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comparison alphafold.xml @ 21:e7f1b552a695 draft

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planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 628c9fdcb77489063145a2307b6bb6a450416dd6-dirty
author galaxy-australia
date Tue, 29 Oct 2024 02:15:36 +0000
parents 6ab1a261520a
children 3f188450ca4f
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20:6ab1a261520a 21:e7f1b552a695
1 <tool id="alphafold" name="Alphafold 2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05"> 1 <tool id="alphafold" name="Alphafold 2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
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@">2.3.2</token> 4 <token name="@TOOL_VERSION@">2.3.2</token>
5 <token name="@TOOL_MINOR_VERSION@">2.3</token> 5 <token name="@TOOL_MINOR_VERSION@">2.3</token>
6 <token name="@VERSION_SUFFIX@">0</token> 6 <token name="@VERSION_SUFFIX@">1</token>
7 <import>macro_output.xml</import> 7 <import>macro_output.xml</import>
8 <import>macro_test_output.xml</import> 8 <import>macro_test_output.xml</import>
9 </macros> 9 </macros>
10 <edam_topics> 10 <edam_topics>
11 <edam_topic>topic_0082</edam_topic> 11 <edam_topic>topic_0082</edam_topic>
116 && python3 '$__tool_directory__/scripts/outputs.py' output/alphafold 116 && python3 '$__tool_directory__/scripts/outputs.py' output/alphafold
117 $outputs.plddts 117 $outputs.plddts
118 $outputs.model_pkls 118 $outputs.model_pkls
119 $outputs.pae_csv 119 $outputs.pae_csv
120 $outputs.plots 120 $outputs.plots
121 #if $model_preset.selection == 'multimer': 121 $outputs.plot_msa
122 --multimer
123 #end if
124 122
125 ## HTML output 123 ## HTML output
126 && mkdir -p '${ html.files_path }' 124 && mkdir -p '${ html.files_path }'
127 && cp output/alphafold/extra/alphafold.html '${html}' 125 && cp output/alphafold/extra/alphafold.html '${html}'
128 && cp output/alphafold/ranked_*.pdb '${html.files_path}' 126 && cp output/alphafold/ranked_*.pdb '${html.files_path}'
133 && (([ -d working ] && cp -r working/* .) || true) 131 && (([ -d working ] && cp -r working/* .) || true)
134 132
135 ]]></command> 133 ]]></command>
136 <inputs> 134 <inputs>
137 <conditional name="fasta_or_text"> 135 <conditional name="fasta_or_text">
138 <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."> 136 <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. We recommend submitting sequences with a maximum length of 3000AA, because run time scales exponentially with sequence length. If multiple-sequence FASTA file provided, multimer mode must be selected.">
139 <option value="history">Use fasta from history</option> 137 <option value="history">Use fasta from history</option>
140 <option value="textbox">Paste sequence into textbox</option> 138 <option value="textbox">Paste sequence into textbox</option>
141 </param> 139 </param>
142 <when value="history"> 140 <when value="history">
143 <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." /> 141 <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." />
234 falsevalue="" 232 falsevalue=""
235 label="pLDDT and PAE matrix plots (per model)" 233 label="pLDDT and PAE matrix plots (per model)"
236 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." 234 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."
237 /> 235 />
238 <param 236 <param
237 name="plot_msa"
238 type="boolean"
239 checked="false"
240 truevalue="--plot-msa"
241 falsevalue=""
242 label="MSA sequence coverage plot"
243 help="A heatmap showing sequence coverage across the multiple sequence alignment (MSA). This plot can help you understand if regions of low confidence are due to poor sequence coverage."
244 />
245 <param
239 name="confidence_scores" 246 name="confidence_scores"
240 type="boolean" 247 type="boolean"
241 checked="false" 248 checked="false"
242 label="Per-model confidence scores" 249 label="Per-model confidence scores"
243 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)." 250 help="A tabular file showing average confidence score for each model. The monomer preset is scored in plddt, the monomer_ptm preset is scored in predicted template modelling (PTM) and the multimer preset is scored in PTM+IPTM (interface PTM)."
244 /> 251 />
245 <param 252 <param
246 name="plddts" 253 name="plddts"
247 type="boolean" 254 type="boolean"
248 checked="false" 255 checked="false"
249 label="Per-residue confidence scores" 256 label="Per-residue confidence scores"
250 truevalue="--plddts" 257 truevalue="--confidence-scores"
251 falsevalue="" 258 falsevalue=""
252 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." 259 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."
253 /> 260 />
254 <param 261 <param
255 name="pae_csv" 262 name="pae_csv"
289 <outputs> 296 <outputs>
290 <expand macro="output_pdb_models" /> 297 <expand macro="output_pdb_models" />
291 <data name="html" format="html" label="${tool.name} on ${on_string}: Visualization" /> 298 <data name="html" format="html" label="${tool.name} on ${on_string}: Visualization" />
292 <!-- Optional outputs --> 299 <!-- Optional outputs -->
293 <expand macro="output_plddts" /> 300 <expand macro="output_plddts" />
301 <expand macro="output_msa_plot" />
294 <expand macro="output_confidence_scores" /> 302 <expand macro="output_confidence_scores" />
295 <expand macro="output_pickles" /> 303 <expand macro="output_pickles" />
296 <expand macro="output_pae_csv" /> 304 <expand macro="output_pae_csv" />
297 <expand macro="output_plots" /> 305 <expand macro="output_plots" />
298 <expand macro="output_relax_json" /> 306 <expand macro="output_relax_json" />
462 | 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. 470 | 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.
463 | Panel b) is only produced for ``monomer_ptm`` and ``multimer`` model presets. 471 | Panel b) is only produced for ``monomer_ptm`` and ``multimer`` model presets.
464 | 472 |
465 | 473 |
466 474
475 *MSA sequence coverage plot (optional)*
476
477 | A heatmap in PNG format showing:
478 | a) Per-position sequence identity to query as a heatmap
479 | b) Per-position sequence coverage as a line plot
480 |
481 | This plot can help you understand if regions of low confidence are due to poor sequence coverage, rather than
482 | limitations of the model or intrinsically unstable regions.
483 |
484 |
485
467 *Model predicted-alignment error matrix (pae_ranked_n.csv)* 486 *Model predicted-alignment error matrix (pae_ranked_n.csv)*
468 487
469 | Per-model predicted-alignment error (PAE) matrix - only available with the ``monomer_ptm`` and ``multimer`` model presets. 488 | Per-model predicted-alignment error (PAE) matrix - only available with the ``monomer_ptm`` and ``multimer`` model presets.
470 | The tool will produce one ``.csv`` output for each PDB model. 489 | The tool will produce one ``.csv`` output for each PDB model.
471 | 490 |