Mercurial > repos > galaxy-australia > alphafold2

comparison alphafold.xml @ 8:ca90d17ff51b draft

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"planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 03537aada92b5fff565ff48dd47c81462c5df47e"
author galaxy-australia
date Fri, 19 Aug 2022 00:29:16 +0000
parents eb085b3dbaf8
children 3bd420ec162d
comparison
equal deleted inserted replaced
7:eb085b3dbaf8 8:ca90d17ff51b
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@">0</token> 5 <token name="@VERSION_SUFFIX@">1</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>
28 #elif $fasta_or_text.input_mode == 'textbox': 28 #elif $fasta_or_text.input_mode == 'textbox':
29 echo '$fasta_or_text.fasta_text' > input.fasta && 29 echo '$fasta_or_text.fasta_text' > input.fasta &&
30 #end if 30 #end if
31 31
32 python3 '$__tool_directory__/validate_fasta.py' input.fasta 32 python3 '$__tool_directory__/validate_fasta.py' input.fasta
33 --min_length \${ALPHAFOLD_AA_LENGTH_MIN:-30} 33 --min_length \${ALPHAFOLD_AA_LENGTH_MIN:-0}
34 --max_length \${ALPHAFOLD_AA_LENGTH_MAX:-2000} 34 --max_length \${ALPHAFOLD_AA_LENGTH_MAX:-0}
35 > alphafold.fasta && 35 > alphafold.fasta &&
36 36
37 ## env vars ------------------------------- 37 ## env vars -------------------------------
38 export TF_FORCE_UNIFIED_MEMORY=1 && 38 export TF_FORCE_UNIFIED_MEMORY=1 &&
39 export XLA_PYTHON_CLIENT_MEM_FRACTION=4.0 && 39 export XLA_PYTHON_CLIENT_MEM_FRACTION=4.0 &&
51 --obsolete_pdbs_path \${ALPHAFOLD_DB:-/data}/pdb_mmcif/obsolete.dat 51 --obsolete_pdbs_path \${ALPHAFOLD_DB:-/data}/pdb_mmcif/obsolete.dat
52 --max_template_date=\$DATE 52 --max_template_date=\$DATE
53 --bfd_database_path \${ALPHAFOLD_DB:-/data}/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt 53 --bfd_database_path \${ALPHAFOLD_DB:-/data}/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt
54 --uniclust30_database_path \${ALPHAFOLD_DB:-/data}/uniclust30/uniclust30_2018_08/uniclust30_2018_08 54 --uniclust30_database_path \${ALPHAFOLD_DB:-/data}/uniclust30/uniclust30_2018_08/uniclust30_2018_08
55 ## Param introduced in AlphaFold v2.1.2: 55 ## Param introduced in AlphaFold v2.1.2:
56 --use_gpu_relax=True 56 --use_gpu_relax=\${ALPHAFOLD_USE_GPU:-True}
57 && 57 &&
58
59 ## Uncomment for "dummy" output - read output from test-data
60 ## cp -r '$__tool_directory__/output' . &&
61 58
62 ## Generate additional outputs ------------ 59 ## Generate additional outputs ------------
63 python3 '$__tool_directory__/gen_extra_outputs.py' output/alphafold $output_plddts && 60 python3 '$__tool_directory__/gen_extra_outputs.py' output/alphafold $output_plddts &&
64 61
65 ## HTML output 62 ## HTML output
73 [ -d working ] && cp -r working/* . 70 [ -d working ] && cp -r working/* .
74 71
75 ]]></command> 72 ]]></command>
76 <inputs> 73 <inputs>
77 <conditional name="fasta_or_text"> 74 <conditional name="fasta_or_text">
78 <param name="input_mode" type="select" label="Fasta Input" help="Single protein sequence to fold. Input can be fasta file from history, or text. Provide only 1 sequence per job."> 75 <param name="input_mode" type="select" label="Fasta Input" help="Single protein sequence to fold. Input can be fasta file from history, or text. Sequence must be valid IUPAC amino acid characters. Provide only 1 sequence per job.">
79 <option value="history">Use fasta from history</option> 76 <option value="history">Use fasta from history</option>
80 <option value="textbox">Paste sequence into textbox</option> 77 <option value="textbox">Paste sequence into textbox</option>
81 </param> 78 </param>
82 <when value="history"> 79 <when value="history">
83 <param name="fasta_file" type="data" format="fasta" label="Fasta file from history" help="Select single fasta protein sequence from your history. If you wish to fold multiple proteins, submit an individual job for each protein." /> 80 <param name="fasta_file" type="data" format="fasta" label="Fasta file from history" help="Select single fasta protein sequence from your history. If you wish to fold multiple proteins, submit an individual job for each protein." />