comparison colabfold_alphafold.xml @ 2:9d65257c56de draft default tip

planemo upload for repository https://github.com/sokrypton/ColabFold commit b01085b7137b002268e0a8e4d75a5e03326638bb
author iuc
date Wed, 21 Aug 2024 07:40:05 +0000
parents 5f7a01f8ea28
children
comparison
equal deleted inserted replaced
1:5f7a01f8ea28 2:9d65257c56de
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">