Mercurial > repos > galaxy-australia > alphafold2

annotate alphafold.xml @ 20:6ab1a261520a draft default tip

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 c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
author galaxy-australia
date Sun, 28 Jul 2024 20:09:55 +0000
parents 2f7702fd0a4c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
20
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
1 <tool id="alphafold" name="Alphafold 2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
5
138feebde7d3 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit c7fcba69096f16e6a5cfc03d363d4db28b16807f"
galaxy-australia
parents: 4
diff changeset
2 <description> - AI-guided 3D structural prediction of proteins</description>
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
3 <macros>
20
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
4 <token name="@TOOL_VERSION@">2.3.2</token>
16
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents: 15
diff changeset
5 <token name="@TOOL_MINOR_VERSION@">2.3</token>
20
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
6 <token name="@VERSION_SUFFIX@">0</token>
15
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
7 <import>macro_output.xml</import>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
8 <import>macro_test_output.xml</import>
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
9 </macros>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
10 <edam_topics>
1
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
11 <edam_topic>topic_0082</edam_topic>
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
12 </edam_topics>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
13 <edam_operations>
1
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
14 <edam_operation>operation_0474</edam_operation>
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
15 </edam_operations>
1
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
16 <xrefs>
14
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
17 <xref type="bio.tools">alphafold_2</xref>
1
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
18 </xrefs>
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
19 <requirements>
20
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
20 <container type="docker">neoformit/alphafold:v2.3.2_0</container>
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
21 </requirements>
17
5b85006245f3 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 2e1eba8094c506a99a844546e8343849d3cef694
galaxy-australia
parents: 16
diff changeset
22 <required_files>
5b85006245f3 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 2e1eba8094c506a99a844546e8343849d3cef694
galaxy-australia
parents: 16
diff changeset
23 <include path="scripts/outputs.py" />
5b85006245f3 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 2e1eba8094c506a99a844546e8343849d3cef694
galaxy-australia
parents: 16
diff changeset
24 <include path="scripts/validate_fasta.py" />
20
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
25 <include path="scripts/alphafold.html" />
17
5b85006245f3 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 2e1eba8094c506a99a844546e8343849d3cef694
galaxy-australia
parents: 16
diff changeset
26 </required_files>
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
27 <command detect_errors="exit_code"><![CDATA[
1
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
28
15
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
29 ## Developers: to test with mock alphafold run, set `export PLANEMO_TESTING=1`
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
30 ## in planemo's gx_venv_n/bin/activate script. AlphaFold outputs will be copied
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
31 ## from the test-data directory instead of running the tool.
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
32
16
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents: 15
diff changeset
33 ## $ALPHAFOLD_DB variable should point to the location containing the versioned
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents: 15
diff changeset
34 ## AlphaFold databases - defaults to /data
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents: 15
diff changeset
35 ## that is the directory should contain a subdir / symlink named identical as
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents: 15
diff changeset
36 ## the value of the TOOL_MINOR_VERSION token which contains the AF reference data
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents: 15
diff changeset
37 ## for the corresponding version
1
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
38
15
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
39 ## Read FASTA input -----------------------------------------------------------
1
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
40 #if $fasta_or_text.input_mode == 'history':
14
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
41 cp '$fasta_or_text.fasta_file' input.fasta
1
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
42 #elif $fasta_or_text.input_mode == 'textbox':
14
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
43 echo '$fasta_or_text.fasta_text' > input.fasta
1
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
44 #end if
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
45
16
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents: 15
diff changeset
46 && python3 '$__tool_directory__/scripts/validate_fasta.py' input.fasta
8
ca90d17ff51b "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 03537aada92b5fff565ff48dd47c81462c5df47e"
galaxy-australia
parents: 7
diff changeset
47 --min_length \${ALPHAFOLD_AA_LENGTH_MIN:-0}
ca90d17ff51b "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 03537aada92b5fff565ff48dd47c81462c5df47e"
galaxy-australia
parents: 7
diff changeset
48 --max_length \${ALPHAFOLD_AA_LENGTH_MAX:-0}
20
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
49 #if $model_preset.selection == 'multimer':
9
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468
galaxy-australia
parents: 8
diff changeset
50 --multimer
19
2f7702fd0a4c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit cd0379c8ecc24977dffa462c1897d402c85fa4e6
galaxy-australia
parents: 18
diff changeset
51 --max-sequences \${ALPHAFOLD_MAX_SEQUENCES:-10}
9
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468
galaxy-australia
parents: 8
diff changeset
52 #end if
14
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
53 > alphafold.fasta
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
54
15
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
55 ## Env vars -------------------------------------------------------------------
14
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
56 && export TF_FORCE_UNIFIED_MEMORY=1
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
57 && export XLA_PYTHON_CLIENT_MEM_FRACTION=4.0
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
58 && export TODAY=`date +"%Y-%m-%d"`
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
59
15
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
60 ## Run AlphaFold -------------------------------------------------------------
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
61 #if os.environ.get('PLANEMO_TESTING'):
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
62 ## Run in testing mode (mocks a successful AlphaFold run by copying outputs)
20
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
63 && echo "Creating dummy outputs for model_preset=$model_preset.selection..."
16
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents: 15
diff changeset
64 && bash '$__tool_directory__/scripts/mock_alphafold.sh' $model_preset
15
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
65 #else:
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
66 ## Run AlphaFold
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
67 && python /app/alphafold/run_alphafold.py
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
68 --fasta_paths alphafold.fasta
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
69 --output_dir output
16
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents: 15
diff changeset
70 --data_dir \${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/
20
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
71 --model_preset=$model_preset.selection
9
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468
galaxy-australia
parents: 8
diff changeset
72
15
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
73 ## Set reference database paths
16
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents: 15
diff changeset
74 --uniref90_database_path \${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/uniref90/uniref90.fasta
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents: 15
diff changeset
75 --mgnify_database_path \${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/mgnify/mgy_clusters_2022_05.fa
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents: 15
diff changeset
76 --template_mmcif_dir \${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/pdb_mmcif/mmcif_files
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents: 15
diff changeset
77 --obsolete_pdbs_path \${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/pdb_mmcif/obsolete.dat
15
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
78 #if $dbs == 'full':
16
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents: 15
diff changeset
79 --bfd_database_path \${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents: 15
diff changeset
80 --uniref30_database_path \${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/uniref30/UniRef30_2021_03
15
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
81 #else
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
82 --db_preset=reduced_dbs
16
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents: 15
diff changeset
83 --small_bfd_database_path \${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/small_bfd/bfd-first_non_consensus_sequences.fasta
15
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
84 #end if
14
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
85
20
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
86 #if $advanced.max_template_date:
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
87 --max_template_date=$advanced.max_template_date
15
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
88 #else
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
89 --max_template_date=\$TODAY
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
90 #end if
9
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468
galaxy-australia
parents: 8
diff changeset
91
20
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
92 --use_gpu_relax=\${ALPHAFOLD_USE_GPU:-True}
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
93
20
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
94 #if $model_preset.selection == 'multimer':
16
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents: 15
diff changeset
95 --pdb_seqres_database_path=\${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/pdb_seqres/pdb_seqres.txt
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents: 15
diff changeset
96 --uniprot_database_path=\${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/uniprot/uniprot.fasta
20
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
97 --num_multimer_predictions_per_model=$model_preset.num_multimer_predictions_per_model
15
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
98 #else
16
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents: 15
diff changeset
99 --pdb70_database_path \${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/pdb70/pdb70
15
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
100 #end if
20
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
101
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
102 ## Galaxy-specific options --------------------------------------------
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
103 ## See https://github.com/neoformit/alphafold/tree/release_2.3.2_galaxy
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
104 #if $advanced.disable_amber_relax:
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
105 --disable_amber_relax
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
106 #end if
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
107
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
108 #if $advanced.limit_model_outputs:
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
109 --output_models=$limit_model_outputs
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
110 #end if
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
111 ## End Galaxy-specific options ----------------------------------------
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
112
15
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
113 #end if
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
114
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
115 ## Generate additional outputs ------------------------------------------------
16
f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
galaxy-australia
parents: 15
diff changeset
116 && python3 '$__tool_directory__/scripts/outputs.py' output/alphafold
15
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
117 $outputs.plddts
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
118 $outputs.model_pkls
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
119 $outputs.pae_csv
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
120 $outputs.plots
20
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
121 #if $model_preset.selection == 'multimer':
9
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468
galaxy-australia
parents: 8
diff changeset
122 --multimer
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468
galaxy-australia
parents: 8
diff changeset
123 #end if
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
124
1
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
galaxy-australia
parents: 0
diff changeset
125 ## HTML output
14
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
126 && mkdir -p '${ html.files_path }'
20
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
127 && cp output/alphafold/extra/alphafold.html '${html}'
14
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
128 && cp output/alphafold/ranked_*.pdb '${html.files_path}'
4
bc99b0a951ec "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 2d7c3d151feaafc3be33ebb0081ec640680fbb4d-dirty"
galaxy-australia
parents: 3
diff changeset
129
bc99b0a951ec "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 2d7c3d151feaafc3be33ebb0081ec640680fbb4d-dirty"
galaxy-australia
parents: 3
diff changeset
130 ## This is a (hacky) fix for a bug that has appeared in multiple Pulsar servers.
bc99b0a951ec "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 2d7c3d151feaafc3be33ebb0081ec640680fbb4d-dirty"
galaxy-australia
parents: 3
diff changeset
131 ## The working directory ends up two levels deep and the visualization html page
bc99b0a951ec "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 2d7c3d151feaafc3be33ebb0081ec640680fbb4d-dirty"
galaxy-australia
parents: 3
diff changeset
132 ## fails to load the PDB files as static assets.
14
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
133 && (([ -d working ] && cp -r working/* .) || true)
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
134
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
135 ]]></command>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
136 <inputs>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
137 <conditional name="fasta_or_text">
14
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
138 <param name="input_mode" type="select" label="Fasta Input" help="Protein sequence(s) to fold. Input can be fasta file from history, or text. Sequence must be valid IUPAC amino acid characters. If multiple-sequence FASTA file provided, multimer mode must be selected.">
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
139 <option value="history">Use fasta from history</option>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
140 <option value="textbox">Paste sequence into textbox</option>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
141 </param>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
142 <when value="history">
9
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468
galaxy-australia
parents: 8
diff changeset
143 <param name="fasta_file" type="data" multiple="false" format="fasta" label="Fasta file from history" help="Select single FASTA protein file from your history. If you wish to fold multiple proteins, submit an individual job for each protein. If you wish to run AlphaFold multimer, please supply multiple sequences in this file." />
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
144 </when>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
145 <when value="textbox">
9
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468
galaxy-australia
parents: 8
diff changeset
146 <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." />
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
147 </when>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
148 </conditional>
9
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468
galaxy-australia
parents: 8
diff changeset
149
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468
galaxy-australia
parents: 8
diff changeset
150 <param
10
072c324f20fc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c8f9b460b5c5f2ef0344719d38f6be9d1a3da573
galaxy-australia
parents: 9
diff changeset
151 name="dbs"
072c324f20fc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c8f9b460b5c5f2ef0344719d38f6be9d1a3da573
galaxy-australia
parents: 9
diff changeset
152 type="select"
072c324f20fc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c8f9b460b5c5f2ef0344719d38f6be9d1a3da573
galaxy-australia
parents: 9
diff changeset
153 display="radio"
072c324f20fc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c8f9b460b5c5f2ef0344719d38f6be9d1a3da573
galaxy-australia
parents: 9
diff changeset
154 label="Select database"
072c324f20fc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c8f9b460b5c5f2ef0344719d38f6be9d1a3da573
galaxy-australia
parents: 9
diff changeset
155 help="The reduced database allows significantly faster run time in
072c324f20fc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c8f9b460b5c5f2ef0344719d38f6be9d1a3da573
galaxy-australia
parents: 9
diff changeset
156 exchange for a small loss in accuracy."
072c324f20fc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c8f9b460b5c5f2ef0344719d38f6be9d1a3da573
galaxy-australia
parents: 9
diff changeset
157 >
072c324f20fc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c8f9b460b5c5f2ef0344719d38f6be9d1a3da573
galaxy-australia
parents: 9
diff changeset
158 <option value="reduced" selected="true">Reduced database</option>
072c324f20fc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c8f9b460b5c5f2ef0344719d38f6be9d1a3da573
galaxy-australia
parents: 9
diff changeset
159 <option value="full">Full database</option>
072c324f20fc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c8f9b460b5c5f2ef0344719d38f6be9d1a3da573
galaxy-australia
parents: 9
diff changeset
160 </param>
072c324f20fc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c8f9b460b5c5f2ef0344719d38f6be9d1a3da573
galaxy-australia
parents: 9
diff changeset
161
20
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
162 <conditional name="model_preset">
10
072c324f20fc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c8f9b460b5c5f2ef0344719d38f6be9d1a3da573
galaxy-australia
parents: 9
diff changeset
163 <param
20
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
164 name="selection"
15
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
165 type="select"
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
166 label="Model preset"
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
167 help="Select which prediction model to run. The monomer model is the most accurate for single protein prediction. The multimer model allows prediction of protein complexes."
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
168 >
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
169 <option value="monomer" selected="true">monomer - default prediction model</option>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
170 <option value="monomer_ptm">
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
171 monomer_ptm - slightly less accurate version of the monomer model, but provides a pairwise alignment error (PAE) matrix
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
172 </option>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
173 <option value="multimer">
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
174 multimer - model a protein complex (requires multi-sequence FASTA input)
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
175 </option>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
176 </param>
20
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
177 <when value="monomer"></when>
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
178 <when value="monomer_ptm"></when>
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
179 <when value="multimer">
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
180 <param
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
181 name="num_multimer_predictions_per_model"
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
182 type="integer"
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
183 value="5"
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
184 label="Multimer predictions per model"
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
185 help="How many predictions (each with a different random seed) will be generated per model. E.g. if this is 2 and there are 5 models then there will be 10 predictions per input. For a small drop in accuracy you may wish to run a single seed per model (default 5, max 10)."
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
186 min="1"
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
187 max="10"
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
188 />
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
189 </when>
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
190 </conditional>
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
191
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
192 <section name="advanced" title="Advanced options" expanded="false">
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
193 <param
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
194 name="max_template_date"
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
195 type="text"
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
196 label="Max template date (yyyy-mm-dd) (optional)"
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
197 help="The model will reference PDB structures deposited before this date only. Defaults to today's date."
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
198 optional="true"
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
199 >
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
200 <sanitizer>
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
201 <valid initial="string.digits">
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
202 <add value="-" />
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
203 </valid>
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
204 </sanitizer>
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
205 <validator type="regex">[0-9]{4}-[0-9]{2}-[0-9]{2}</validator>
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
206 </param>
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
207
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
208 <param
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
209 name="disable_amber_relax"
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
210 type="boolean"
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
211 label="Disable Amber relaxation"
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
212 value="false"
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
213 optional="true"
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
214 help="Amber relaxation can be disabled to speed up processing time. Amber relaxation is used to refine predicted structures by removing stereochemical violations, resulting in more accurate prediction of side-chain geometry. Disabling this option with large proteins may lead to artefacts in the predicted structure. Disabling amber relax will result in the unrelaxed models being collected as PDB outputs."
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
215 />
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
216
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
217 <param
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
218 name="limit_model_outputs"
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
219 type="integer"
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
220 label="Limit model outputs"
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
221 value="5"
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
222 help="Limit the number of models to output. The top N models will be output, where N is the value entered here (default 5). Please note that the top-ranking model is not always the correct one, and it is usually recommended to inspect multiple models. Reducing the number of models will result in a slight reduction in run time."
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
223 min="1"
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
224 max="5"
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
225 />
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
226 </section>
9
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468
galaxy-australia
parents: 8
diff changeset
227
14
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
228 <section name="outputs" title="Optional outputs" expanded="false">
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
229 <param
15
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
230 name="plots"
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
231 type="boolean"
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
232 checked="false"
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
233 truevalue="--plot"
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
234 falsevalue=""
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
235 label="pLDDT and PAE matrix plots (per model)"
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
236 help="A two-panel plot showing pLDDT against residue position (left) and PAE (paired-alignment error) as a heatmap image with residue numbers running along vertical and horizontal axes and color at each pixel indicating PAE value for the corresponding pair of residues. (right). PAE heatmap is only produced with monomer_ptm and multimer model presets."
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
237 />
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
238 <param
14
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
239 name="confidence_scores"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
240 type="boolean"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
241 checked="false"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
242 label="Per-model confidence scores"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
243 help="A tabular file showing average confidence score for each model (predicted template modelling (PTM) score; interface PTM is incorporated into this score for multimer predictions)."
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
244 />
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
245 <param
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
246 name="plddts"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
247 type="boolean"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
248 checked="false"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
249 label="Per-residue confidence scores"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
250 truevalue="--plddts"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
251 falsevalue=""
15
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
252 help="Alphafold produces a pLDDT score between 0-100 for each residue in the folded models. High scores represent high confidence in placement for the residue, while low scoring residues have lower confidence. This output is a tabular file with five rows (one for each output PDB model), with each column providing a pLDDT score for a single residue."
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
253 />
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
254 <param
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
255 name="pae_csv"
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
256 type="boolean"
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
257 checked="false"
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
258 truevalue="--pae"
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
259 falsevalue=""
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
260 label="Paired-alignment error (PAE)"
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
261 help="A CSV-formatted matrix for each model. Only available for monomer_ptm and multimer model presets. Predicted aligned error (PAE) gives a distance error for every pair of residues. It gives AlphaFold's estimate of position error at residue X when the predicted and true structures are aligned on residue Y. Values range from 0 - 35 Angstroms."
14
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
262 />
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
263 <param
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
264 name="model_pkls"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
265 type="boolean"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
266 checked="false"
15
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
267 truevalue="--pkl"
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
268 falsevalue=""
14
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
269 label="ranked_*.pkl"
15
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
270 help="A pickle file containing metrics used for the assessment of the model's accuracy. These include per-residue pLDDT scores (see above), predicted TM (Template Modelling) score, which is a global superposition metric and predicted aligned error (a matrix size (number of residues) x (number of residues) where each position describes the confidence of the residue's 3D position relative to another residue in the model; can be used for the interpretation of relative positions of domains). Pickle files can be read and processed using the Python 'pickle' library (requires the jax Python library). Outputs are named respective to PDB outputs."
14
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
271 />
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
272 <param
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
273 name="relax_json"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
274 type="boolean"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
275 checked="false"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
276 label="relax_metrics.json"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
277 help="A JSON-formatted text file containing relax metrics (mostly remaining violations)."
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
278 />
20
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
279 <param
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
280 name="timings_json"
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
281 type="boolean"
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
282 checked="false"
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
283 label="timings.json"
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
284 help="A JSON file with timings reported for each phase of the AlphaFold run."
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
285 />
14
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
286 </section>
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
287 </inputs>
9
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468
galaxy-australia
parents: 8
diff changeset
288
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
289 <outputs>
15
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
290 <expand macro="output_pdb_models" />
14
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
291 <data name="html" format="html" label="${tool.name} on ${on_string}: Visualization" />
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
292 <!-- Optional outputs -->
15
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
293 <expand macro="output_plddts" />
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
294 <expand macro="output_confidence_scores" />
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
295 <expand macro="output_pickles" />
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
296 <expand macro="output_pae_csv" />
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
297 <expand macro="output_plots" />
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
298 <expand macro="output_relax_json" />
20
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
299 <expand macro="output_timings_json" />
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
300 </outputs>
14
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
301
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
302 <tests>
15
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
303 <!-- Test monomer with default outputs -->
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
304 <test expect_num_outputs="6">
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
305 <conditional name="fasta_or_text">
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
306 <param name="input_mode" value="history"/>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
307 <param name="fasta_file" value="test1.fasta"/>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
308 </conditional>
20
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
309 <param name="model_preset|selection" value="monomer"/>
15
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
310 <expand macro="test_output_pdb_models" />
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
311 </test>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
312
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
313 <!-- Test monomer with all outputs -->
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
314 <test expect_num_outputs="19">
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
315 <conditional name="fasta_or_text">
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
316 <param name="input_mode" value="history"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
317 <param name="fasta_file" value="test1.fasta"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
318 </conditional>
20
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
319 <param name="model_preset|selection" value="monomer"/>
15
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
320 <param name="outputs|plots" value="true"/>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
321 <param name="outputs|confidence_scores" value="true"/>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
322 <param name="outputs|plddts" value="true"/>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
323 <param name="outputs|pae_csv" value="true"/>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
324 <param name="outputs|model_pkls" value="true"/>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
325 <param name="outputs|relax_json" value="true"/>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
326 <expand macro="test_output_plots_1" />
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
327 <expand macro="test_output_confidence_scores" />
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
328 <expand macro="test_output_plddts" />
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
329 <expand macro="test_output_pdb_models" />
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
330 <expand macro="test_output_pickles" />
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
331 <expand macro="test_output_relax_json" />
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
332 </test>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
333
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
334 <!-- Test monomer_ptm with all outputs -->
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
335 <test expect_num_outputs="24">
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
336 <conditional name="fasta_or_text">
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
337 <param name="input_mode" value="history"/>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
338 <param name="fasta_file" value="test1.fasta"/>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
339 </conditional>
20
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
340 <param name="model_preset|selection" value="monomer_ptm"/>
15
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
341 <param name="outputs|plots" value="true"/>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
342 <param name="outputs|confidence_scores" value="true"/>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
343 <param name="outputs|plddts" value="true"/>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
344 <param name="outputs|pae_csv" value="true"/>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
345 <param name="outputs|model_pkls" value="true"/>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
346 <param name="outputs|relax_json" value="true"/>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
347 <expand macro="test_output_plots_2" />
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
348 <expand macro="test_output_confidence_scores" />
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
349 <expand macro="test_output_plddts" />
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
350 <expand macro="test_output_pdb_models" />
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
351 <expand macro="test_output_pickles" />
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
352 <expand macro="test_output_relax_json" />
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
353 <expand macro="test_output_pae_csv" />
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
354 </test>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
355
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
356 <!-- Test multimer with all outputs -->
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
357 <test expect_num_outputs="24">
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
358 <conditional name="fasta_or_text">
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
359 <param name="input_mode" value="history"/>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
360 <param name="fasta_file" value="multimer.fasta"/>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
361 </conditional>
20
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
362 <param name="model_preset|selection" value="multimer"/>
15
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
363 <param name="outputs|plots" value="true"/>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
364 <param name="outputs|confidence_scores" value="true"/>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
365 <param name="outputs|plddts" value="true"/>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
366 <param name="outputs|pae_csv" value="true"/>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
367 <param name="outputs|model_pkls" value="true"/>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
368 <param name="outputs|relax_json" value="true"/>
20
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
369 <param name="outputs|timings_json" value="true"/>
15
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
370 <expand macro="test_output_plots_3" />
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
371 <expand macro="test_output_confidence_scores" />
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
372 <expand macro="test_output_plddts" />
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
373 <expand macro="test_output_pdb_models" />
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
374 <expand macro="test_output_pickles" />
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
375 <expand macro="test_output_relax_json" />
20
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
376 <expand macro="test_output_timings_json" />
15
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
377 <expand macro="test_output_pae_csv" />
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
378 </test>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
379 </tests>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
380 <help><![CDATA[
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
381
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
382 .. class:: infomark
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
383
14
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
384 | AlphaFold v2: AI-guided 3D structural prediction of proteins
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
385 |
20
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
386 | **NOTE: this tool packages** `a modified branch of AlphaFold v2.3.2. <https://github.com/neoformit/alphafold/tree/release_2.3.2_galaxy>`_
14
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
387 |
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
388 | This means that the neural network has been trained on PDBs with a release
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
389 | date before 2021-09-30 (the training cutoff was 2018-04-30 until ``v2.3.0``).
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
390 |
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
391 | Find out more in the technical and release notes:
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
392 |
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
393
20
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
394 - `Release notes for v2.3.2 <https://github.com/deepmind/alphafold/releases/tag/v2.3.2>`_
14
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
395 - `Technical notes for v2.3 <https://github.com/deepmind/alphafold/blob/main/docs/technical_note_v2.3.0.md>`_
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
396
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
397 **What it does**
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
398
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
399 *What is AlphaFold?*
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
400
14
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
401 | AlphaFold is a program which uses neural networks to predict the tertiary (3D) structure of proteins. AlphaFold accepts an amino acid sequence in Fasta format, which will be "folded" into a 3D model.
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
402 |
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
403
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
404 *What makes AlphaFold different?*
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
405
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
406 | The ability to use computers to predict 3D protein structures with high accuracy is desirable because it removes the time-consuming and costly process of determining structures experimentally.
14
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
407 | In-silico protein folding has been an active field of research for decades, but existing tools were slower and far less reliable than AlphaFold.
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
408 | AlphaFold represents a leap forward by regularly predicting structures to atomic-level accuracy, even when no similar structures are known.
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
409 |
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
410
9
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468
galaxy-australia
parents: 8
diff changeset
411
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
412 **Input**
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
413
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
414 *Amino acid sequence*
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
415
9
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468
galaxy-australia
parents: 8
diff changeset
416 | AlphaFold monomer (default) accepts a **single amino acid sequence** in FASTA format.
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
417 | You can choose to input either a file from your Galaxy history or paste a sequence into a text box.
9
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468
galaxy-australia
parents: 8
diff changeset
418 | If you choose the ``multimer`` option, you can supply a FASTA file containing **multiple sequences** to be folded concurrently into a multimer.
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468
galaxy-australia
parents: 8
diff changeset
419 |
20
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
420 | For pairwise screening of target-candidate with multimer, you can submit a list of paired protein sequences in batch mode (i.e. two protein sequences in each FASTA file).
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
421 |
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
422
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
423 **Outputs**
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
424
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
425 *Visualization*
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
426
9
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468
galaxy-australia
parents: 8
diff changeset
427 An interactive 3D graphic of the best predicted molecular structures.
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468
galaxy-australia
parents: 8
diff changeset
428 This output can be opened in Galaxy to give a visual impression of the results, with different structural representations to choose from.
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468
galaxy-australia
parents: 8
diff changeset
429 Open the "Visualization" history output by clicking on the "view data" icon:
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
430
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
431 .. image:: https://github.com/usegalaxy-au/galaxy-local-tools/blob/1a8d3e8daa7ccc5a345ca377697735ab95ed0666/tools/alphafold/static/img/alphafold-visualization.png?raw=true
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
432 :height: 520
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
433 :alt: Result visualization
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
434
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
435 |
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
436
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
437 *PDB files*
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
438
20
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
439 | PDB (Protein Data Bank) files (5 by default) are be created, ordered by rank, as predicted by AlphaFold. The tool produces 5 models by default, but this can be reduced with the "Limit model outputs" for a reduced run time.
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
440 | These files describe the molecular structures and can be used for downstream analysis. e.g. *in silico* molecular docking.
14
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
441 | **PLEASE NOTE** that all outputs have been renamed to their respective rank order, including model and model.pkl files.
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
442 |
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
443
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
444 *Model confidence scores (optional)*
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
445
9
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468
galaxy-australia
parents: 8
diff changeset
446 | This optional output produces a file which describes the confidence scores for each model (based on `pLDDTs <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3799472/>`_, or the ``iptm+ptm`` score if run in multimer mode) which may be useful for downstream analysis.
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468
galaxy-australia
parents: 8
diff changeset
447 | Model confidence scores are also included as a column (replacing ``bFactor``) in the default PDB output.
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468
galaxy-australia
parents: 8
diff changeset
448 |
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468
galaxy-australia
parents: 8
diff changeset
449 |
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468
galaxy-australia
parents: 8
diff changeset
450
14
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
451 *Model data files (ranked_n.pkl)*
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
452
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
453 | Per-model data stored in pickle files (a Python binary data format). These files can be used as inputs to downstream analysis software (such as Chimera X) for visualizing structures and computing kinetics between protein multimers and domains.
15
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
454 | The tool will produce one ``.pkl`` output for each PDB model.
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
455 |
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
456 |
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
457
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
458 *pLDDT + PAE plots (optional)*
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
459
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
460 | A two-panel figure in PNG format showing:
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
461 | a) pLDDT score plotted against residue position
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
462 | b) a heatmap of predicted-alignment error (PAE) with residue position running along vertical and horizontal axes and color at each pixel indicating PAE value for the corresponding pair of residues.
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
463 | Panel b) is only produced for ``monomer_ptm`` and ``multimer`` model presets.
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
464 |
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
465 |
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
466
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
467 *Model predicted-alignment error matrix (pae_ranked_n.csv)*
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
468
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
469 | Per-model predicted-alignment error (PAE) matrix - only available with the ``monomer_ptm`` and ``multimer`` model presets.
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
470 | The tool will produce one ``.csv`` output for each PDB model.
14
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
471 |
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
472 |
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
473
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
474 *relax_metrics.json (optional)*
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
475
15
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
476 | A JSON-formatted text file containing relax metrics (primarily remaining violations).
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
477 |
14
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
478 |
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
479
20
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
480 *timings.json (optional)*
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
481
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
482 | A JSON-formatted text file containing the timings for each phase of the prediction.
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
483 |
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
484 |
6ab1a261520a planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
galaxy-australia
parents: 19
diff changeset
485
9
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468
galaxy-australia
parents: 8
diff changeset
486 **AlphaFold configuration**
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468
galaxy-australia
parents: 8
diff changeset
487
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468
galaxy-australia
parents: 8
diff changeset
488 | We have configured AlphaFold to run with the parameters suggested by default on `AlphaFold's GitHub <https://github.com/deepmind/alphafold>`_.
15
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
galaxy-australia
parents: 14
diff changeset
489 | This means that it runs with Amber relaxation enabled, with relaxed PDB models collected as output datasets (ranked\_*.pdb files). If there are additonal parameters that you would like to interact with, please `send a support request to Galaxy AU <https://site.usegalaxy.org.au/request/support>`_, or open an issue on `our GitHub <https://github.com/usegalaxy-au/tools-au>`_.
9
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468
galaxy-australia
parents: 8
diff changeset
490 |
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
491 |
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
492
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
493 **External Resources**
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
494
14
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
495 We highly recommend checking out the
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
496 `Alphafold Protein Structure Database <https://alphafold.ebi.ac.uk/>`_,
9
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468
galaxy-australia
parents: 8
diff changeset
497 which contains pre-computed structures for over 200 million known proteins.
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468
galaxy-australia
parents: 8
diff changeset
498 See also:
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
499
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
500 - `Google Deepmind's article on AlphaFold <https://deepmind.com/blog/article/alphafold-a-solution-to-a-50-year-old-grand-challenge-in-biology>`_
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
501 - `AlphaFold source code on GitHub <https://github.com/deepmind/alphafold>`_
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
502
14
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
503 *Downstream analysis*
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
504
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
505 | Obtaining a protein structure prediction is the first step in many analyses.
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
506 | The 3D models created by AlphaFold can be used in downstream analysis, including the following:
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
507 |
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
508
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
509 - Inspecting protein features
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
510 3D viewers (pymol, chimera, ngl, blender) can be used to inspect active sites, regulatory domains, binding sites.
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
511 - Molecular docking
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
512 3D structures can be used to predict the binding affinity of different compounds.
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
513 This is especially useful in screening drug candidates.
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
514 - Protein-protein interactions
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
515 Proteins associate in many biological processes, including intracellular signalling pathways and protein complex formation.
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
516 To predict these interactions, other programs may ingest 3D models predicted by AlphaFold. Proprietary softwares include `GOLD <https://www.ccdc.cam.ac.uk/solutions/csd-discovery/components/gold/>`_ and `SeeSAR <https://www.biosolveit.de/SeeSAR>`_, but many `free and open-source options <https://en.wikipedia.org/wiki/List_of_protein-ligand_docking_software>`_ are available such as `AutoDock <https://autodock.scripps.edu/>`_, `SwissDock <http://www.swissdock.ch/>`_, `DockQ <https://github.com/bjornwallner/DockQ>`_, `MM-Align <https://zhanggroup.org/MM-align/>`_ and `TM-Align <https://zhanggroup.org/TM-align/>`_. Protein-protein interactions are often inferred from AlphaFold-Multimer predictions, which provide a level of confidence in binding affinity between homomer/heteromer subunits.
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
galaxy-australia
parents: 13
diff changeset
517
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
518 ]]></help>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
519 <citations>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
520 <citation type="doi">https://doi.org/10.1038/s41586-021-03819-2</citation>
9
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468
galaxy-australia
parents: 8
diff changeset
521 <citation type="doi">https://doi.org/10.1101/2021.10.04.463034</citation>
0
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
522 </citations>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
523 </tool>