Mercurial > repos > iuc > semibin_train

comparison train.xml @ 2:35c4a1990ba2 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
author iuc
date Tue, 25 Mar 2025 15:50:55 +0000
parents f9f3d70127c2
children be96c5251f2d
comparison
equal deleted inserted replaced
1:f9f3d70127c2 2:35c4a1990ba2
24 #else 24 #else
25 ln -s '$e' '${identifier}.fasta' && 25 ln -s '$e' '${identifier}.fasta' &&
26 #end if 26 #end if
27 #end for 27 #end for
28 #end if 28 #end if
29 SemiBin train 29 SemiBin2 train_semi
30 --mode '$mode.select'
31 #if $mode.select == 'single' 30 #if $mode.select == 'single'
32 --input-fasta 'contigs.fasta' 31 --input-fasta 'contigs.fasta'
33 --data '$mode.data' 32 --data '$mode.data'
34 --data-split '$mode.data_split' 33 --data-split '$mode.data_split'
35 --cannot-link '$mode.cannot_link' 34 --cannot-link '$mode.cannot_link'
36 #else 35 #else
36 --train-from-many
37 #for $e in $mode.input_fasta 37 #for $e in $mode.input_fasta
38 --input-fasta '${e.element_identifier}.fasta' 38 --input-fasta '${e.element_identifier}.fasta'
39 #end for 39 #end for
40 #for $e in $mode.data 40 #for $e in $mode.data
41 --data '$e' 41 --data '$e'
99 <conditional name="min_len"> 99 <conditional name="min_len">
100 <param name="method" value="min-len"/> 100 <param name="method" value="min-len"/>
101 <param name="min_len" value="2500" /> 101 <param name="min_len" value="2500" />
102 </conditional> 102 </conditional>
103 <param name="orf_finder" value="prodigal"/> 103 <param name="orf_finder" value="prodigal"/>
104 <param name="random-seed" value="0"/> 104 <param name="random_seed" value="0"/>
105 <param name="epoches" value="1"/> 105 <param name="epoches" value="1"/>
106 <param name="batch_size" value="2048"/> 106 <param name="batch_size" value="2048"/>
107 <output name="model" ftype="h5"> 107 <output name="model" ftype="h5">
108 <assert_contents> 108 <assert_contents>
109 <has_size value="3119000" delta="2000" /> 109 <has_size value="3119000" delta="2000" />
121 <conditional name="min_len"> 121 <conditional name="min_len">
122 <param name="method" value="ratio"/> 122 <param name="method" value="ratio"/>
123 <param name="ratio" value="0.05" /> 123 <param name="ratio" value="0.05" />
124 </conditional> 124 </conditional>
125 <param name="orf_finder" value="prodigal"/> 125 <param name="orf_finder" value="prodigal"/>
126 <param name="random-seed" value="0"/> 126 <param name="random_seed" value="0"/>
127 <param name="epoches" value="20"/> 127 <param name="epoches" value="20"/>
128 <param name="batch_size" value="2048"/> 128 <param name="batch_size" value="2048"/>
129 <output name="model" ftype="h5"> 129 <output name="model" ftype="h5">
130 <assert_contents> 130 <assert_contents>
131 <has_size value="3119000" delta="2000" /> 131 <has_size value="3119000" delta="2000" />