alphafold2: alphafold.xml annotate

annotate alphafold.xml @ 15:a58f7eb0df2c draft

planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5

author	galaxy-australia
date	Fri, 10 Mar 2023 02:48:07 +0000
parents	d00e15139065
children	f9eb041c518c

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>
15 a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	5 <token name="@VERSION_SUFFIX@">1</token>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	6 <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	7 <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	8 </macros>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	9 <edam_topics>
1 6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86" galaxy-australia parents: 0 diff changeset	10 <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	11 </edam_topics>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	12 <edam_operations>
1 6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86" galaxy-australia parents: 0 diff changeset	13 <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	14 </edam_operations>
1 6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86" galaxy-australia parents: 0 diff changeset	15 <xrefs>
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	16 <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	17 </xrefs>
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	18 <requirements>
15 a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	19 <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	20 </requirements>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	21 <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	22
15 a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	23 ## 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	24 ## 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	25 ## 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	26
1 6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86" galaxy-australia parents: 0 diff changeset	27 ## $ALPHAFOLD_DB variable should point to the location of the AlphaFold
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86" galaxy-australia parents: 0 diff changeset	28 ## databases - defaults to /data
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86" galaxy-australia parents: 0 diff changeset	29
15 a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	30 ## 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	31 #if $fasta_or_text.input_mode == 'history':
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	32 cp '$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	33 #elif $fasta_or_text.input_mode == 'textbox':
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	34 echo '$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	35 #end if
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	36
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	37 && python3 '$__tool_directory__/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	38 --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	39 --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	40 #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	41 --multimer
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	42 #end if
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	43 > alphafold.fasta
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	44
15 a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	45 ## Env vars -------------------------------------------------------------------
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	46 && 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	47 && 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	48 && 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	49
15 a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	50 ## Run AlphaFold -------------------------------------------------------------
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	51 #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	52 ## 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	53 && echo "Creating dummy outputs for model_preset=$model_preset..."
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	54 && bash '$__tool_directory__/mock_alphafold.sh' $model_preset
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	55 #else:
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	56 ## Run AlphaFold
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	57 && python /app/alphafold/run_alphafold.py
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	58 --fasta_paths alphafold.fasta
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	59 --output_dir output
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	60 --data_dir \${ALPHAFOLD_DB:-/data}
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	61 --model_preset=$model_preset
9 3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	62
15 a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	63 ## Set reference database paths
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	64 --uniref90_database_path \${ALPHAFOLD_DB:-/data}/uniref90/uniref90.fasta
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	65 --mgnify_database_path \${ALPHAFOLD_DB:-/data}/mgnify/mgy_clusters_2022_05.fa
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	66 --template_mmcif_dir \${ALPHAFOLD_DB:-/data}/pdb_mmcif/mmcif_files
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	67 --obsolete_pdbs_path \${ALPHAFOLD_DB:-/data}/pdb_mmcif/obsolete.dat
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	68 #if $dbs == 'full':
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	69 --bfd_database_path \${ALPHAFOLD_DB:-/data}/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	70 --uniref30_database_path \${ALPHAFOLD_DB:-/data}/uniref30/UniRef30_2021_03
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	71 #else
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	72 --db_preset=reduced_dbs
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	73 --small_bfd_database_path \${ALPHAFOLD_DB:-/data}/small_bfd/bfd-first_non_consensus_sequences.fasta
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	74 #end if
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	75
15 a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	76 #if $max_template_date:
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	77 --max_template_date=$max_template_date
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	78 #else
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	79 --max_template_date=\$TODAY
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	80 #end if
9 3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	81
15 a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	82 --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	83
15 a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	84 #if $model_preset == 'multimer':
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	85 --pdb_seqres_database_path=\${ALPHAFOLD_DB:-/data}/pdb_seqres/pdb_seqres.txt
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	86 --uniprot_database_path=\${ALPHAFOLD_DB:-/data}/uniprot/uniprot.fasta
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	87 --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	88 #else
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	89 --pdb70_database_path \${ALPHAFOLD_DB:-/data}/pdb70/pdb70
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	90 #end if
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	91 #end if
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	92
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	93 ## Generate additional outputs ------------------------------------------------
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	94 && python3 '$__tool_directory__/outputs.py' output/alphafold
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	95 $outputs.plddts
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	96 $outputs.model_pkls
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	97 $outputs.pae_csv
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	98 $outputs.plots
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	99 #if $model_preset == 'multimer':
9 3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	100 --multimer
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	101 #end if
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	102
1 6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86" galaxy-australia parents: 0 diff changeset	103 ## HTML output
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	104 && mkdir -p '${ html.files_path }'
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	105 && 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	106 && 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	107
bc99b0a951ec "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 2d7c3d151feaafc3be33ebb0081ec640680fbb4d-dirty" galaxy-australia parents: 3 diff changeset	108 ## 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	109 ## 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	110 ## 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	111 && (([ -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	112
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	113 ]]></command>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	114 <inputs>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	115 <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	116 <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	117 <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	118 <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	119 </param>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	120 <when value="history">
9 3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	121 <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	122 </when>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	123 <when value="textbox">
9 3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	124 <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	125 </when>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	126 </conditional>
9 3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	127
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	128 <param
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	129 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	130 type="text"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	131 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	132 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	133 optional="true"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	134 >
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	135 <sanitizer>
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	136 <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	137 <add value="-" />
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	138 </valid>
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	139 </sanitizer>
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	140 <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	141 </param>
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	142
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	143 <param
10 072c324f20fc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c8f9b460b5c5f2ef0344719d38f6be9d1a3da573 galaxy-australia parents: 9 diff changeset	144 name="dbs"
072c324f20fc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c8f9b460b5c5f2ef0344719d38f6be9d1a3da573 galaxy-australia parents: 9 diff changeset	145 type="select"
072c324f20fc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c8f9b460b5c5f2ef0344719d38f6be9d1a3da573 galaxy-australia parents: 9 diff changeset	146 display="radio"
072c324f20fc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c8f9b460b5c5f2ef0344719d38f6be9d1a3da573 galaxy-australia parents: 9 diff changeset	147 label="Select database"
072c324f20fc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c8f9b460b5c5f2ef0344719d38f6be9d1a3da573 galaxy-australia parents: 9 diff changeset	148 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	149 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	150 >
072c324f20fc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c8f9b460b5c5f2ef0344719d38f6be9d1a3da573 galaxy-australia parents: 9 diff changeset	151 <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	152 <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	153 </param>
072c324f20fc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c8f9b460b5c5f2ef0344719d38f6be9d1a3da573 galaxy-australia parents: 9 diff changeset	154
072c324f20fc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c8f9b460b5c5f2ef0344719d38f6be9d1a3da573 galaxy-australia parents: 9 diff changeset	155 <param
15 a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	156 name="model_preset"
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	157 type="select"
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	158 label="Model preset"
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	159 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	160 >
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	161 <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	162 <option value="monomer_ptm">
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	163 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	164 </option>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	165 <option value="multimer">
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	166 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	167 </option>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	168 </param>
9 3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	169
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	170 <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	171 <param
15 a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	172 name="plots"
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	173 type="boolean"
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	174 checked="false"
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	175 truevalue="--plot"
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	176 falsevalue=""
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	177 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	178 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	179 />
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	180 <param
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	181 name="confidence_scores"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	182 type="boolean"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	183 checked="false"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	184 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	185 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	186 />
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	187 <param
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	188 name="plddts"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	189 type="boolean"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	190 checked="false"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	191 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	192 truevalue="--plddts"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	193 falsevalue=""
15 a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	194 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	195 />
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	196 <param
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	197 name="pae_csv"
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	198 type="boolean"
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	199 checked="false"
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	200 truevalue="--pae"
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	201 falsevalue=""
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	202 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	203 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	204 />
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	205 <param
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	206 name="model_pkls"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	207 type="boolean"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	208 checked="false"
15 a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	209 truevalue="--pkl"
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	210 falsevalue=""
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	211 label="ranked_*.pkl"
15 a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	212 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	213 />
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	214 <param
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	215 name="relax_json"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	216 type="boolean"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	217 checked="false"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	218 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	219 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	220 />
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	221 </section>
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	222 </inputs>
9 3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	223
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	224 <outputs>
15 a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	225 <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	226 <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	227 <!-- Optional outputs -->
15 a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	228 <expand macro="output_plddts" />
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	229 <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	230 <expand macro="output_pickles" />
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	231 <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	232 <expand macro="output_plots" />
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	233 <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	234 </outputs>
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	235
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	236 <tests>
15 a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	237 <!-- 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	238 <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	239 <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	240 <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	241 <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	242 </conditional>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	243 <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	244 <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	245 </test>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	246
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	247 <!-- 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	248 <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	249 <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	250 <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	251 <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	252 </conditional>
15 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 <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	255 <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	256 <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	257 <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	258 <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	259 <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	260 <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	261 <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	262 <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	263 <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	264 <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	265 <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	266 </test>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	267
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	268 <!-- 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	269 <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	270 <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	271 <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	272 <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	273 </conditional>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	274 <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	275 <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	276 <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	277 <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	278 <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	279 <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	280 <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	281 <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	282 <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	283 <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	284 <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	285 <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	286 <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	287 <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	288 </test>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	289
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	290 <!-- 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	291 <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	292 <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	293 <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	294 <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	295 </conditional>
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	296 <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	297 <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	298 <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	299 <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	300 <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	301 <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	302 <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	303 <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	304 <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	305 <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	306 <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	307 <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	308 <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	309 <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	310 </test>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	311 </tests>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	312 <help><![CDATA[
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	313
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	314 .. class:: infomark
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	315
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	316 \| 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	317 \|
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	318 \| 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	319 \|
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	320 \| 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	321 \| 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	322 \|
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	323 \| 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	324 \|
0 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 - `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	327 - `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	328
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	329 \| 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	330 \|
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	331
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	332 What it does
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	333
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	334 What is AlphaFold?
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 \| 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	337 \|
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	338
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	339 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	340
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	341 \| 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	342 \| 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	343 \| 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	344 \|
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	345
9 3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	346
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	347 Input
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 Amino acid sequence
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	350
9 3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	351 \| 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	352 \| 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	353 \| 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	354 \|
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	355 \|
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	356
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	357 Outputs
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 Visualization
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 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	362 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	363 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	364
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	365 .. 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	366 :height: 520
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	367 :alt: Result visualization
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 \|
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	370
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	371 PDB files
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	372
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	373 \| 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	374 \| 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	375 \| 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	376 \|
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	377
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	378 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	379
9 3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	380 \| 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	381 \| 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	382 \|
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	383 \|
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	384
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	385 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	386
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	387 \| 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	388 \| 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	389 \|
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	390 \|
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	391
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	392 pLDDT + PAE plots (optional)
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	393
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	394 \| 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	395 \| 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	396 \| 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	397 \| 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	398 \|
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 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	402
a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	403 \| 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	404 \| 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	405 \|
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	406 \|
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	407
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	408 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	409
15 a58f7eb0df2c planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5 galaxy-australia parents: 14 diff changeset	410 \| 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	411 \|
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	412 \|
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	413
9 3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	414 AlphaFold configuration
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	415
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	416 \| 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	417 \| 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	418 \|
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	419 \|
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	420
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	421 External Resources
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	422
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	423 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	424 `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	425 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	426 See also:
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	427
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	428 - `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	429 - `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	430
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	431 Downstream analysis
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	432
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	433 \| 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	434 \| 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	435 \|
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	436
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	437 - Inspecting protein features
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	438 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	439 - Molecular docking
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	440 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	441 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	442 - Protein-protein interactions
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	443 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	444 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	445
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	446 ]]></help>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	447 <citations>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	448 <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	449 <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	450 </citations>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	451 </tool>

Mercurial > repos > galaxy-australia > alphafold2

annotate alphafold.xml @ 15:a58f7eb0df2c draft