Mercurial > repos > iuc > semibin_train
comparison train.xml @ 0:08cc1cd58f38 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
author | iuc |
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date | Fri, 14 Oct 2022 21:42:14 +0000 |
parents | |
children | 43df7a4c33a2 |
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-1:000000000000 | 0:08cc1cd58f38 |
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1 <tool id="semibin_train" name="SemiBin: Train" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> | |
2 <description> | |
3 the semi-supervised deep learning model | |
4 </description> | |
5 <macros> | |
6 <import>macros.xml</import> | |
7 </macros> | |
8 <expand macro="biotools"/> | |
9 <expand macro="requirements"/> | |
10 <expand macro="version"/> | |
11 <command detect_errors="exit_code"><![CDATA[ | |
12 #import re | |
13 #if $mode.select == 'single' | |
14 #if $mode.input_fasta.ext.endswith(".gz") | |
15 gunzip -c '$mode.input_fasta' > 'contigs.fasta' && | |
16 #else | |
17 ln -s '$mode.input_fasta' 'contigs.fasta' && | |
18 #end if | |
19 #else | |
20 #for $e in $mode.input_fasta | |
21 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($e.element_identifier)) | |
22 #if $e.ext.endswith(".gz") | |
23 gunzip -c '$e' > '${identifier}.fasta' && | |
24 #else | |
25 ln -s '$e' '${identifier}.fasta' && | |
26 #end if | |
27 #end for | |
28 #end if | |
29 SemiBin train | |
30 --mode '$mode.select' | |
31 #if $mode.select == 'single' | |
32 --input-fasta 'contigs.fasta' | |
33 --data '$mode.data' | |
34 --data-split '$mode.data_split' | |
35 --cannot-link '$mode.cannot_link' | |
36 #else | |
37 #for $e in $mode.input_fasta | |
38 --input-fasta '${e.element_identifier}.fasta' | |
39 #end for | |
40 #for $e in $mode.data | |
41 --data '$e' | |
42 #end for | |
43 #for $e in $mode.data_split | |
44 --data-split '$e' | |
45 #end for | |
46 #for $e in $mode.cannot_link | |
47 --cannot-link '$e' | |
48 #end for | |
49 #end if | |
50 --output 'output' | |
51 --threads \${GALAXY_SLOTS:-1} | |
52 --epoches $epoches | |
53 --batch-size $batch_size | |
54 --random-seed $random_seed | |
55 #if $min_len.method == 'min-len' | |
56 --min-len $min_len.min_len | |
57 #else if $min_len.method == 'ratio' | |
58 --ratio $min_len.ratio | |
59 #end if | |
60 --orf-finder '$orf_finder' | |
61 ]]></command> | |
62 <inputs> | |
63 <conditional name="mode"> | |
64 <param argument="select" type="select" label="Mode to train the models"> | |
65 <option value="single" selected="true">From one sample</option> | |
66 <option value="several">From multiple samples (train model across several samples can get better pre-trained model for single-sample binning)</option> | |
67 </param> | |
68 <when value="single"> | |
69 <param argument="--input-fasta" type="data" format="fasta,fasta.gz" label="Contig sequences"/> | |
70 <param argument="--data" type="data" format="csv" label="Train data"/> | |
71 <param argument="--data-split" type="data" format="csv" label="Split train data"/> | |
72 <param argument="--cannot-link" type="data" format="txt" label="Cannot-link constraints"/> | |
73 </when> | |
74 <when value="several"> | |
75 <param argument="--input-fasta" type="data" multiple="true" format="fasta,fasta.gz" label="Contig sequences"/> | |
76 <param argument="--data" type="data" format="csv" multiple="true" label="Train data"/> | |
77 <param argument="--data-split" type="data" format="csv" multiple="true" label="Split train data"/> | |
78 <param argument="--cannot-link" type="data" format="txt" multiple="true" label="Cannot-link constraints"/> | |
79 </when> | |
80 </conditional> | |
81 <expand macro="min_len"/> | |
82 <expand macro="orf-finder"/> | |
83 <expand macro="random-seed"/> | |
84 <expand macro="epoches"/> | |
85 <expand macro="batch-size"/> | |
86 </inputs> | |
87 <outputs> | |
88 <expand macro="train_output"/> | |
89 </outputs> | |
90 <tests> | |
91 <test expect_num_outputs="1"> | |
92 <conditional name="mode"> | |
93 <param name="select" value="single"/> | |
94 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/> | |
95 <param name="data" ftype="csv" value="data.csv"/> | |
96 <param name="data_split" ftype="csv" value="data_split.csv"/> | |
97 <param name="cannot_link" ftype="txt" value="cannot.txt"/> | |
98 </conditional> | |
99 <conditional name="min_len"> | |
100 <param name="method" value="min-len"/> | |
101 <param name="min_len" value="2500" /> | |
102 </conditional> | |
103 <param name="orf_finder" value="prodigal"/> | |
104 <param name="random-seed" value="0"/> | |
105 <param name="epoches" value="1"/> | |
106 <param name="batch_size" value="2048"/> | |
107 <output name="model" ftype="h5"> | |
108 <assert_contents> | |
109 <has_size value="3119000" delta="1000" /> | |
110 </assert_contents> | |
111 </output> | |
112 </test> | |
113 <test expect_num_outputs="1"> | |
114 <conditional name="mode"> | |
115 <param name="select" value="several"/> | |
116 <param name="input_fasta" ftype="fasta" value="input_single.fasta,input_single_2.fasta,input_single_3.fasta"/> | |
117 <param name="data" ftype="csv" value="data.csv,data.csv,data.csv"/> | |
118 <param name="data_split" ftype="csv" value="data_split.csv,data_split.csv,data_split.csv"/> | |
119 <param name="cannot_link" ftype="txt" value="cannot.txt,cannot.txt,cannot.txt"/> | |
120 </conditional> | |
121 <conditional name="min_len"> | |
122 <param name="method" value="ratio"/> | |
123 <param name="ratio" value="0.05" /> | |
124 </conditional> | |
125 <param name="orf_finder" value="prodigal"/> | |
126 <param name="random-seed" value="0"/> | |
127 <param name="epoches" value="20"/> | |
128 <param name="batch_size" value="2048"/> | |
129 <output name="model" ftype="h5"> | |
130 <assert_contents> | |
131 <has_size value="3119000" delta="1000" /> | |
132 </assert_contents> | |
133 </output> | |
134 </test> | |
135 </tests> | |
136 <help><![CDATA[ | |
137 @HELP_HEADER@ | |
138 | |
139 This tool trains the semi-supervised deep learning model | |
140 | |
141 Inputs | |
142 ====== | |
143 | |
144 @HELP_INPUT_FASTA@ | |
145 @HELP_CANNOT@ | |
146 @HELP_DATA@ | |
147 | |
148 Outputs | |
149 ======= | |
150 | |
151 @HELP_MODEL@ | |
152 ]]></help> | |
153 <expand macro="citations"/> | |
154 </tool> |