "Creating dummy outputs for model_preset=$model_preset..." 57 && echo "Creating dummy outputs for model_preset=$model_preset..."
54 && bash '$__tool_directory__/mock_alphafold.sh' $model_preset 58 && bash '$__tool_directory__/scripts/mock_alphafold.sh' $model_preset
55 #else: 59 #else:
56 ## Run AlphaFold 60 ## Run AlphaFold
57 && python /app/alphafold/run_alphafold.py 61 && python /app/alphafold/run_alphafold.py
58 --fasta_paths alphafold.fasta 62 --fasta_paths alphafold.fasta
59 --output_dir output 63 --output_dir output
60 --data_dir \${ALPHAFOLD_DB:-/data} 64 --data_dir \${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/
61 --model_preset=$model_preset 65 --model_preset=$model_preset
62 66
63 ## Set reference database paths 67 ## Set reference database paths
64 --uniref90_database_path \${ALPHAFOLD_DB:-/data}/uniref90/uniref90.fasta 68 --uniref90_database_path \${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/uniref90/uniref90.fasta
65 --mgnify_database_path \${ALPHAFOLD_DB:-/data}/mgnify/mgy_clusters_2022_05.fa 69 --mgnify_database_path \${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/mgnify/mgy_clusters_2022_05.fa
66 --template_mmcif_dir \${ALPHAFOLD_DB:-/data}/pdb_mmcif/mmcif_files 70 --template_mmcif_dir \${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/pdb_mmcif/mmcif_files
67 --obsolete_pdbs_path \${ALPHAFOLD_DB:-/data}/pdb_mmcif/obsolete.dat 71 --obsolete_pdbs_path \${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/pdb_mmcif/obsolete.dat
68 #if $dbs == 'full': 72 #if $dbs == 'full':
69 --bfd_database_path \${ALPHAFOLD_DB:-/data}/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt 73 --bfd_database_path \${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt
70 --uniref30_database_path \${ALPHAFOLD_DB:-/data}/uniref30/UniRef30_2021_03 74 --uniref30_database_path \${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/uniref30/UniRef30_2021_03
71 #else 75 #else
72 --db_preset=reduced_dbs 76 --db_preset=reduced_dbs
73 --small_bfd_database_path \${ALPHAFOLD_DB:-/data}/small_bfd/bfd-first_non_consensus_sequences.fasta 77 --small_bfd_database_path \${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/small_bfd/bfd-first_non_consensus_sequences.fasta
74 #end if 78 #end if
75 79
76 #if $max_template_date: 80 #if $max_template_date:
77 --max_template_date=$max_template_date 81 --max_template_date=$max_template_date
78 #else 82 #else
80 #end if 84 #end if
81 85
82 --use_gpu_relax=\${ALPHAFOLD_USE_GPU:-True} ## introduced in v2.1.2 86 --use_gpu_relax=\${ALPHAFOLD_USE_GPU:-True} ## introduced in v2.1.2
83 87
84 #if $model_preset == 'multimer': 88 #if $model_preset == 'multimer':
85 --pdb_seqres_database_path=\${ALPHAFOLD_DB:-/data}/pdb_seqres/pdb_seqres.txt 89 --pdb_seqres_database_path=\${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/pdb_seqres/pdb_seqres.txt
86 --uniprot_database_path=\${ALPHAFOLD_DB:-/data}/uniprot/uniprot.fasta 90 --uniprot_database_path=\${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/uniprot/uniprot.fasta
87 --num_multimer_predictions_per_model=1 ## introduced in v2.2.0 91 --num_multimer_predictions_per_model=1 ## introduced in v2.2.0
88 #else 92 #else
89 --pdb70_database_path \${ALPHAFOLD_DB:-/data}/pdb70/pdb70 93 --pdb70_database_path \${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/pdb70/pdb70
90 #end if 94 #end if
91 #end if 95 #end if
92 96
93 ## Generate additional outputs ------------------------------------------------ 97 ## Generate additional outputs ------------------------------------------------
94 && python3 '$__tool_directory__/outputs.py' output/alphafold 98 && python3 '$__tool_directory__/scripts/outputs.py' output/alphafold
95 $outputs.plddts 99 $outputs.plddts
96 $outputs.model_pkls 100 $outputs.model_pkls
97 $outputs.pae_csv 101 $outputs.pae_csv
98 $outputs.plots 102 $outputs.plots
99 #if $model_preset == 'multimer': 103 #if $model_preset == 'multimer':