alphafold2: alphafold.xml annotate

annotate alphafold.xml @ 19:2f7702fd0a4c draft default tip

planemo upload for repository https://github.com/usegalaxy-au/tools-au commit cd0379c8ecc24977dffa462c1897d402c85fa4e6

author	galaxy-australia
date	Wed, 08 May 2024 06:26:55 +0000
parents	e4a053d67e24
children

rev	line source
5 138feebde7d3 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit c7fcba69096f16e6a5cfc03d363d4db28b16807f" galaxy-australia parents: 4 diff changeset	1 <tool id="alphafold" name="Alphafold 2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
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>
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	4 <token name="@TOOL_VERSION@">2.3.1</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>
19 2f7702fd0a4c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit cd0379c8ecc24977dffa462c1897d402c85fa4e6 galaxy-australia parents: 18 diff changeset	6 <token name="@VERSION_SUFFIX@">5</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>
15 a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	20 <container type="docker">neoformit/alphafold:v2.3.1_2</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" />
5b85006245f3 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 2e1eba8094c506a99a844546e8343849d3cef694 galaxy-australia parents: 16 diff changeset	25 <include path="alphafold.html" />
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}
15 a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	49 #if $model_preset == '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)
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	63 && echo "Creating dummy outputs for model_preset=$model_preset..."
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' $model_preset
15 a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	65 #else:
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	66 ## Run AlphaFold
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	67 && python /app/alphafold/run_alphafold.py
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	68 --fasta_paths alphafold.fasta
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	69 --output_dir output
16 f9eb041c518c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty galaxy-australia parents: 15 diff changeset	70 --data_dir \${ALPHAFOLD_DB:-/data}/@TOOL_MINOR_VERSION@/
15 a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	71 --model_preset=$model_preset
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
15 a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	86 #if $max_template_date:
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	87 --max_template_date=$max_template_date
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
15 a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	92 --use_gpu_relax=\${ALPHAFOLD_USE_GPU:-True} ## introduced in v2.1.2
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	93
15 a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	94 #if $model_preset == '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
15 a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	97 --num_multimer_predictions_per_model=1 ## introduced in v2.2.0
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
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	101 #end if
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	102
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	103 ## 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	104 && 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	105 $outputs.plddts
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	106 $outputs.model_pkls
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	107 $outputs.pae_csv
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	108 $outputs.plots
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	109 #if $model_preset == 'multimer':
9 3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	110 --multimer
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	111 #end if
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	112
1 6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86" galaxy-australia parents: 0 diff changeset	113 ## HTML output
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	114 && mkdir -p '${ html.files_path }'
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	115 && cp '$__tool_directory__/alphafold.html' '${html}'
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	116 && 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	117
bc99b0a951ec "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 2d7c3d151feaafc3be33ebb0081ec640680fbb4d-dirty" galaxy-australia parents: 3 diff changeset	118 ## 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	119 ## 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	120 ## 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	121 && (([ -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	122
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	123 ]]></command>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	124 <inputs>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	125 <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	126 <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	127 <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	128 <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	129 </param>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	130 <when value="history">
9 3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	131 <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	132 </when>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	133 <when value="textbox">
9 3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	134 <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	135 </when>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	136 </conditional>
9 3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	137
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	138 <param
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	139 name="max_template_date"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	140 type="text"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	141 label="Max template date (yyyy-mm-dd) (optional)"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	142 help="The model will reference PDB structures deposited before this date only. Defaults to today's date."
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	143 optional="true"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	144 >
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	145 <sanitizer>
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	146 <valid initial="string.digits">
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	147 <add value="-" />
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	148 </valid>
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	149 </sanitizer>
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	150 <validator type="regex">[0-9]{4}-[0-9]{2}-[0-9]{2}</validator>
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	151 </param>
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	152
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	153 <param
10 072c324f20fc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c8f9b460b5c5f2ef0344719d38f6be9d1a3da573 galaxy-australia parents: 9 diff changeset	154 name="dbs"
072c324f20fc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c8f9b460b5c5f2ef0344719d38f6be9d1a3da573 galaxy-australia parents: 9 diff changeset	155 type="select"
072c324f20fc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c8f9b460b5c5f2ef0344719d38f6be9d1a3da573 galaxy-australia parents: 9 diff changeset	156 display="radio"
072c324f20fc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c8f9b460b5c5f2ef0344719d38f6be9d1a3da573 galaxy-australia parents: 9 diff changeset	157 label="Select database"
072c324f20fc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c8f9b460b5c5f2ef0344719d38f6be9d1a3da573 galaxy-australia parents: 9 diff changeset	158 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	159 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	160 >
072c324f20fc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c8f9b460b5c5f2ef0344719d38f6be9d1a3da573 galaxy-australia parents: 9 diff changeset	161 <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	162 <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	163 </param>
072c324f20fc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c8f9b460b5c5f2ef0344719d38f6be9d1a3da573 galaxy-australia parents: 9 diff changeset	164
072c324f20fc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c8f9b460b5c5f2ef0344719d38f6be9d1a3da573 galaxy-australia parents: 9 diff changeset	165 <param
15 a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	166 name="model_preset"
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	167 type="select"
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	168 label="Model preset"
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	169 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	170 >
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	171 <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	172 <option value="monomer_ptm">
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	173 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	174 </option>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	175 <option value="multimer">
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	176 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	177 </option>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	178 </param>
9 3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	179
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	180 <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	181 <param
15 a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	182 name="plots"
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	183 type="boolean"
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	184 checked="false"
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	185 truevalue="--plot"
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	186 falsevalue=""
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	187 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	188 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	189 />
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	190 <param
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	191 name="confidence_scores"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	192 type="boolean"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	193 checked="false"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	194 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	195 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	196 />
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	197 <param
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	198 name="plddts"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	199 type="boolean"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	200 checked="false"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	201 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	202 truevalue="--plddts"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	203 falsevalue=""
15 a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	204 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	205 />
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	206 <param
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	207 name="pae_csv"
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	208 type="boolean"
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	209 checked="false"
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	210 truevalue="--pae"
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	211 falsevalue=""
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	212 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	213 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	214 />
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	215 <param
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	216 name="model_pkls"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	217 type="boolean"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	218 checked="false"
15 a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	219 truevalue="--pkl"
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	220 falsevalue=""
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	221 label="ranked_*.pkl"
15 a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	222 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	223 />
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	224 <param
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	225 name="relax_json"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	226 type="boolean"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	227 checked="false"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	228 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	229 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	230 />
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	231 </section>
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	232 </inputs>
9 3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	233
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	234 <outputs>
15 a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	235 <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	236 <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	237 <!-- Optional outputs -->
15 a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	238 <expand macro="output_plddts" />
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	239 <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	240 <expand macro="output_pickles" />
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	241 <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	242 <expand macro="output_plots" />
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	243 <expand macro="output_relax_json" />
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	244 </outputs>
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	245
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	246 <tests>
15 a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	247 <!-- 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	248 <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	249 <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	250 <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	251 <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	252 </conditional>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	253 <param name="model_preset" value="monomer"/>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	254 <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	255 </test>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	256
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	257 <!-- 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	258 <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	259 <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	260 <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	261 <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	262 </conditional>
15 a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	263 <param name="model_preset" value="monomer"/>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	264 <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	265 <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	266 <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	267 <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	268 <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	269 <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	270 <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	271 <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	272 <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	273 <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	274 <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	275 <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	276 </test>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	277
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	278 <!-- 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	279 <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	280 <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	281 <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	282 <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	283 </conditional>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	284 <param name="model_preset" value="monomer_ptm"/>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	285 <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	286 <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	287 <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	288 <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	289 <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	290 <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	291 <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	292 <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	293 <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	294 <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	295 <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	296 <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	297 <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	298 </test>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	299
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	300 <!-- 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	301 <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	302 <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	303 <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	304 <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	305 </conditional>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	306 <param name="model_preset" value="multimer"/>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	307 <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	308 <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	309 <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	310 <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	311 <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	312 <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	313 <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	314 <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	315 <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	316 <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	317 <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	318 <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	319 <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	320 </test>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	321 </tests>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	322 <help><![CDATA[
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	323
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	324 .. class:: infomark
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	325
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	326 \| 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	327 \|
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	328 \| NOTE: this tool packages AlphaFold v2.3.1.
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	329 \|
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	330 \| 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	331 \| 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	332 \|
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	333 \| 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	334 \|
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	335
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	336 - `Release notes for v2.3.1 <https://github.com/deepmind/alphafold/releases/tag/v2.3.1>`_
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	337 - `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	338
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	339 \| If you want to use AlphaFold trained against an older cutoff date, switch to Galaxy version ``2.1.2`` (which was trained to data up to 2018-04-30).
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	340 \|
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	341
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	342 What it does
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	343
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	344 What is AlphaFold?
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	345
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	346 \| 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	347 \|
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	348
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	349 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	350
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	351 \| 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	352 \| 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	353 \| 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	354 \|
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	355
9 3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	356
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	357 Input
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	358
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	359 Amino acid sequence
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	360
9 3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	361 \| 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	362 \| 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	363 \| 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	364 \|
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	365 \|
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	366
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	367 Outputs
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	368
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	369 Visualization
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	370
9 3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	371 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	372 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	373 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	374
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	375 .. 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	376 :height: 520
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	377 :alt: Result visualization
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	378
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	379 \|
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	380
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	381 PDB files
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	382
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	383 \| Five PDB (Protein Data Bank) files are be created, ordered by rank, as predicted by AlphaFold.
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	384 \| 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	385 \| 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	386 \|
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	387
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	388 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	389
9 3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	390 \| 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	391 \| 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	392 \|
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	393 \|
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	394
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	395 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	396
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	397 \| 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	398 \| 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	399 \|
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	400 \|
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	401
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	402 pLDDT + PAE plots (optional)
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	403
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	404 \| 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	405 \| 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	406 \| 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	407 \| 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	408 \|
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	409 \|
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	410
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	411 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	412
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	413 \| 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	414 \| 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	415 \|
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	416 \|
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	417
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	418 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	419
15 a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	420 \| 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	421 \|
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	422 \|
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	423
9 3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	424 AlphaFold configuration
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	425
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	426 \| 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	427 \| 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	428 \|
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	429 \|
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 External Resources
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	432
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	433 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	434 `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	435 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	436 See also:
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	437
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	438 - `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	439 - `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	440
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	441 Downstream analysis
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	442
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	443 \| 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	444 \| 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	445 \|
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	446
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	447 - Inspecting protein features
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	448 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	449 - Molecular docking
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	450 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	451 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	452 - Protein-protein interactions
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	453 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	454 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	455
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	456 ]]></help>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	457 <citations>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	458 <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	459 <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	460 </citations>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	461 </tool>

Mercurial > repos > galaxy-australia > alphafold2

annotate alphafold.xml @ 19:2f7702fd0a4c draft default tip