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annotate alphafold.xml @ 8:ca90d17ff51b draft

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"planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 03537aada92b5fff565ff48dd47c81462c5df47e"
author galaxy-australia
date Fri, 19 Aug 2022 00:29:16 +0000
parents eb085b3dbaf8
children 3bd420ec162d
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1 <tool id="alphafold" name="Alphafold 2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
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2 <description> - AI-guided 3D structural prediction of proteins</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">2.1.2</token>
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5 <token name="@VERSION_SUFFIX@">1</token>
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6 </macros>
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7 <edam_topics>
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8 <edam_topic>topic_0082</edam_topic>
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9 </edam_topics>
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10 <edam_operations>
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11 <edam_operation>operation_0474</edam_operation>
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12 </edam_operations>
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13 <xrefs>
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14 <xref type="bio.tools">alphafold_2.0</xref>
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15 </xrefs>
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16 <requirements>
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17 <container type="docker">neoformit/alphafold:v2.1.2_0</container>
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18 </requirements>
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19 <command detect_errors="exit_code"><![CDATA[
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6c92e000d684 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
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21 ## $ALPHAFOLD_DB variable should point to the location of the AlphaFold
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22 ## databases - defaults to /data
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24 ## fasta setup ----------------------------
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25 #if $fasta_or_text.input_mode == 'history':
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26 cp '$fasta_or_text.fasta_file' input.fasta &&
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27
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28 #elif $fasta_or_text.input_mode == 'textbox':
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29 echo '$fasta_or_text.fasta_text' > input.fasta &&
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30 #end if
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31
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32 python3 '$__tool_directory__/validate_fasta.py' input.fasta
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33 --min_length \${ALPHAFOLD_AA_LENGTH_MIN:-0}
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34 --max_length \${ALPHAFOLD_AA_LENGTH_MAX:-0}
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35 > alphafold.fasta &&
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36
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37 ## env vars -------------------------------
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38 export TF_FORCE_UNIFIED_MEMORY=1 &&
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39 export XLA_PYTHON_CLIENT_MEM_FRACTION=4.0 &&
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40 export DATE=`date +"%Y-%m-%d"` &&
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41
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42 ## run alphafold -------------------------
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43 python /app/alphafold/run_alphafold.py
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44 --fasta_paths alphafold.fasta
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45 --output_dir output
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46 --data_dir \${ALPHAFOLD_DB:-/data}
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47 --uniref90_database_path \${ALPHAFOLD_DB:-/data}/uniref90/uniref90.fasta
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48 --mgnify_database_path \${ALPHAFOLD_DB:-/data}/mgnify/mgy_clusters_2018_12.fa
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49 --pdb70_database_path \${ALPHAFOLD_DB:-/data}/pdb70/pdb70
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50 --template_mmcif_dir \${ALPHAFOLD_DB:-/data}/pdb_mmcif/mmcif_files
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51 --obsolete_pdbs_path \${ALPHAFOLD_DB:-/data}/pdb_mmcif/obsolete.dat
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52 --max_template_date=\$DATE
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53 --bfd_database_path \${ALPHAFOLD_DB:-/data}/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt
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54 --uniclust30_database_path \${ALPHAFOLD_DB:-/data}/uniclust30/uniclust30_2018_08/uniclust30_2018_08
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55 ## Param introduced in AlphaFold v2.1.2:
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56 --use_gpu_relax=\${ALPHAFOLD_USE_GPU:-True}
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57 &&
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58
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59 ## Generate additional outputs ------------
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60 python3 '$__tool_directory__/gen_extra_outputs.py' output/alphafold $output_plddts &&
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61
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62 ## HTML output
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63 mkdir -p '${ html.files_path }' &&
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64 cp '$__tool_directory__/alphafold.html' '${html}' &&
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65 cp output/alphafold/ranked_*.pdb '${html.files_path}' &&
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66
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67 ## This is a (hacky) fix for a bug that has appeared in multiple Pulsar servers.
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68 ## The working directory ends up two levels deep and the visualization html page
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69 ## fails to load the PDB files as static assets.
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70 [ -d working ] && cp -r working/* .
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71
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72 ]]></command>
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73 <inputs>
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74 <conditional name="fasta_or_text">
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75 <param name="input_mode" type="select" label="Fasta Input" help="Single protein sequence to fold. Input can be fasta file from history, or text. Sequence must be valid IUPAC amino acid characters. Provide only 1 sequence per job.">
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76 <option value="history">Use fasta from history</option>
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77 <option value="textbox">Paste sequence into textbox</option>
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78 </param>
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79 <when value="history">
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80 <param name="fasta_file" type="data" format="fasta" label="Fasta file from history" help="Select single fasta protein sequence from your history. If you wish to fold multiple proteins, submit an individual job for each protein." />
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81 </when>
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82 <when value="textbox">
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
83 <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." />
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
84 </when>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
85 </conditional>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
86 <param name="output_plddts" type="boolean" checked="false" label="Output per-residue confidence scores" truevalue="--plddts" falsevalue="" 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. Sections of low confidence often occur in disordered regions. " />
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
87 </inputs>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
88 <outputs>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
89 <data name="model5" format="pdb" from_work_dir="output/alphafold/ranked_4.pdb" label="${tool.name} on ${on_string}: Model 5"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
90 <data name="model4" format="pdb" from_work_dir="output/alphafold/ranked_3.pdb" label="${tool.name} on ${on_string}: Model 4"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
91 <data name="model3" format="pdb" from_work_dir="output/alphafold/ranked_2.pdb" label="${tool.name} on ${on_string}: Model 3"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
92 <data name="model2" format="pdb" from_work_dir="output/alphafold/ranked_1.pdb" label="${tool.name} on ${on_string}: Model 2"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
93 <data name="model1" format="pdb" from_work_dir="output/alphafold/ranked_0.pdb" label="${tool.name} on ${on_string}: Model 1"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
94 <data name="confidence_scores" format="tsv" from_work_dir="output/alphafold/model_confidence_scores.tsv" label="${tool.name} on ${on_string}: Model confidence scores"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
95 <data name="plddts" format="tsv" from_work_dir="output/alphafold/plddts.tsv" label="${tool.name} on ${on_string}: Per-residue confidence scores (plddts)">
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
96 <filter>(output_plddts)</filter>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
97 </data>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
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98 <data name="html" format="html" label="${tool.name} on ${on_string}: Visualization" />
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
99 </outputs>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
100 <tests>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
101 <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
102 <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
103 <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
104 <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
105 </conditional>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
106 <param name="output_plddts" value="true"/>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
107 <output name="plddts">
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
108 <assert_contents>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
109 <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
110 <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
111 <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
112 </assert_contents>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
113 </output>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
114 <output name="confidence_scores">
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
115 <assert_contents>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
116 <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
117 <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
118 <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
119 </assert_contents>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
120 </output>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
121 <output name="model1">
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
122 <assert_contents>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
123 <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
124 <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
125 <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
126 </assert_contents>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
127 </output>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
128 <output name="model2">
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
129 <assert_contents>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
130 <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
131 <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
132 <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
133 </assert_contents>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
134 </output>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
135 <output name="model3">
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
136 <assert_contents>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
137 <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
138 <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
139 <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
140 </assert_contents>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
141 </output>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
142 <output name="model4">
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
143 <assert_contents>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
144 <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
145 <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
146 <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
147 </assert_contents>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
148 </output>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
149 <output name="model5">
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
150 <assert_contents>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
151 <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
152 <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
153 <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
154 </assert_contents>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
155 </output>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
156 </test>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
157 </tests>
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
158 <help><![CDATA[
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
159
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
160 .. class:: infomark
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
161
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
162 **What it does**
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
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diff changeset
163
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
164 | AlphaFold v2.0: AI-guided 3D structure prediction of proteins
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
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165 |
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
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166
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
parents:
diff changeset
167 *What is AlphaFold?*
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
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168
7ae9d78b06f5 "planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
galaxy-australia
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169 | 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), then will 'fold' that sequence into a 3D model.
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170 | NOTE: AlphaFold has a number of versions - this tool uses AlphaFold v2.0.
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171 |
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172
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173 *What makes AlphaFold different?*
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174
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175 | 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.
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176 | In-silico protein folding has been an active field of research for decades, but existing tools ran more slowly and with less reliability than AlphaFold.
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177 | AlphaFold represents a leap forward by regularly predicting structures to atomic-level accuracy, even when no similar structures are known.
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178 |
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179
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180 *Downstream analysis*
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181
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182 | Obtaining a protein fold is the first step in many analyses.
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183 | The 3D models created by AlphaFold can be used in downstream analysis, including the following:
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184 |
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185
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186 - Inspecting protein features
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187 3D viewers (pymol, chimera, ngl, blender) can be used to inspect active sites, regulatory domains, binding sites.
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188 - Molecular docking
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189 3D structures can be used to predict the binding affinity of different compounds.
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190 This is especially useful in screening drug candidates.
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191 - Protein-protein interactions
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192 Proteins associate in many biological processes, including intracellular signalling pathways and protein complex formation.
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193 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/>`_ and `SwissDock <http://www.swissdock.ch/>`_.
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194
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195 **Input**
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196
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197 *Amino acid sequence*
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198
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199 | AlphaFold accepts a **single amino acid sequence** in FASTA format.
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200 | You can choose to input either a file from your Galaxy history or paste a sequence into a text box.
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201 | Please paste only a single sequence - we can only process a single sequence per job.
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202 | Multiple sequences will return an error.
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203 |
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204
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205 **Outputs**
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206
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207 *Visualization*
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208
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209 | An interactive 3D graphic of the best predicted molecular structures.
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210 | This output can be opened in Galaxy to give a visual impression of the results, with different structural representations to choose from.
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211 | Open the "Visualization" history output by clicking on the "view data" icon:
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212 |
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213
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214 .. image:: https://github.com/usegalaxy-au/galaxy-local-tools/blob/1a8d3e8daa7ccc5a345ca377697735ab95ed0666/tools/alphafold/static/img/alphafold-visualization.png?raw=true
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215 :height: 520
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216 :alt: Result visualization
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217
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218 |
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219
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220 *PDB files*
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221
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222 | Five PDB (Protein Data Bank) files will be created for the best ranking models predicted by AlphaFold.
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223 | These files describe the molecular structures and can be used for downstream analysis. e.g. *in silico* molecular docking.
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224 |
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225
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226 *Model confidence scores (optional)*
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227
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228 | 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/>`_) which may be useful for downstream analysis.
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229 | Model confidence scores are also included as a column in the default PDB output.
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230 |
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231
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232 **External Resources**
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233
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234 We recommend checking out the
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235 `Alphafold Protein Structure Database <https://alphafold.ebi.ac.uk/>`_,
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236 which contains predicted sequences for thousands of Human proteins. See also:
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237
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238 - `Google Deepmind's article on AlphaFold <https://deepmind.com/blog/article/alphafold-a-solution-to-a-50-year-old-grand-challenge-in-biology>`_
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239 - `AlphaFold source code on GitHub <https://github.com/deepmind/alphafold>`_
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240
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241 ]]></help>
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242 <citations>
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243 <citation type="doi">https://doi.org/10.1038/s41586-021-03819-2</citation>
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244 </citations>
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245 </tool>