alphafold2: alphafold.xml annotate

annotate alphafold.xml @ 14:d00e15139065 draft

planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty

author	galaxy-australia
date	Tue, 28 Feb 2023 01:15:42 +0000
parents	c0e71cb2bd1b
children	a58f7eb0df2c

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>
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	5 <token name="@VERSION_SUFFIX@">0</token>
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	6 </macros>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	7 <edam_topics>
1 6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86" galaxy-australia parents: 0 diff changeset	8 <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	9 </edam_topics>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	10 <edam_operations>
1 6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86" galaxy-australia parents: 0 diff changeset	11 <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	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 <xrefs>
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	14 <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	15 </xrefs>
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	16 <requirements>
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	17 <container type="docker">neoformit/alphafold:v2.3.1_1</container>
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	18 </requirements>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	19 <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	20
6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86" galaxy-australia parents: 0 diff changeset	21 ## $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	22 ## 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	23
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	24 ## 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	25 #if $fasta_or_text.input_mode == 'history':
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	26 cp '$fasta_or_text.fasta_file' input.fasta
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	27
1 6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86" galaxy-australia parents: 0 diff changeset	28 #elif $fasta_or_text.input_mode == 'textbox':
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	29 echo '$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	30 #end if
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	31
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	32 && 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	33 --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	34 --max_length \${ALPHAFOLD_AA_LENGTH_MAX:-0}
9 3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	35 #if $multimer:
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	36 --multimer
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	37 #end if
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	38 > alphafold.fasta
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	39
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	40 ## Env vars -------------------------------
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	41 && 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	42 && 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	43 && 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	44
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	45 ## Run alphafold -------------------------
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	46 && python /app/alphafold/run_alphafold.py
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	47 --fasta_paths alphafold.fasta
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	48 --output_dir output
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	49 --data_dir \${ALPHAFOLD_DB:-/data}
10 072c324f20fc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c8f9b460b5c5f2ef0344719d38f6be9d1a3da573 galaxy-australia parents: 9 diff changeset	50
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	51 ## Set reference database paths
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	52 --uniref90_database_path \${ALPHAFOLD_DB:-/data}/uniref90/uniref90.fasta
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	53 --mgnify_database_path \${ALPHAFOLD_DB:-/data}/mgnify/mgy_clusters_2022_05.fa
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	54 --template_mmcif_dir \${ALPHAFOLD_DB:-/data}/pdb_mmcif/mmcif_files
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	55 --obsolete_pdbs_path \${ALPHAFOLD_DB:-/data}/pdb_mmcif/obsolete.dat
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	56 #if $dbs == 'full':
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	57 --bfd_database_path \${ALPHAFOLD_DB:-/data}/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	58 --uniref30_database_path \${ALPHAFOLD_DB:-/data}/uniref30/UniRef30_2021_03
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	59 #else
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	60 --db_preset=reduced_dbs
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	61 --small_bfd_database_path \${ALPHAFOLD_DB:-/data}/small_bfd/bfd-first_non_consensus_sequences.fasta
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	62 #end if
9 3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	63
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	64 #if $max_template_date:
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	65 --max_template_date=$max_template_date
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	66 #else
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	67 --max_template_date=\$TODAY
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	68 #end if
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	69
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	70 --use_gpu_relax=\${ALPHAFOLD_USE_GPU:-True} ## introduced in v2.1.2
9 3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	71
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	72 #if $multimer:
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	73 --model_preset=multimer
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	74 --pdb_seqres_database_path=\${ALPHAFOLD_DB:-/data}/pdb_seqres/pdb_seqres.txt
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	75 --uniprot_database_path=\${ALPHAFOLD_DB:-/data}/uniprot/uniprot.fasta
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	76 --num_multimer_predictions_per_model=1 ## introduced in v2.2.0
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	77 #else
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	78 --pdb70_database_path \${ALPHAFOLD_DB:-/data}/pdb70/pdb70
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	79 #end if
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	80
1 6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86" galaxy-australia parents: 0 diff changeset	81 ## Generate additional outputs ------------
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	82 && python3 '$__tool_directory__/outputs.py' output/alphafold $outputs.plddts
9 3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	83 #if $multimer:
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	84 --multimer
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	85 #end if
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	86
1 6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86" galaxy-australia parents: 0 diff changeset	87 ## HTML output
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	88 && mkdir -p '${ html.files_path }'
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	89 && 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	90 && 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	91
bc99b0a951ec "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 2d7c3d151feaafc3be33ebb0081ec640680fbb4d-dirty" galaxy-australia parents: 3 diff changeset	92 ## 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	93 ## 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	94 ## 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	95 && (([ -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	96
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	97 ]]></command>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	98 <inputs>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	99 <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	100 <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	101 <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	102 <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	103 </param>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	104 <when value="history">
9 3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	105 <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	106 </when>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	107 <when value="textbox">
9 3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	108 <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	109 </when>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	110 </conditional>
9 3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	111
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	112 <param
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	113 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	114 type="text"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	115 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	116 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	117 optional="true"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	118 >
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	119 <sanitizer>
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	120 <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	121 <add value="-" />
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	122 </valid>
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	123 </sanitizer>
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	124 <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	125 </param>
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	126
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	127 <param
10 072c324f20fc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c8f9b460b5c5f2ef0344719d38f6be9d1a3da573 galaxy-australia parents: 9 diff changeset	128 name="dbs"
072c324f20fc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c8f9b460b5c5f2ef0344719d38f6be9d1a3da573 galaxy-australia parents: 9 diff changeset	129 type="select"
072c324f20fc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c8f9b460b5c5f2ef0344719d38f6be9d1a3da573 galaxy-australia parents: 9 diff changeset	130 display="radio"
072c324f20fc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c8f9b460b5c5f2ef0344719d38f6be9d1a3da573 galaxy-australia parents: 9 diff changeset	131 label="Select database"
072c324f20fc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c8f9b460b5c5f2ef0344719d38f6be9d1a3da573 galaxy-australia parents: 9 diff changeset	132 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	133 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	134 >
072c324f20fc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c8f9b460b5c5f2ef0344719d38f6be9d1a3da573 galaxy-australia parents: 9 diff changeset	135 <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	136 <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	137 </param>
072c324f20fc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c8f9b460b5c5f2ef0344719d38f6be9d1a3da573 galaxy-australia parents: 9 diff changeset	138
072c324f20fc planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c8f9b460b5c5f2ef0344719d38f6be9d1a3da573 galaxy-australia parents: 9 diff changeset	139 <param
9 3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	140 name="multimer"
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	141 type="boolean"
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	142 checked="false"
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	143 label="Multimer mode"
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	144 help="Fold a protein multimer from multiple input sequences. You must input multiple sequences in FASTA to run this mode."
9 3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	145 />
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	146
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	147 <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	148 <param
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	149 name="confidence_scores"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	150 type="boolean"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	151 checked="false"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	152 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	153 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	154 />
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	155 <param
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	156 name="plddts"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	157 type="boolean"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	158 checked="false"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	159 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	160 truevalue="--plddts"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	161 falsevalue=""
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	162 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. These data have been parsed from the model pickle files (below)."
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	163 />
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	164 <param
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	165 name="model_pkls"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	166 type="boolean"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	167 checked="false"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	168 label="ranked_*.pkl"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	169 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. Outputs are named respectively to PDB outputs."
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	170 />
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	171 <param
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	172 name="relax_json"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	173 type="boolean"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	174 checked="false"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	175 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	176 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	177 />
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	178 </section>
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	179 </inputs>
9 3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	180
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	181 <outputs>
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	182 <data name="model5" format="pdb" from_work_dir="output/alphafold/ranked_4.pdb" label="${tool.name} on ${on_string}: PDB ranked 4"/>
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	183 <data name="model4" format="pdb" from_work_dir="output/alphafold/ranked_3.pdb" label="${tool.name} on ${on_string}: PDB ranked 3"/>
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	184 <data name="model3" format="pdb" from_work_dir="output/alphafold/ranked_2.pdb" label="${tool.name} on ${on_string}: PDB ranked 2"/>
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	185 <data name="model2" format="pdb" from_work_dir="output/alphafold/ranked_1.pdb" label="${tool.name} on ${on_string}: PDB ranked 1"/>
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	186 <data name="model1" format="pdb" from_work_dir="output/alphafold/ranked_0.pdb" label="${tool.name} on ${on_string}: PDB ranked 0"/>
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	187 <data name="html" format="html" label="${tool.name} on ${on_string}: Visualization" />
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	188
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	189 <!-- Optional outputs -->
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	190 <data
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	191 name="output_confidence_scores"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	192 format="tabular"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	193 from_work_dir="output/alphafold/extra/model_confidence_scores.tsv"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	194 label="${tool.name} on ${on_string}: Model confidence scores"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	195 >
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	196 <filter>outputs['confidence_scores']</filter>
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	197 </data>
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	198
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	199 <data
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	200 name="output_plddts"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	201 format="tabular"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	202 from_work_dir="output/alphafold/extra/plddts.tsv"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	203 label="${tool.name} on ${on_string}: Per-residue confidence scores (plddts)"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	204 >
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	205 <filter>outputs['plddts']</filter>
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	206 </data>
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	207
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	208 <data
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	209 name="output_ranked_4_pkl"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	210 format="binary"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	211 from_work_dir="output/alphafold/extra/ranked_4.pkl"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	212 label="${tool.name} on ${on_string}: ranked_4.pkl"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	213 >
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	214 <filter>outputs['model_pkls']</filter>
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	215 </data>
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	216 <data
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	217 name="output_ranked_3_pkl"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	218 format="binary"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	219 from_work_dir="output/alphafold/extra/ranked_3.pkl"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	220 label="${tool.name} on ${on_string}: ranked_3.pkl"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	221 >
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	222 <filter>outputs['model_pkls']</filter>
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	223 </data>
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	224 <data
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	225 name="output_ranked_2_pkl"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	226 format="binary"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	227 from_work_dir="output/alphafold/extra/ranked_2.pkl"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	228 label="${tool.name} on ${on_string}: ranked_2.pkl"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	229 >
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	230 <filter>outputs['model_pkls']</filter>
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	231 </data>
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	232 <data
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	233 name="output_ranked_1_pkl"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	234 format="binary"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	235 from_work_dir="output/alphafold/extra/ranked_1.pkl"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	236 label="${tool.name} on ${on_string}: ranked_1.pkl"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	237 >
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	238 <filter>outputs['model_pkls']</filter>
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	239 </data>
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	240 <data
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	241 name="output_ranked_0_pkl"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	242 format="binary"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	243 from_work_dir="output/alphafold/extra/ranked_0.pkl"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	244 label="${tool.name} on ${on_string}: ranked_0.pkl"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	245 >
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	246 <filter>outputs['model_pkls']</filter>
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	247 </data>
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	248 <data
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	249 name="output_relax_json"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	250 format="json"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	251 from_work_dir="output/alphafold/extra/relax_metrics_ranked.json"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	252 label="${tool.name} on ${on_string}: relax_metrics_ranked.json"
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	253 >
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	254 <filter>outputs['relax_json']</filter>
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	255 </data>
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	256 </outputs>
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	257
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	258 <tests>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	259 <test expect_num_outputs="8">
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	260 <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	261 <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	262 <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	263 </conditional>
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	264 <param name="plddts" value="true"/>
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	265 <output name="output_plddts">
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	266 <assert_contents>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	267 <has_n_columns n="2"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	268 <has_n_lines n="6"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	269 <has_size value="2900" delta="300"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	270 </assert_contents>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	271 </output>
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	272 <output name="output_confidence_scores">
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	273 <assert_contents>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	274 <has_n_columns n="2"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	275 <has_n_lines n="6"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	276 <has_size value="70" delta="50"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	277 </assert_contents>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	278 </output>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	279 <output name="model1">
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	280 <assert_contents>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	281 <has_n_columns n="12"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	282 <has_n_lines n="1517"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	283 <has_size value="123000" delta="10000"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	284 </assert_contents>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	285 </output>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	286 <output name="model2">
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	287 <assert_contents>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	288 <has_n_columns n="12"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	289 <has_n_lines n="1517"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	290 <has_size value="123000" delta="10000"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	291 </assert_contents>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	292 </output>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	293 <output name="model3">
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	294 <assert_contents>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	295 <has_n_columns n="12"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	296 <has_n_lines n="1517"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	297 <has_size value="123000" delta="10000"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	298 </assert_contents>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	299 </output>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	300 <output name="model4">
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	301 <assert_contents>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	302 <has_n_columns n="12"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	303 <has_n_lines n="1517"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	304 <has_size value="123000" delta="10000"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	305 </assert_contents>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	306 </output>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	307 <output name="model5">
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	308 <assert_contents>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	309 <has_n_columns n="12"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	310 <has_n_lines n="1517"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	311 <has_size value="123000" delta="10000"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	312 </assert_contents>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	313 </output>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	314 </test>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	315 </tests>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	316 <help><![CDATA[
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	317
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	318 .. class:: infomark
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	319
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	320 \| 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	321 \|
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	322 \| 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	323 \|
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	324 \| 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	325 \| 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	326 \|
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	327 \| 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	328 \|
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	329
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	330 - `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	331 - `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	332
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	333 \| 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	334 \|
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 What it does
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	337
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	338 What is AlphaFold?
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	339
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	340 \| 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	341 \|
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	342
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	343 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	344
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	345 \| 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	346 \| 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	347 \| 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	348 \|
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	349
9 3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	350
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	351 Input
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	352
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	353 Amino acid sequence
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	354
9 3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	355 \| 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	356 \| 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	357 \| 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	358 \|
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	359 \|
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	360
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	361 Outputs
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	362
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	363 Visualization
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	364
9 3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	365 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	366 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	367 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	368
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	369 .. 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	370 :height: 520
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	371 :alt: Result visualization
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	372
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	373 \|
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	374
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	375 PDB files
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	376
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	377 \| 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	378 \| 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	379 \| 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	380 \|
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	381
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	382 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	383
9 3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	384 \| 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	385 \| 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	386 \|
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	387 \|
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	388
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	389 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	390
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	391 \| 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.
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	392 \| The tool will produce one ``.pkl`` output for each of the PDB models.
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	393 \|
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	394 \|
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	395
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	396 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	397
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	398 \| 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	399 \|
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	400
9 3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	401 AlphaFold configuration
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	402
3bd420ec162d planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468 galaxy-australia parents: 8 diff changeset	403 \| We have configured AlphaFold to run with the parameters suggested by default on `AlphaFold's GitHub <https://github.com/deepmind/alphafold>`_.
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	404 \| This means that it runs with Amber relaxation enabled, with relaxed PDB models collected as output datasets. 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	405 \|
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	406 \|
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	407
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	408 External Resources
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	409
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	410 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	411 `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	412 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	413 See also:
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	414
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	415 - `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	416 - `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	417
14 d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	418 Downstream analysis
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	419
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	420 \| 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	421 \| 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	422 \|
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	423
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	424 - Inspecting protein features
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	425 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	426 - Molecular docking
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	427 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	428 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	429 - Protein-protein interactions
d00e15139065 planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty galaxy-australia parents: 13 diff changeset	430 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	431 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	432
0 7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	433 ]]></help>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	434 <citations>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	435 <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	436 <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	437 </citations>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty" galaxy-australia parents: diff changeset	438 </tool>

Mercurial > repos > galaxy-australia > alphafold2

annotate alphafold.xml @ 14:d00e15139065 draft