Mercurial > repos > iuc > colabfold_alphafold
comparison colabfold_alphafold.xml @ 2:9d65257c56de draft default tip
planemo upload for repository https://github.com/sokrypton/ColabFold commit b01085b7137b002268e0a8e4d75a5e03326638bb
author | iuc |
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date | Wed, 21 Aug 2024 07:40:05 +0000 |
parents | 5f7a01f8ea28 |
children |
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1:5f7a01f8ea28 | 2:9d65257c56de |
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41 $output_options.save_pair_representations | 41 $output_options.save_pair_representations |
42 --jobname-prefix "galaxy" | 42 --jobname-prefix "galaxy" |
43 input_data | 43 input_data |
44 output | 44 output |
45 && cd output | 45 && cd output |
46 && mv *.a3m output.a3m | 46 && mkdir a3m_out |
47 && mkdir png_out | 47 && mkdir png_out |
48 && mkdir json_out | 48 && mkdir json_out |
49 && mkdir pdb_out | 49 && mkdir pdb_out |
50 && mv ./*.a3m a3m_out | |
50 && mv ./*.png png_out | 51 && mv ./*.png png_out |
51 && mv ./*.json json_out | 52 && mv ./*.json json_out |
52 && mv ./*.pdb pdb_out | 53 && mv ./*.pdb pdb_out |
53 && mv json_out/config.json . | 54 && mv json_out/config.json . |
54 #if $output_options.save_all: | 55 #if $output_options.save_all: |
115 </collection> | 116 </collection> |
116 <collection name="npy" type="list" format="npy" label="${tool.name} on ${on_string}: Numpy embeddings"> | 117 <collection name="npy" type="list" format="npy" label="${tool.name} on ${on_string}: Numpy embeddings"> |
117 <discover_datasets format="npy" pattern="__name_and_ext__" directory="output/npy_out"/> | 118 <discover_datasets format="npy" pattern="__name_and_ext__" directory="output/npy_out"/> |
118 <filter>output_options['save_single_representations'] or output_options['save_pair_representations']</filter> | 119 <filter>output_options['save_single_representations'] or output_options['save_pair_representations']</filter> |
119 </collection> | 120 </collection> |
120 <data name="a3m_out" format="a3m" from_work_dir="output/output.a3m" label="${tool.name} on ${on_string}: a3m file"/> | 121 <collection name="a3m" type="list" format="a3m" label="${tool.name} on ${on_string}: a3m files"> |
122 <discover_datasets format="a3m" pattern="__name_and_ext__" directory="output/a3m_out"/> | |
123 </collection> | |
121 </outputs> | 124 </outputs> |
122 <tests> | 125 <tests> |
123 <test expect_failure="true" expect_exit_code="1"> | 126 <test expect_failure="true" expect_exit_code="1"> |
124 <param name="input" value="input.tar"/> | 127 <param name="input" value="input.tar"/> |
125 <section name="advanced"> | 128 <section name="advanced"> |