Mercurial > repos > galaxy-australia > alphafold2

comparison macro_output.xml @ 23:2891385d6ace draft

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planemo upload for repository https://github.com/usegalaxy-au/tools-au commit b347c6ccc82b14fcbff360b3357050d1d43e3ef5-dirty
author galaxy-australia
date Wed, 16 Apr 2025 05:46:58 +0000
parents e7f1b552a695
children 31f648b7555a
comparison
equal deleted inserted replaced
22:3f188450ca4f 23:2891385d6ace
1 <macros> 1 <macros>
2 <xml name="output_pdb_models"> 2 <xml name="output_pdb_models">
3 <data name="model5" format="pdb" from_work_dir="output/alphafold/ranked_4.pdb" label="${tool.name} on ${on_string}: PDB ranked 4"> 3 <data name="model5" format="pdb" from_work_dir="output/alphafold/ranked_4.pdb" label="${tool.name} on ${on_string}: PDB ranked 4">
4 <filter>advanced['limit_model_outputs'] > 4</filter> 4 <filter>advanced['limit_model_outputs'] > 4</filter>
5 <filter>not advanced['exit_after_msa']</filter>
5 </data> 6 </data>
6 <data name="model4" format="pdb" from_work_dir="output/alphafold/ranked_3.pdb" label="${tool.name} on ${on_string}: PDB ranked 3"> 7 <data name="model4" format="pdb" from_work_dir="output/alphafold/ranked_3.pdb" label="${tool.name} on ${on_string}: PDB ranked 3">
7 <filter>advanced['limit_model_outputs'] > 3</filter> 8 <filter>advanced['limit_model_outputs'] > 3</filter>
9 <filter>not advanced['exit_after_msa']</filter>
8 </data> 10 </data>
9 <data name="model3" format="pdb" from_work_dir="output/alphafold/ranked_2.pdb" label="${tool.name} on ${on_string}: PDB ranked 2"> 11 <data name="model3" format="pdb" from_work_dir="output/alphafold/ranked_2.pdb" label="${tool.name} on ${on_string}: PDB ranked 2">
10 <filter>advanced['limit_model_outputs'] > 2</filter> 12 <filter>advanced['limit_model_outputs'] > 2</filter>
13 <filter>not advanced['exit_after_msa']</filter>
11 </data> 14 </data>
12 <data name="model2" format="pdb" from_work_dir="output/alphafold/ranked_1.pdb" label="${tool.name} on ${on_string}: PDB ranked 1"> 15 <data name="model2" format="pdb" from_work_dir="output/alphafold/ranked_1.pdb" label="${tool.name} on ${on_string}: PDB ranked 1">
13 <filter>advanced['limit_model_outputs'] > 1</filter> 16 <filter>advanced['limit_model_outputs'] > 1</filter>
14 </data> 17 <filter>not advanced['exit_after_msa']</filter>
15 <data name="model1" format="pdb" from_work_dir="output/alphafold/ranked_0.pdb" label="${tool.name} on ${on_string}: PDB ranked 0"/> 18 </data>
19 <data name="model1" format="pdb" from_work_dir="output/alphafold/ranked_0.pdb" label="${tool.name} on ${on_string}: PDB ranked 0">
20 <filter>not advanced['exit_after_msa']</filter>
21 </data>
16 </xml> 22 </xml>
17 23
18 <xml name="output_pae_csv"> 24 <xml name="output_pae_csv">
19 <data 25 <data
20 name="pae_ranked_4" 26 name="pae_ranked_4"
23 label="${tool.name} on ${on_string}: pae_ranked_4.csv" 29 label="${tool.name} on ${on_string}: pae_ranked_4.csv"
24 > 30 >
25 <filter>outputs['pae_csv']</filter> 31 <filter>outputs['pae_csv']</filter>
26 <filter>model_preset != "monomer"</filter> 32 <filter>model_preset != "monomer"</filter>
27 <filter>advanced['limit_model_outputs'] > 4</filter> 33 <filter>advanced['limit_model_outputs'] > 4</filter>
34 <filter>not advanced['exit_after_msa']</filter>
28 </data> 35 </data>
29 <data 36 <data
30 name="pae_ranked_3" 37 name="pae_ranked_3"
31 format="csv" 38 format="csv"
32 from_work_dir="output/alphafold/extra/pae_ranked_3.csv" 39 from_work_dir="output/alphafold/extra/pae_ranked_3.csv"
33 label="${tool.name} on ${on_string}: pae_ranked_3.csv" 40 label="${tool.name} on ${on_string}: pae_ranked_3.csv"
34 > 41 >
35 <filter>outputs['pae_csv']</filter> 42 <filter>outputs['pae_csv']</filter>
36 <filter>model_preset != "monomer"</filter> 43 <filter>model_preset != "monomer"</filter>
37 <filter>advanced['limit_model_outputs'] > 3</filter> 44 <filter>advanced['limit_model_outputs'] > 3</filter>
45 <filter>not advanced['exit_after_msa']</filter>
38 </data> 46 </data>
39 <data 47 <data
40 name="pae_ranked_2" 48 name="pae_ranked_2"
41 format="csv" 49 format="csv"
42 from_work_dir="output/alphafold/extra/pae_ranked_2.csv" 50 from_work_dir="output/alphafold/extra/pae_ranked_2.csv"
43 label="${tool.name} on ${on_string}: pae_ranked_2.csv" 51 label="${tool.name} on ${on_string}: pae_ranked_2.csv"
44 > 52 >
45 <filter>outputs['pae_csv']</filter> 53 <filter>outputs['pae_csv']</filter>
46 <filter>model_preset != "monomer"</filter> 54 <filter>model_preset != "monomer"</filter>
47 <filter>advanced['limit_model_outputs'] > 2</filter> 55 <filter>advanced['limit_model_outputs'] > 2</filter>
56 <filter>not advanced['exit_after_msa']</filter>
48 </data> 57 </data>
49 <data 58 <data
50 name="pae_ranked_1" 59 name="pae_ranked_1"
51 format="csv" 60 format="csv"
52 from_work_dir="output/alphafold/extra/pae_ranked_1.csv" 61 from_work_dir="output/alphafold/extra/pae_ranked_1.csv"
53 label="${tool.name} on ${on_string}: pae_ranked_1.csv" 62 label="${tool.name} on ${on_string}: pae_ranked_1.csv"
54 > 63 >
55 <filter>outputs['pae_csv']</filter> 64 <filter>outputs['pae_csv']</filter>
56 <filter>model_preset != "monomer"</filter> 65 <filter>model_preset != "monomer"</filter>
57 <filter>advanced['limit_model_outputs'] > 1</filter> 66 <filter>advanced['limit_model_outputs'] > 1</filter>
67 <filter>not advanced['exit_after_msa']</filter>
58 </data> 68 </data>
59 <data 69 <data
60 name="pae_ranked_0" 70 name="pae_ranked_0"
61 format="csv" 71 format="csv"
62 from_work_dir="output/alphafold/extra/pae_ranked_0.csv" 72 from_work_dir="output/alphafold/extra/pae_ranked_0.csv"
63 label="${tool.name} on ${on_string}: pae_ranked_0.csv" 73 label="${tool.name} on ${on_string}: pae_ranked_0.csv"
64 > 74 >
65 <filter>outputs['pae_csv']</filter> 75 <filter>outputs['pae_csv']</filter>
66 <filter>model_preset != "monomer"</filter> 76 <filter>model_preset != "monomer"</filter>
77 <filter>not advanced['exit_after_msa']</filter>
67 </data> 78 </data>
68 </xml> 79 </xml>
69 80
70 <xml name="output_pickles"> 81 <xml name="output_pickles">
71 <data 82 <data
74 from_work_dir="output/alphafold/extra/ranked_4.pkl" 85 from_work_dir="output/alphafold/extra/ranked_4.pkl"
75 label="${tool.name} on ${on_string}: ranked_4.pkl" 86 label="${tool.name} on ${on_string}: ranked_4.pkl"
76 > 87 >
77 <filter>outputs['model_pkls']</filter> 88 <filter>outputs['model_pkls']</filter>
78 <filter>advanced['limit_model_outputs'] > 4</filter> 89 <filter>advanced['limit_model_outputs'] > 4</filter>
90 <filter>not advanced['exit_after_msa']</filter>
79 </data> 91 </data>
80 <data 92 <data
81 name="output_ranked_3_pkl" 93 name="output_ranked_3_pkl"
82 format="binary" 94 format="binary"
83 from_work_dir="output/alphafold/extra/ranked_3.pkl" 95 from_work_dir="output/alphafold/extra/ranked_3.pkl"
84 label="${tool.name} on ${on_string}: ranked_3.pkl" 96 label="${tool.name} on ${on_string}: ranked_3.pkl"
85 > 97 >
86 <filter>outputs['model_pkls']</filter> 98 <filter>outputs['model_pkls']</filter>
87 <filter>advanced['limit_model_outputs'] > 3</filter> 99 <filter>advanced['limit_model_outputs'] > 3</filter>
100 <filter>not advanced['exit_after_msa']</filter>
88 </data> 101 </data>
89 <data 102 <data
90 name="output_ranked_2_pkl" 103 name="output_ranked_2_pkl"
91 format="binary" 104 format="binary"
92 from_work_dir="output/alphafold/extra/ranked_2.pkl" 105 from_work_dir="output/alphafold/extra/ranked_2.pkl"
93 label="${tool.name} on ${on_string}: ranked_2.pkl" 106 label="${tool.name} on ${on_string}: ranked_2.pkl"
94 > 107 >
95 <filter>outputs['model_pkls']</filter> 108 <filter>outputs['model_pkls']</filter>
96 <filter>advanced['limit_model_outputs'] > 2</filter> 109 <filter>advanced['limit_model_outputs'] > 2</filter>
110 <filter>not advanced['exit_after_msa']</filter>
97 </data> 111 </data>
98 <data 112 <data
99 name="output_ranked_1_pkl" 113 name="output_ranked_1_pkl"
100 format="binary" 114 format="binary"
101 from_work_dir="output/alphafold/extra/ranked_1.pkl" 115 from_work_dir="output/alphafold/extra/ranked_1.pkl"
102 label="${tool.name} on ${on_string}: ranked_1.pkl" 116 label="${tool.name} on ${on_string}: ranked_1.pkl"
103 > 117 >
104 <filter>outputs['model_pkls']</filter> 118 <filter>outputs['model_pkls']</filter>
105 <filter>advanced['limit_model_outputs'] > 1</filter> 119 <filter>advanced['limit_model_outputs'] > 1</filter>
120 <filter>not advanced['exit_after_msa']</filter>
106 </data> 121 </data>
107 <data 122 <data
108 name="output_ranked_0_pkl" 123 name="output_ranked_0_pkl"
109 format="binary" 124 format="binary"
110 from_work_dir="output/alphafold/extra/ranked_0.pkl" 125 from_work_dir="output/alphafold/extra/ranked_0.pkl"
111 label="${tool.name} on ${on_string}: ranked_0.pkl" 126 label="${tool.name} on ${on_string}: ranked_0.pkl"
112 > 127 >
113 <filter>outputs['model_pkls']</filter> 128 <filter>outputs['model_pkls']</filter>
129 <filter>not advanced['exit_after_msa']</filter>
114 </data> 130 </data>
115 </xml> 131 </xml>
116 132
117 <xml name="output_plots"> 133 <xml name="output_plots">
118 <data 134 <data
121 from_work_dir="output/alphafold/extra/ranked_4.png" 137 from_work_dir="output/alphafold/extra/ranked_4.png"
122 label="${tool.name} on ${on_string}: pLDDT/PAE plot ranked 4" 138 label="${tool.name} on ${on_string}: pLDDT/PAE plot ranked 4"
123 > 139 >
124 <filter>outputs['plots']</filter> 140 <filter>outputs['plots']</filter>
125 <filter>advanced['limit_model_outputs'] > 4</filter> 141 <filter>advanced['limit_model_outputs'] > 4</filter>
142 <filter>not advanced['exit_after_msa']</filter>
126 </data> 143 </data>
127 <data 144 <data
128 name="plot_ranked_3" 145 name="plot_ranked_3"
129 format="png" 146 format="png"
130 from_work_dir="output/alphafold/extra/ranked_3.png" 147 from_work_dir="output/alphafold/extra/ranked_3.png"
131 label="${tool.name} on ${on_string}: pLDDT/PAE plot ranked 3" 148 label="${tool.name} on ${on_string}: pLDDT/PAE plot ranked 3"
132 > 149 >
133 <filter>outputs['plots']</filter> 150 <filter>outputs['plots']</filter>
134 <filter>advanced['limit_model_outputs'] > 3</filter> 151 <filter>advanced['limit_model_outputs'] > 3</filter>
152 <filter>not advanced['exit_after_msa']</filter>
135 </data> 153 </data>
136 <data 154 <data
137 name="plot_ranked_2" 155 name="plot_ranked_2"
138 format="png" 156 format="png"
139 from_work_dir="output/alphafold/extra/ranked_2.png" 157 from_work_dir="output/alphafold/extra/ranked_2.png"
140 label="${tool.name} on ${on_string}: pLDDT/PAE plot ranked 2" 158 label="${tool.name} on ${on_string}: pLDDT/PAE plot ranked 2"
141 > 159 >
142 <filter>outputs['plots']</filter> 160 <filter>outputs['plots']</filter>
143 <filter>advanced['limit_model_outputs'] > 2</filter> 161 <filter>advanced['limit_model_outputs'] > 2</filter>
162 <filter>not advanced['exit_after_msa']</filter>
144 </data> 163 </data>
145 <data 164 <data
146 name="plot_ranked_1" 165 name="plot_ranked_1"
147 format="png" 166 format="png"
148 from_work_dir="output/alphafold/extra/ranked_1.png" 167 from_work_dir="output/alphafold/extra/ranked_1.png"
149 label="${tool.name} on ${on_string}: pLDDT/PAE plot ranked 1" 168 label="${tool.name} on ${on_string}: pLDDT/PAE plot ranked 1"
150 > 169 >
151 <filter>outputs['plots']</filter> 170 <filter>outputs['plots']</filter>
152 <filter>advanced['limit_model_outputs'] > 1</filter> 171 <filter>advanced['limit_model_outputs'] > 1</filter>
172 <filter>not advanced['exit_after_msa']</filter>
153 </data> 173 </data>
154 <data 174 <data
155 name="plot_ranked_0" 175 name="plot_ranked_0"
156 format="png" 176 format="png"
157 from_work_dir="output/alphafold/extra/ranked_0.png" 177 from_work_dir="output/alphafold/extra/ranked_0.png"
158 label="${tool.name} on ${on_string}: pLDDT/PAE plot ranked 0" 178 label="${tool.name} on ${on_string}: pLDDT/PAE plot ranked 0"
159 > 179 >
160 <filter>outputs['plots']</filter> 180 <filter>outputs['plots']</filter>
181 <filter>not advanced['exit_after_msa']</filter>
161 </data> 182 </data>
162 </xml> 183 </xml>
163 184
164 <xml name="output_confidence_scores"> 185 <xml name="output_confidence_scores">
165 <data 186 <data
167 format="tabular" 188 format="tabular"
168 from_work_dir="output/alphafold/extra/model_confidence_scores.tsv" 189 from_work_dir="output/alphafold/extra/model_confidence_scores.tsv"
169 label="${tool.name} on ${on_string}: Model confidence scores" 190 label="${tool.name} on ${on_string}: Model confidence scores"
170 > 191 >
171 <filter>outputs['confidence_scores']</filter> 192 <filter>outputs['confidence_scores']</filter>
193 <filter>not advanced['exit_after_msa']</filter>
172 </data> 194 </data>
173 </xml> 195 </xml>
174 196
175 <xml name="output_msa_plot"> 197 <xml name="output_msa_plot">
176 <data 198 <data
178 format="png" 200 format="png"
179 from_work_dir="output/alphafold/extra/msa_coverage.png" 201 from_work_dir="output/alphafold/extra/msa_coverage.png"
180 label="${tool.name} on ${on_string}: MSA plot" 202 label="${tool.name} on ${on_string}: MSA plot"
181 > 203 >
182 <filter>outputs['plot_msa']</filter> 204 <filter>outputs['plot_msa']</filter>
205 <filter>not advanced['exit_after_msa']</filter>
183 </data> 206 </data>
184 </xml> 207 </xml>
185 208
186 <xml name="output_plddts"> 209 <xml name="output_plddts">
187 <data 210 <data
189 format="tabular" 212 format="tabular"
190 from_work_dir="output/alphafold/extra/plddts.tsv" 213 from_work_dir="output/alphafold/extra/plddts.tsv"
191 label="${tool.name} on ${on_string}: Per-residue confidence scores (plddts)" 214 label="${tool.name} on ${on_string}: Per-residue confidence scores (plddts)"
192 > 215 >
193 <filter>outputs['plddts']</filter> 216 <filter>outputs['plddts']</filter>
217 <filter>not advanced['exit_after_msa']</filter>
194 </data> 218 </data>
195 </xml> 219 </xml>
196 220
197 <xml name="output_relax_json"> 221 <xml name="output_relax_json">
198 <data 222 <data
200 format="json" 224 format="json"
201 from_work_dir="output/alphafold/extra/relax_metrics_ranked.json" 225 from_work_dir="output/alphafold/extra/relax_metrics_ranked.json"
202 label="${tool.name} on ${on_string}: relax_metrics_ranked.json" 226 label="${tool.name} on ${on_string}: relax_metrics_ranked.json"
203 > 227 >
204 <filter>outputs['relax_json']</filter> 228 <filter>outputs['relax_json']</filter>
229 <filter>not advanced['exit_after_msa']</filter>
205 </data> 230 </data>
206 </xml> 231 </xml>
207 232
208 <xml name="output_timings_json"> 233 <xml name="output_timings_json">
209 <data 234 <data
211 format="json" 236 format="json"
212 from_work_dir="output/alphafold/timings.json" 237 from_work_dir="output/alphafold/timings.json"
213 label="${tool.name} on ${on_string}: timings.json" 238 label="${tool.name} on ${on_string}: timings.json"
214 > 239 >
215 <filter>outputs['timings_json']</filter> 240 <filter>outputs['timings_json']</filter>
216 </data> 241 <filter>not advanced['exit_after_msa']</filter>
242 </data>
243 </xml>
244
245 <xml name="output_msa">
246 <collection name="output_msa" type="list" label="${tool.name} on ${on_string}: MSAs">
247 <discover_datasets
248 pattern="__designation_and_ext__"
249 directory="output/alphafold/extra/msas"
250 format="zip"
251 visible="false"
252 />
253 <filter>outputs['msa'] or advanced['exit_after_msa']</filter>
254 </collection>
217 </xml> 255 </xml>
218 </macros> 256 </macros>