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comparison comebin.xml @ 1:15f6ef1d7c96 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit a298275e9754bf6bc71e5ee794121bbc6b3d426c
author iuc
date Wed, 30 Jul 2025 11:47:15 +0000
parents 2576c9132481
children ddfb9c10740a
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0:2576c9132481 1:15f6ef1d7c96
33 ]]> 33 ]]>
34 </command> 34 </command>
35 <inputs> 35 <inputs>
36 <param name="assembly_file" type="data" format="fasta" label="Metagenomic assembly file"/> 36 <param name="assembly_file" type="data" format="fasta" label="Metagenomic assembly file"/>
37 <param name="bam_files" type="data" format="bam" multiple="true" label="Input bam file(s)"/> 37 <param name="bam_files" type="data" format="bam" multiple="true" label="Input bam file(s)"/>
38 <param name="learning" type="integer" default_value="6" label="Views for contrastive multiple-view learning"/> 38 <param name="learning" type="integer" value="6" label="Views for contrastive multiple-view learning"/>
39 <param name="loss" type="float" default_value="0.15" label="Temperature in loss function" help="0.07 is recommended for assemblies with an N50 > 10000"/> 39 <param name="loss" type="float" value="0.15" label="Temperature in loss function" help="0.07 is recommended for assemblies with an N50 > 10000"/>
40 <param name="emb_comebin" type="integer" default_value="2048" label="Embedding size for COMEBin network"/> 40 <param name="emb_comebin" type="integer" value="2048" label="Embedding size for COMEBin network"/>
41 <param name="emb_cov" type="integer" default_value="2048" label="Embedding size for coverage network"/> 41 <param name="emb_cov" type="integer" value="2048" label="Embedding size for coverage network"/>
42 <param name="batch" type="integer" default_value="1024" label="Batch size"/> 42 <param name="batch" type="integer" value="1024" label="Batch size"/>
43 </inputs> 43 </inputs>
44 <outputs> 44 <outputs>
45 <collection name="bins" type="list" format="fasta" label="${tool.name}: BINS"> 45 <collection name="bins" type="list" format="fasta" label="${tool.name}: BINS">
46 <discover_datasets pattern="__name__" directory="outputs/comebin_res/comebin_res_bins/"/> 46 <discover_datasets pattern="__name__" directory="outputs/comebin_res/comebin_res_bins/"/>
47 </collection> 47 </collection>