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planemo upload for repository https://github.com/usegalaxy-au/tools-au commit fd45a857a71358e7e5375dcfb5043cdc8560c5a5
author galaxy-australia
date Fri, 10 Mar 2023 02:48:07 +0000
parents d00e15139065
children f9eb041c518c
comparison
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14:d00e15139065 15:a58f7eb0df2c
1 <tool id="alphafold" name="Alphafold 2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> 1 <tool id="alphafold" name="Alphafold 2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
2 <description> - AI-guided 3D structural prediction of proteins</description> 2 <description> - AI-guided 3D structural prediction of proteins</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">2.3.1</token> 4 <token name="@TOOL_VERSION@">2.3.1</token>
5 <token name="@VERSION_SUFFIX@">0</token> 5 <token name="@VERSION_SUFFIX@">1</token>
6 <import>macro_output.xml</import>
7 <import>macro_test_output.xml</import>
6 </macros> 8 </macros>
7 <edam_topics> 9 <edam_topics>
8 <edam_topic>topic_0082</edam_topic> 10 <edam_topic>topic_0082</edam_topic>
9 </edam_topics> 11 </edam_topics>
10 <edam_operations> 12 <edam_operations>
12 </edam_operations> 14 </edam_operations>
13 <xrefs> 15 <xrefs>
14 <xref type="bio.tools">alphafold_2</xref> 16 <xref type="bio.tools">alphafold_2</xref>
15 </xrefs> 17 </xrefs>
16 <requirements> 18 <requirements>
17 <container type="docker">neoformit/alphafold:v2.3.1_1</container> 19 <container type="docker">neoformit/alphafold:v2.3.1_2</container>
18 </requirements> 20 </requirements>
19 <command detect_errors="exit_code"><![CDATA[ 21 <command detect_errors="exit_code"><![CDATA[
20 22
23 ## Developers: to test with mock alphafold run, set `export PLANEMO_TESTING=1`
24 ## in planemo's gx_venv_n/bin/activate script. AlphaFold outputs will be copied
25 ## from the test-data directory instead of running the tool.
26
21 ## $ALPHAFOLD_DB variable should point to the location of the AlphaFold 27 ## $ALPHAFOLD_DB variable should point to the location of the AlphaFold
22 ## databases - defaults to /data 28 ## databases - defaults to /data
23 29
24 ## Read FASTA input ---------------------------- 30 ## Read FASTA input -----------------------------------------------------------
25 #if $fasta_or_text.input_mode == 'history': 31 #if $fasta_or_text.input_mode == 'history':
26 cp '$fasta_or_text.fasta_file' input.fasta 32 cp '$fasta_or_text.fasta_file' input.fasta
27
28 #elif $fasta_or_text.input_mode == 'textbox': 33 #elif $fasta_or_text.input_mode == 'textbox':
29 echo '$fasta_or_text.fasta_text' > input.fasta 34 echo '$fasta_or_text.fasta_text' > input.fasta
30 #end if 35 #end if
31 36
32 && python3 '$__tool_directory__/validate_fasta.py' input.fasta 37 && python3 '$__tool_directory__/validate_fasta.py' input.fasta
33 --min_length \${ALPHAFOLD_AA_LENGTH_MIN:-0} 38 --min_length \${ALPHAFOLD_AA_LENGTH_MIN:-0}
34 --max_length \${ALPHAFOLD_AA_LENGTH_MAX:-0} 39 --max_length \${ALPHAFOLD_AA_LENGTH_MAX:-0}
35 #if $multimer: 40 #if $model_preset == 'multimer':
36 --multimer 41 --multimer
37 #end if 42 #end if
38 > alphafold.fasta 43 > alphafold.fasta
39 44
40 ## Env vars ------------------------------- 45 ## Env vars -------------------------------------------------------------------
41 && export TF_FORCE_UNIFIED_MEMORY=1 46 && export TF_FORCE_UNIFIED_MEMORY=1
42 && export XLA_PYTHON_CLIENT_MEM_FRACTION=4.0 47 && export XLA_PYTHON_CLIENT_MEM_FRACTION=4.0
43 && export TODAY=`date +"%Y-%m-%d"` 48 && export TODAY=`date +"%Y-%m-%d"`
44 49
45 ## Run alphafold ------------------------- 50 ## Run AlphaFold -------------------------------------------------------------
46 && python /app/alphafold/run_alphafold.py 51 #if os.environ.get('PLANEMO_TESTING'):
47 --fasta_paths alphafold.fasta 52 ## Run in testing mode (mocks a successful AlphaFold run by copying outputs)
48 --output_dir output 53 && echo "Creating dummy outputs for model_preset=$model_preset..."
49 --data_dir \${ALPHAFOLD_DB:-/data} 54 && bash '$__tool_directory__/mock_alphafold.sh' $model_preset
50 55 #else:
51 ## Set reference database paths 56 ## Run AlphaFold
52 --uniref90_database_path \${ALPHAFOLD_DB:-/data}/uniref90/uniref90.fasta 57 && python /app/alphafold/run_alphafold.py
53 --mgnify_database_path \${ALPHAFOLD_DB:-/data}/mgnify/mgy_clusters_2022_05.fa 58 --fasta_paths alphafold.fasta
54 --template_mmcif_dir \${ALPHAFOLD_DB:-/data}/pdb_mmcif/mmcif_files 59 --output_dir output
55 --obsolete_pdbs_path \${ALPHAFOLD_DB:-/data}/pdb_mmcif/obsolete.dat 60 --data_dir \${ALPHAFOLD_DB:-/data}
56 #if $dbs == 'full': 61 --model_preset=$model_preset
57 --bfd_database_path \${ALPHAFOLD_DB:-/data}/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt 62
58 --uniref30_database_path \${ALPHAFOLD_DB:-/data}/uniref30/UniRef30_2021_03 63 ## Set reference database paths
59 #else 64 --uniref90_database_path \${ALPHAFOLD_DB:-/data}/uniref90/uniref90.fasta
60 --db_preset=reduced_dbs 65 --mgnify_database_path \${ALPHAFOLD_DB:-/data}/mgnify/mgy_clusters_2022_05.fa
61 --small_bfd_database_path \${ALPHAFOLD_DB:-/data}/small_bfd/bfd-first_non_consensus_sequences.fasta 66 --template_mmcif_dir \${ALPHAFOLD_DB:-/data}/pdb_mmcif/mmcif_files
62 #end if 67 --obsolete_pdbs_path \${ALPHAFOLD_DB:-/data}/pdb_mmcif/obsolete.dat
63 68 #if $dbs == 'full':
64 #if $max_template_date: 69 --bfd_database_path \${ALPHAFOLD_DB:-/data}/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt
65 --max_template_date=$max_template_date 70 --uniref30_database_path \${ALPHAFOLD_DB:-/data}/uniref30/UniRef30_2021_03
66 #else 71 #else
67 --max_template_date=\$TODAY 72 --db_preset=reduced_dbs
68 #end if 73 --small_bfd_database_path \${ALPHAFOLD_DB:-/data}/small_bfd/bfd-first_non_consensus_sequences.fasta
69 74 #end if
70 --use_gpu_relax=\${ALPHAFOLD_USE_GPU:-True} ## introduced in v2.1.2 75
71 76 #if $max_template_date:
72 #if $multimer: 77 --max_template_date=$max_template_date
73 --model_preset=multimer 78 #else
74 --pdb_seqres_database_path=\${ALPHAFOLD_DB:-/data}/pdb_seqres/pdb_seqres.txt 79 --max_template_date=\$TODAY
75 --uniprot_database_path=\${ALPHAFOLD_DB:-/data}/uniprot/uniprot.fasta 80 #end if
76 --num_multimer_predictions_per_model=1 ## introduced in v2.2.0 81
77 #else 82 --use_gpu_relax=\${ALPHAFOLD_USE_GPU:-True} ## introduced in v2.1.2
78 --pdb70_database_path \${ALPHAFOLD_DB:-/data}/pdb70/pdb70 83
79 #end if 84 #if $model_preset == 'multimer':
80 85 --pdb_seqres_database_path=\${ALPHAFOLD_DB:-/data}/pdb_seqres/pdb_seqres.txt
81 ## Generate additional outputs ------------ 86 --uniprot_database_path=\${ALPHAFOLD_DB:-/data}/uniprot/uniprot.fasta
82 && python3 '$__tool_directory__/outputs.py' output/alphafold $outputs.plddts 87 --num_multimer_predictions_per_model=1 ## introduced in v2.2.0
83 #if $multimer: 88 #else
89 --pdb70_database_path \${ALPHAFOLD_DB:-/data}/pdb70/pdb70
90 #end if
91 #end if
92
93 ## Generate additional outputs ------------------------------------------------
94 && python3 '$__tool_directory__/outputs.py' output/alphafold
95 $outputs.plddts
96 $outputs.model_pkls
97 $outputs.pae_csv
98 $outputs.plots
99 #if $model_preset == 'multimer':
84 --multimer 100 --multimer
85 #end if 101 #end if
86 102
87 ## HTML output 103 ## HTML output
88 && mkdir -p '${ html.files_path }' 104 && mkdir -p '${ html.files_path }'
135 <option value="reduced" selected="true">Reduced database</option> 151 <option value="reduced" selected="true">Reduced database</option>
136 <option value="full">Full database</option> 152 <option value="full">Full database</option>
137 </param> 153 </param>
138 154
139 <param 155 <param
140 name="multimer" 156 name="model_preset"
141 type="boolean" 157 type="select"
142 checked="false" 158 label="Model preset"
143 label="Multimer mode" 159 help="Select which prediction model to run. The monomer model is the most accurate for single protein prediction. The multimer model allows prediction of protein complexes."
144 help="Fold a protein multimer from multiple input sequences. You must input multiple sequences in FASTA to run this mode." 160 >
145 /> 161 <option value="monomer" selected="true">monomer - default prediction model</option>
162 <option value="monomer_ptm">
163 monomer_ptm - slightly less accurate version of the monomer model, but provides a pairwise alignment error (PAE) matrix
164 </option>
165 <option value="multimer">
166 multimer - model a protein complex (requires multi-sequence FASTA input)
167 </option>
168 </param>
146 169
147 <section name="outputs" title="Optional outputs" expanded="false"> 170 <section name="outputs" title="Optional outputs" expanded="false">
171 <param
172 name="plots"
173 type="boolean"
174 checked="false"
175 truevalue="--plot"
176 falsevalue=""
177 label="pLDDT and PAE matrix plots (per model)"
178 help="A two-panel plot showing pLDDT against residue position (left) and PAE (paired-alignment error) as a heatmap image with residue numbers running along vertical and horizontal axes and color at each pixel indicating PAE value for the corresponding pair of residues. (right). PAE heatmap is only produced with monomer_ptm and multimer model presets."
179 />
148 <param 180 <param
149 name="confidence_scores" 181 name="confidence_scores"
150 type="boolean" 182 type="boolean"
151 checked="false" 183 checked="false"
152 label="Per-model confidence scores" 184 label="Per-model confidence scores"
157 type="boolean" 189 type="boolean"
158 checked="false" 190 checked="false"
159 label="Per-residue confidence scores" 191 label="Per-residue confidence scores"
160 truevalue="--plddts" 192 truevalue="--plddts"
161 falsevalue="" 193 falsevalue=""
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)." 194 help="Alphafold produces a pLDDT score between 0-100 for each residue in the folded models. High scores represent high confidence in placement for the residue, while low scoring residues have lower confidence. This output is a tabular file with five rows (one for each output PDB model), with each column providing a pLDDT score for a single residue."
195 />
196 <param
197 name="pae_csv"
198 type="boolean"
199 checked="false"
200 truevalue="--pae"
201 falsevalue=""
202 label="Paired-alignment error (PAE)"
203 help="A CSV-formatted matrix for each model. Only available for monomer_ptm and multimer model presets. Predicted aligned error (PAE) gives a distance error for every pair of residues. It gives AlphaFold's estimate of position error at residue X when the predicted and true structures are aligned on residue Y. Values range from 0 - 35 Angstroms."
163 /> 204 />
164 <param 205 <param
165 name="model_pkls" 206 name="model_pkls"
166 type="boolean" 207 type="boolean"
167 checked="false" 208 checked="false"
209 truevalue="--pkl"
210 falsevalue=""
168 label="ranked_*.pkl" 211 label="ranked_*.pkl"
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." 212 help="A pickle file containing metrics used for the assessment of the model's accuracy. These include per-residue pLDDT scores (see above), predicted TM (Template Modelling) score, which is a global superposition metric and predicted aligned error (a matrix size (number of residues) x (number of residues) where each position describes the confidence of the residue's 3D position relative to another residue in the model; can be used for the interpretation of relative positions of domains). Pickle files can be read and processed using the Python 'pickle' library (requires the jax Python library). Outputs are named respective to PDB outputs."
170 /> 213 />
171 <param 214 <param
172 name="relax_json" 215 name="relax_json"
173 type="boolean" 216 type="boolean"
174 checked="false" 217 checked="false"
177 /> 220 />
178 </section> 221 </section>
179 </inputs> 222 </inputs>
180 223
181 <outputs> 224 <outputs>
182 <data name="model5" format="pdb" from_work_dir="output/alphafold/ranked_4.pdb" label="${tool.name} on ${on_string}: PDB ranked 4"/> 225 <expand macro="output_pdb_models" />
183 <data name="model4" format="pdb" from_work_dir="output/alphafold/ranked_3.pdb" label="${tool.name} on ${on_string}: PDB ranked 3"/>
184 <data name="model3" format="pdb" from_work_dir="output/alphafold/ranked_2.pdb" label="${tool.name} on ${on_string}: PDB ranked 2"/>
185 <data name="model2" format="pdb" from_work_dir="output/alphafold/ranked_1.pdb" label="${tool.name} on ${on_string}: PDB ranked 1"/>
186 <data name="model1" format="pdb" from_work_dir="output/alphafold/ranked_0.pdb" label="${tool.name} on ${on_string}: PDB ranked 0"/>
187 <data name="html" format="html" label="${tool.name} on ${on_string}: Visualization" /> 226 <data name="html" format="html" label="${tool.name} on ${on_string}: Visualization" />
188
189 <!-- Optional outputs --> 227 <!-- Optional outputs -->
190 <data 228 <expand macro="output_plddts" />
191 name="output_confidence_scores" 229 <expand macro="output_confidence_scores" />
192 format="tabular" 230 <expand macro="output_pickles" />
193 from_work_dir="output/alphafold/extra/model_confidence_scores.tsv" 231 <expand macro="output_pae_csv" />
194 label="${tool.name} on ${on_string}: Model confidence scores" 232 <expand macro="output_plots" />
195 > 233 <expand macro="output_relax_json" />
196 <filter>outputs['confidence_scores']</filter>
197 </data>
198
199 <data
200 name="output_plddts"
201 format="tabular"
202 from_work_dir="output/alphafold/extra/plddts.tsv"
203 label="${tool.name} on ${on_string}: Per-residue confidence scores (plddts)"
204 >
205 <filter>outputs['plddts']</filter>
206 </data>
207
208 <data
209 name="output_ranked_4_pkl"
210 format="binary"
211 from_work_dir="output/alphafold/extra/ranked_4.pkl"
212 label="${tool.name} on ${on_string}: ranked_4.pkl"
213 >
214 <filter>outputs['model_pkls']</filter>
215 </data>
216 <data
217 name="output_ranked_3_pkl"
218 format="binary"
219 from_work_dir="output/alphafold/extra/ranked_3.pkl"
220 label="${tool.name} on ${on_string}: ranked_3.pkl"
221 >
222 <filter>outputs['model_pkls']</filter>
223 </data>
224 <data
225 name="output_ranked_2_pkl"
226 format="binary"
227 from_work_dir="output/alphafold/extra/ranked_2.pkl"
228 label="${tool.name} on ${on_string}: ranked_2.pkl"
229 >
230 <filter>outputs['model_pkls']</filter>
231 </data>
232 <data
233 name="output_ranked_1_pkl"
234 format="binary"
235 from_work_dir="output/alphafold/extra/ranked_1.pkl"
236 label="${tool.name} on ${on_string}: ranked_1.pkl"
237 >
238 <filter>outputs['model_pkls']</filter>
239 </data>
240 <data
241 name="output_ranked_0_pkl"
242 format="binary"
243 from_work_dir="output/alphafold/extra/ranked_0.pkl"
244 label="${tool.name} on ${on_string}: ranked_0.pkl"
245 >
246 <filter>outputs['model_pkls']</filter>
247 </data>
248 <data
249 name="output_relax_json"
250 format="json"
251 from_work_dir="output/alphafold/extra/relax_metrics_ranked.json"
252 label="${tool.name} on ${on_string}: relax_metrics_ranked.json"
253 >
254 <filter>outputs['relax_json']</filter>
255 </data>
256 </outputs> 234 </outputs>
257 235
258 <tests> 236 <tests>
259 <test expect_num_outputs="8"> 237 <!-- Test monomer with default outputs -->
238 <test expect_num_outputs="6">
260 <conditional name="fasta_or_text"> 239 <conditional name="fasta_or_text">
261 <param name="input_mode" value="history"/> 240 <param name="input_mode" value="history"/>
262 <param name="fasta_file" value="test1.fasta"/> 241 <param name="fasta_file" value="test1.fasta"/>
263 </conditional> 242 </conditional>
264 <param name="plddts" value="true"/> 243 <param name="model_preset" value="monomer"/>
265 <output name="output_plddts"> 244 <expand macro="test_output_pdb_models" />
266 <assert_contents> 245 </test>
267 <has_n_columns n="2"/> 246
268 <has_n_lines n="6"/> 247 <!-- Test monomer with all outputs -->
269 <has_size value="2900" delta="300"/> 248 <test expect_num_outputs="19">
270 </assert_contents> 249 <conditional name="fasta_or_text">
271 </output> 250 <param name="input_mode" value="history"/>
272 <output name="output_confidence_scores"> 251 <param name="fasta_file" value="test1.fasta"/>
273 <assert_contents> 252 </conditional>
274 <has_n_columns n="2"/> 253 <param name="model_preset" value="monomer"/>
275 <has_n_lines n="6"/> 254 <param name="outputs|plots" value="true"/>
276 <has_size value="70" delta="50"/> 255 <param name="outputs|confidence_scores" value="true"/>
277 </assert_contents> 256 <param name="outputs|plddts" value="true"/>
278 </output> 257 <param name="outputs|pae_csv" value="true"/>
279 <output name="model1"> 258 <param name="outputs|model_pkls" value="true"/>
280 <assert_contents> 259 <param name="outputs|relax_json" value="true"/>
281 <has_n_columns n="12"/> 260 <expand macro="test_output_plots_1" />
282 <has_n_lines n="1517"/> 261 <expand macro="test_output_confidence_scores" />
283 <has_size value="123000" delta="10000"/> 262 <expand macro="test_output_plddts" />
284 </assert_contents> 263 <expand macro="test_output_pdb_models" />
285 </output> 264 <expand macro="test_output_pickles" />
286 <output name="model2"> 265 <expand macro="test_output_relax_json" />
287 <assert_contents> 266 </test>
288 <has_n_columns n="12"/> 267
289 <has_n_lines n="1517"/> 268 <!-- Test monomer_ptm with all outputs -->
290 <has_size value="123000" delta="10000"/> 269 <test expect_num_outputs="24">
291 </assert_contents> 270 <conditional name="fasta_or_text">
292 </output> 271 <param name="input_mode" value="history"/>
293 <output name="model3"> 272 <param name="fasta_file" value="test1.fasta"/>
294 <assert_contents> 273 </conditional>
295 <has_n_columns n="12"/> 274 <param name="model_preset" value="monomer_ptm"/>
296 <has_n_lines n="1517"/> 275 <param name="outputs|plots" value="true"/>
297 <has_size value="123000" delta="10000"/> 276 <param name="outputs|confidence_scores" value="true"/>
298 </assert_contents> 277 <param name="outputs|plddts" value="true"/>
299 </output> 278 <param name="outputs|pae_csv" value="true"/>
300 <output name="model4"> 279 <param name="outputs|model_pkls" value="true"/>
301 <assert_contents> 280 <param name="outputs|relax_json" value="true"/>
302 <has_n_columns n="12"/> 281 <expand macro="test_output_plots_2" />
303 <has_n_lines n="1517"/> 282 <expand macro="test_output_confidence_scores" />
304 <has_size value="123000" delta="10000"/> 283 <expand macro="test_output_plddts" />
305 </assert_contents> 284 <expand macro="test_output_pdb_models" />
306 </output> 285 <expand macro="test_output_pickles" />
307 <output name="model5"> 286 <expand macro="test_output_relax_json" />
308 <assert_contents> 287 <expand macro="test_output_pae_csv" />
309 <has_n_columns n="12"/> 288 </test>
310 <has_n_lines n="1517"/> 289
311 <has_size value="123000" delta="10000"/> 290 <!-- Test multimer with all outputs -->
312 </assert_contents> 291 <test expect_num_outputs="24">
313 </output> 292 <conditional name="fasta_or_text">
293 <param name="input_mode" value="history"/>
294 <param name="fasta_file" value="multimer.fasta"/>
295 </conditional>
296 <param name="model_preset" value="multimer"/>
297 <param name="outputs|plots" value="true"/>
298 <param name="outputs|confidence_scores" value="true"/>
299 <param name="outputs|plddts" value="true"/>
300 <param name="outputs|pae_csv" value="true"/>
301 <param name="outputs|model_pkls" value="true"/>
302 <param name="outputs|relax_json" value="true"/>
303 <expand macro="test_output_plots_3" />
304 <expand macro="test_output_confidence_scores" />
305 <expand macro="test_output_plddts" />
306 <expand macro="test_output_pdb_models" />
307 <expand macro="test_output_pickles" />
308 <expand macro="test_output_relax_json" />
309 <expand macro="test_output_pae_csv" />
314 </test> 310 </test>
315 </tests> 311 </tests>
316 <help><![CDATA[ 312 <help><![CDATA[
317 313
318 .. class:: infomark 314 .. class:: infomark
387 | 383 |
388 384
389 *Model data files (ranked_n.pkl)* 385 *Model data files (ranked_n.pkl)*
390 386
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. 387 | Per-model data stored in pickle files (a Python binary data format). These files can be used as inputs to downstream analysis software (such as Chimera X) for visualizing structures and computing kinetics between protein multimers and domains.
392 | The tool will produce one ``.pkl`` output for each of the PDB models. 388 | The tool will produce one ``.pkl`` output for each PDB model.
389 |
390 |
391
392 *pLDDT + PAE plots (optional)*
393
394 | A two-panel figure in PNG format showing:
395 | a) pLDDT score plotted against residue position
396 | b) a heatmap of predicted-alignment error (PAE) with residue position running along vertical and horizontal axes and color at each pixel indicating PAE value for the corresponding pair of residues.
397 | Panel b) is only produced for ``monomer_ptm`` and ``multimer`` model presets.
398 |
399 |
400
401 *Model predicted-alignment error matrix (pae_ranked_n.csv)*
402
403 | Per-model predicted-alignment error (PAE) matrix - only available with the ``monomer_ptm`` and ``multimer`` model presets.
404 | The tool will produce one ``.csv`` output for each PDB model.
393 | 405 |
394 | 406 |
395 407
396 *relax_metrics.json (optional)* 408 *relax_metrics.json (optional)*
397 409
398 | A JSON-formatted text file containing relax metrics (mostly remaining violations). 410 | A JSON-formatted text file containing relax metrics (primarily remaining violations).
411 |
399 | 412 |
400 413
401 **AlphaFold configuration** 414 **AlphaFold configuration**
402 415
403 | We have configured AlphaFold to run with the parameters suggested by default on `AlphaFold's GitHub <https://github.com/deepmind/alphafold>`_. 416 | We have configured AlphaFold to run with the parameters suggested by default on `AlphaFold's GitHub <https://github.com/deepmind/alphafold>`_.
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>`_. 417 | This means that it runs with Amber relaxation enabled, with relaxed PDB models collected as output datasets (ranked\_*.pdb files). If there are additonal parameters that you would like to interact with, please `send a support request to Galaxy AU <https://site.usegalaxy.org.au/request/support>`_, or open an issue on `our GitHub <https://github.com/usegalaxy-au/tools-au>`_.
405 | 418 |
406 | 419 |
407 420
408 **External Resources** 421 **External Resources**
409 422