Mercurial > repos > galaxy-australia > alphafold2

comparison macro_output.xml @ 20:6ab1a261520a draft

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planemo upload for repository https://github.com/usegalaxy-au/tools-au commit c3a90eb12ada44d477541baa4dd6182be29cd554-dirty
author galaxy-australia
date Sun, 28 Jul 2024 20:09:55 +0000
parents a58f7eb0df2c
children e7f1b552a695
comparison
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19:2f7702fd0a4c 20:6ab1a261520a
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 ${on_string}: PDB ranked 4">
4 <data name="model4" format="pdb" from_work_dir="output/alphafold/ranked_3.pdb" label="${tool.name} on ${on_string}: PDB ranked 3"/> 4 <filter>advanced['limit_model_outputs'] > 4</filter>
5 <data name="model3" format="pdb" from_work_dir="output/alphafold/ranked_2.pdb" label="${tool.name} on ${on_string}: PDB ranked 2"/> 5 </data>
6 <data name="model2" format="pdb" from_work_dir="output/alphafold/ranked_1.pdb" label="${tool.name} on ${on_string}: PDB ranked 1"/> 6 <data name="model4" format="pdb" from_work_dir="output/alphafold/ranked_3.pdb" label="${tool.name} on ${on_string}: PDB ranked 3">
7 <filter>advanced['limit_model_outputs'] > 3</filter>
8 </data>
9 <data name="model3" format="pdb" from_work_dir="output/alphafold/ranked_2.pdb" label="${tool.name} on ${on_string}: PDB ranked 2">
10 <filter>advanced['limit_model_outputs'] > 2</filter>
11 </data>
12 <data name="model2" format="pdb" from_work_dir="output/alphafold/ranked_1.pdb" label="${tool.name} on ${on_string}: PDB ranked 1">
13 <filter>advanced['limit_model_outputs'] > 1</filter>
14 </data>
7 <data name="model1" format="pdb" from_work_dir="output/alphafold/ranked_0.pdb" label="${tool.name} on ${on_string}: PDB ranked 0"/> 15 <data name="model1" format="pdb" from_work_dir="output/alphafold/ranked_0.pdb" label="${tool.name} on ${on_string}: PDB ranked 0"/>
8 </xml> 16 </xml>
9 17
10 <xml name="output_pae_csv"> 18 <xml name="output_pae_csv">
11 <data 19 <data
14 from_work_dir="output/alphafold/extra/pae_ranked_4.csv" 22 from_work_dir="output/alphafold/extra/pae_ranked_4.csv"
15 label="${tool.name} on ${on_string}: pae_ranked_4.csv" 23 label="${tool.name} on ${on_string}: pae_ranked_4.csv"
16 > 24 >
17 <filter>outputs['pae_csv']</filter> 25 <filter>outputs['pae_csv']</filter>
18 <filter>model_preset != "monomer"</filter> 26 <filter>model_preset != "monomer"</filter>
27 <filter>advanced['limit_model_outputs'] > 4</filter>
19 </data> 28 </data>
20 <data 29 <data
21 name="pae_ranked_3" 30 name="pae_ranked_3"
22 format="csv" 31 format="csv"
23 from_work_dir="output/alphafold/extra/pae_ranked_3.csv" 32 from_work_dir="output/alphafold/extra/pae_ranked_3.csv"
24 label="${tool.name} on ${on_string}: pae_ranked_3.csv" 33 label="${tool.name} on ${on_string}: pae_ranked_3.csv"
25 > 34 >
26 <filter>outputs['pae_csv']</filter> 35 <filter>outputs['pae_csv']</filter>
27 <filter>model_preset != "monomer"</filter> 36 <filter>model_preset != "monomer"</filter>
37 <filter>advanced['limit_model_outputs'] > 3</filter>
28 </data> 38 </data>
29 <data 39 <data
30 name="pae_ranked_2" 40 name="pae_ranked_2"
31 format="csv" 41 format="csv"
32 from_work_dir="output/alphafold/extra/pae_ranked_2.csv" 42 from_work_dir="output/alphafold/extra/pae_ranked_2.csv"
33 label="${tool.name} on ${on_string}: pae_ranked_2.csv" 43 label="${tool.name} on ${on_string}: pae_ranked_2.csv"
34 > 44 >
35 <filter>outputs['pae_csv']</filter> 45 <filter>outputs['pae_csv']</filter>
36 <filter>model_preset != "monomer"</filter> 46 <filter>model_preset != "monomer"</filter>
47 <filter>advanced['limit_model_outputs'] > 2</filter>
37 </data> 48 </data>
38 <data 49 <data
39 name="pae_ranked_1" 50 name="pae_ranked_1"
40 format="csv" 51 format="csv"
41 from_work_dir="output/alphafold/extra/pae_ranked_1.csv" 52 from_work_dir="output/alphafold/extra/pae_ranked_1.csv"
42 label="${tool.name} on ${on_string}: pae_ranked_1.csv" 53 label="${tool.name} on ${on_string}: pae_ranked_1.csv"
43 > 54 >
44 <filter>outputs['pae_csv']</filter> 55 <filter>outputs['pae_csv']</filter>
45 <filter>model_preset != "monomer"</filter> 56 <filter>model_preset != "monomer"</filter>
57 <filter>advanced['limit_model_outputs'] > 1</filter>
46 </data> 58 </data>
47 <data 59 <data
48 name="pae_ranked_0" 60 name="pae_ranked_0"
49 format="csv" 61 format="csv"
50 from_work_dir="output/alphafold/extra/pae_ranked_0.csv" 62 from_work_dir="output/alphafold/extra/pae_ranked_0.csv"
61 format="binary" 73 format="binary"
62 from_work_dir="output/alphafold/extra/ranked_4.pkl" 74 from_work_dir="output/alphafold/extra/ranked_4.pkl"
63 label="${tool.name} on ${on_string}: ranked_4.pkl" 75 label="${tool.name} on ${on_string}: ranked_4.pkl"
64 > 76 >
65 <filter>outputs['model_pkls']</filter> 77 <filter>outputs['model_pkls']</filter>
78 <filter>advanced['limit_model_outputs'] > 4</filter>
66 </data> 79 </data>
67 <data 80 <data
68 name="output_ranked_3_pkl" 81 name="output_ranked_3_pkl"
69 format="binary" 82 format="binary"
70 from_work_dir="output/alphafold/extra/ranked_3.pkl" 83 from_work_dir="output/alphafold/extra/ranked_3.pkl"
71 label="${tool.name} on ${on_string}: ranked_3.pkl" 84 label="${tool.name} on ${on_string}: ranked_3.pkl"
72 > 85 >
73 <filter>outputs['model_pkls']</filter> 86 <filter>outputs['model_pkls']</filter>
87 <filter>advanced['limit_model_outputs'] > 3</filter>
74 </data> 88 </data>
75 <data 89 <data
76 name="output_ranked_2_pkl" 90 name="output_ranked_2_pkl"
77 format="binary" 91 format="binary"
78 from_work_dir="output/alphafold/extra/ranked_2.pkl" 92 from_work_dir="output/alphafold/extra/ranked_2.pkl"
79 label="${tool.name} on ${on_string}: ranked_2.pkl" 93 label="${tool.name} on ${on_string}: ranked_2.pkl"
80 > 94 >
81 <filter>outputs['model_pkls']</filter> 95 <filter>outputs['model_pkls']</filter>
96 <filter>advanced['limit_model_outputs'] > 2</filter>
82 </data> 97 </data>
83 <data 98 <data
84 name="output_ranked_1_pkl" 99 name="output_ranked_1_pkl"
85 format="binary" 100 format="binary"
86 from_work_dir="output/alphafold/extra/ranked_1.pkl" 101 from_work_dir="output/alphafold/extra/ranked_1.pkl"
87 label="${tool.name} on ${on_string}: ranked_1.pkl" 102 label="${tool.name} on ${on_string}: ranked_1.pkl"
88 > 103 >
89 <filter>outputs['model_pkls']</filter> 104 <filter>outputs['model_pkls']</filter>
105 <filter>advanced['limit_model_outputs'] > 1</filter>
90 </data> 106 </data>
91 <data 107 <data
92 name="output_ranked_0_pkl" 108 name="output_ranked_0_pkl"
93 format="binary" 109 format="binary"
94 from_work_dir="output/alphafold/extra/ranked_0.pkl" 110 from_work_dir="output/alphafold/extra/ranked_0.pkl"
104 format="png" 120 format="png"
105 from_work_dir="output/alphafold/extra/ranked_4.png" 121 from_work_dir="output/alphafold/extra/ranked_4.png"
106 label="${tool.name} on ${on_string}: pLDDT/PAE plot ranked 4" 122 label="${tool.name} on ${on_string}: pLDDT/PAE plot ranked 4"
107 > 123 >
108 <filter>outputs['plots']</filter> 124 <filter>outputs['plots']</filter>
125 <filter>advanced['limit_model_outputs'] > 4</filter>
109 </data> 126 </data>
110 <data 127 <data
111 name="plot_ranked_3" 128 name="plot_ranked_3"
112 format="png" 129 format="png"
113 from_work_dir="output/alphafold/extra/ranked_3.png" 130 from_work_dir="output/alphafold/extra/ranked_3.png"
114 label="${tool.name} on ${on_string}: pLDDT/PAE plot ranked 3" 131 label="${tool.name} on ${on_string}: pLDDT/PAE plot ranked 3"
115 > 132 >
116 <filter>outputs['plots']</filter> 133 <filter>outputs['plots']</filter>
134 <filter>advanced['limit_model_outputs'] > 3</filter>
117 </data> 135 </data>
118 <data 136 <data
119 name="plot_ranked_2" 137 name="plot_ranked_2"
120 format="png" 138 format="png"
121 from_work_dir="output/alphafold/extra/ranked_2.png" 139 from_work_dir="output/alphafold/extra/ranked_2.png"
122 label="${tool.name} on ${on_string}: pLDDT/PAE plot ranked 2" 140 label="${tool.name} on ${on_string}: pLDDT/PAE plot ranked 2"
123 > 141 >
124 <filter>outputs['plots']</filter> 142 <filter>outputs['plots']</filter>
143 <filter>advanced['limit_model_outputs'] > 2</filter>
125 </data> 144 </data>
126 <data 145 <data
127 name="plot_ranked_1" 146 name="plot_ranked_1"
128 format="png" 147 format="png"
129 from_work_dir="output/alphafold/extra/ranked_1.png" 148 from_work_dir="output/alphafold/extra/ranked_1.png"
130 label="${tool.name} on ${on_string}: pLDDT/PAE plot ranked 1" 149 label="${tool.name} on ${on_string}: pLDDT/PAE plot ranked 1"
131 > 150 >
132 <filter>outputs['plots']</filter> 151 <filter>outputs['plots']</filter>
152 <filter>advanced['limit_model_outputs'] > 1</filter>
133 </data> 153 </data>
134 <data 154 <data
135 name="plot_ranked_0" 155 name="plot_ranked_0"
136 format="png" 156 format="png"
137 from_work_dir="output/alphafold/extra/ranked_0.png" 157 from_work_dir="output/alphafold/extra/ranked_0.png"
171 label="${tool.name} on ${on_string}: relax_metrics_ranked.json" 191 label="${tool.name} on ${on_string}: relax_metrics_ranked.json"
172 > 192 >
173 <filter>outputs['relax_json']</filter> 193 <filter>outputs['relax_json']</filter>
174 </data> 194 </data>
175 </xml> 195 </xml>
196
197 <xml name="output_timings_json">
198 <data
199 name="output_timings_json"
200 format="json"
201 from_work_dir="output/alphafold/timings.json"
202 label="${tool.name} on ${on_string}: timings.json"
203 >
204 <filter>outputs['timings_json']</filter>
205 </data>
206 </xml>
176 </macros> 207 </macros>