Mercurial > repos > iuc > semibin_train

annotate train.xml @ 6:3215ab8a94de draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
author iuc
date Tue, 28 Oct 2025 08:20:57 +0000
parents 2344bc30a326
children
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08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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1 <tool id="semibin_train" name="SemiBin: Train" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>
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3 the semi-supervised deep learning model
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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4 </description>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="biotools"/>
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9 <expand macro="requirements"/>
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10 <expand macro="version"/>
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11 <command detect_errors="exit_code"><![CDATA[
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12 #import re
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13 #if $mode.select == 'single'
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14 ln -s '$mode.input_fasta' 'contigs.$input_fasta.ext' &&
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15 #else
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16 #for $e in $mode.input_fasta
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17 #set $identifier = re.sub('[^\s\w\-]', '_', str($e.element_identifier))
3215ab8a94de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
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18 ln -s '$e' '${identifier}.$e.ext' &&
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19 #end for
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20 #end if
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21 SemiBin2 train_semi
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22 #if $mode.select == 'single'
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23 --input-fasta 'contigs.$input_fasta.ext'
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24 --data '$mode.data'
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25 --data-split '$mode.data_split'
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26 --cannot-link '$mode.cannot_link'
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27 #else
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28 --train-from-many
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29 --input-fasta
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30 #for $e in $mode.input_fasta
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31 #set $identifier = re.sub('[^\s\w\-]', '_', str($e.element_identifier))
3215ab8a94de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
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32 '${identifier}.$e.ext'
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33 #end for
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34 --data
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35 #for $e in $mode.data
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36 '$e'
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37 #end for
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38 --data-split
3215ab8a94de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
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39 #for $e in $mode.data_split
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40 '$e'
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41 #end for
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42 --cannot-link
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43 #for $e in $mode.cannot_link
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44 '$e'
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45 #end for
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46 #end if
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47 --output 'output'
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48 --threads \${GALAXY_SLOTS:-1}
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49 --epoches $epoches
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50 --batch-size $batch_size
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51 --random-seed $random_seed
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52 #if $min_len.method == 'min-len'
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53 --min-len $min_len.min_len
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54 #else if $min_len.method == 'ratio'
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55 --ratio $min_len.ratio
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56 #end if
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57 --orf-finder '$orf_finder'
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58 ]]></command>
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59 <inputs>
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60 <conditional name="mode">
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61 <param argument="select" type="select" label="Mode to train the models">
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62 <option value="single" selected="true">From one sample</option>
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63 <option value="several">From multiple samples (train model across several samples can get better pre-trained model for single-sample binning)</option>
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64 </param>
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65 <when value="single">
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66 <param argument="--input-fasta" type="data" format="fasta,fasta.gz,fasta.bz2" label="Contig sequences"/>
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67 <param argument="--data" type="data" format="csv" label="Train data"/>
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68 <param argument="--data-split" type="data" format="csv" label="Split train data"/>
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69 <param argument="--cannot-link" type="data" format="txt" label="Cannot-link constraints"/>
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70 </when>
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71 <when value="several">
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72 <param argument="--input-fasta" type="data" multiple="true" format="fasta,fasta.gz,fasta.bz2" label="Contig sequences"/>
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73 <param argument="--data" type="data" format="csv" multiple="true" label="Train data"/>
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74 <param argument="--data-split" type="data" format="csv" multiple="true" label="Split train data"/>
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75 <param argument="--cannot-link" type="data" format="txt" multiple="true" label="Cannot-link constraints"/>
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76 </when>
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77 </conditional>
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78 <expand macro="min_len"/>
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79 <expand macro="orf-finder"/>
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80 <expand macro="random-seed"/>
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81 <expand macro="epoches"/>
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82 <expand macro="batch-size"/>
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83 </inputs>
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84 <outputs>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
85 <expand macro="train_output"/>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
86 </outputs>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
87 <tests>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
88 <test expect_num_outputs="1">
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
89 <conditional name="mode">
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
90 <param name="select" value="single"/>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
91 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
92 <param name="data" ftype="csv" value="data.csv"/>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
93 <param name="data_split" ftype="csv" value="data_split.csv"/>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
94 <param name="cannot_link" ftype="txt" value="cannot.txt"/>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
95 </conditional>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
96 <conditional name="min_len">
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
97 <param name="method" value="min-len"/>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
98 <param name="min_len" value="2500" />
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
99 </conditional>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
100 <param name="orf_finder" value="prodigal"/>
3
2344bc30a326 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 2
diff changeset
101 <param name="random_seed" value="0"/>
0
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
102 <param name="epoches" value="1"/>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
103 <param name="batch_size" value="2048"/>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
104 <output name="model" ftype="h5">
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
105 <assert_contents>
1
43df7a4c33a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
iuc
parents: 0
diff changeset
106 <has_size value="3119000" delta="2000" />
0
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
107 </assert_contents>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
108 </output>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
109 </test>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
110 <test expect_num_outputs="1">
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
111 <conditional name="mode">
6
3215ab8a94de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
iuc
parents: 3
diff changeset
112 <param name="select" value="single"/>
3215ab8a94de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
iuc
parents: 3
diff changeset
113 <param name="input_fasta" ftype="fasta.bz2" value="input_single.fasta.bz2"/>
3215ab8a94de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
iuc
parents: 3
diff changeset
114 <param name="data" ftype="csv" value="data.csv"/>
3215ab8a94de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
iuc
parents: 3
diff changeset
115 <param name="data_split" ftype="csv" value="data_split.csv"/>
3215ab8a94de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
iuc
parents: 3
diff changeset
116 <param name="cannot_link" ftype="txt" value="cannot.txt"/>
3215ab8a94de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
iuc
parents: 3
diff changeset
117 </conditional>
3215ab8a94de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
iuc
parents: 3
diff changeset
118 <conditional name="min_len">
3215ab8a94de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
iuc
parents: 3
diff changeset
119 <param name="method" value="min-len"/>
3215ab8a94de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
iuc
parents: 3
diff changeset
120 <param name="min_len" value="2500" />
3215ab8a94de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
iuc
parents: 3
diff changeset
121 </conditional>
3215ab8a94de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
iuc
parents: 3
diff changeset
122 <param name="orf_finder" value="prodigal"/>
3215ab8a94de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
iuc
parents: 3
diff changeset
123 <param name="random_seed" value="0"/>
3215ab8a94de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
iuc
parents: 3
diff changeset
124 <param name="epoches" value="1"/>
3215ab8a94de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
iuc
parents: 3
diff changeset
125 <param name="batch_size" value="2048"/>
3215ab8a94de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
iuc
parents: 3
diff changeset
126 <output name="model" ftype="h5">
3215ab8a94de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
iuc
parents: 3
diff changeset
127 <assert_contents>
3215ab8a94de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
iuc
parents: 3
diff changeset
128 <has_size value="3119000" delta="2000" />
3215ab8a94de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
iuc
parents: 3
diff changeset
129 </assert_contents>
3215ab8a94de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
iuc
parents: 3
diff changeset
130 </output>
3215ab8a94de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
iuc
parents: 3
diff changeset
131 </test>
3215ab8a94de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
iuc
parents: 3
diff changeset
132 <test expect_num_outputs="1">
3215ab8a94de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
iuc
parents: 3
diff changeset
133 <conditional name="mode">
3215ab8a94de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
iuc
parents: 3
diff changeset
134 <param name="select" value="single"/>
3215ab8a94de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
iuc
parents: 3
diff changeset
135 <param name="input_fasta" ftype="fasta.gz" value="input_single.fasta.gz"/>
3215ab8a94de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
iuc
parents: 3
diff changeset
136 <param name="data" ftype="csv" value="data.csv"/>
3215ab8a94de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
iuc
parents: 3
diff changeset
137 <param name="data_split" ftype="csv" value="data_split.csv"/>
3215ab8a94de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
iuc
parents: 3
diff changeset
138 <param name="cannot_link" ftype="txt" value="cannot.txt"/>
3215ab8a94de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
iuc
parents: 3
diff changeset
139 </conditional>
3215ab8a94de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
iuc
parents: 3
diff changeset
140 <conditional name="min_len">
3215ab8a94de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
iuc
parents: 3
diff changeset
141 <param name="method" value="min-len"/>
3215ab8a94de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
iuc
parents: 3
diff changeset
142 <param name="min_len" value="2500" />
3215ab8a94de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
iuc
parents: 3
diff changeset
143 </conditional>
3215ab8a94de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
iuc
parents: 3
diff changeset
144 <param name="orf_finder" value="prodigal"/>
3215ab8a94de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
iuc
parents: 3
diff changeset
145 <param name="random_seed" value="0"/>
3215ab8a94de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
iuc
parents: 3
diff changeset
146 <param name="epoches" value="1"/>
3215ab8a94de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
iuc
parents: 3
diff changeset
147 <param name="batch_size" value="2048"/>
3215ab8a94de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
iuc
parents: 3
diff changeset
148 <output name="model" ftype="h5">
3215ab8a94de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
iuc
parents: 3
diff changeset
149 <assert_contents>
3215ab8a94de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
iuc
parents: 3
diff changeset
150 <has_size value="3119000" delta="2000" />
3215ab8a94de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
iuc
parents: 3
diff changeset
151 </assert_contents>
3215ab8a94de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
iuc
parents: 3
diff changeset
152 </output>
3215ab8a94de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
iuc
parents: 3
diff changeset
153 </test>
3215ab8a94de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
iuc
parents: 3
diff changeset
154 <test expect_num_outputs="1">
3215ab8a94de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin commit 2c08a2e49a2844efe92340c5a9e9c8323e4a33d6
iuc
parents: 3
diff changeset
155 <conditional name="mode">
0
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
156 <param name="select" value="several"/>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
157 <param name="input_fasta" ftype="fasta" value="input_single.fasta,input_single_2.fasta,input_single_3.fasta"/>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
158 <param name="data" ftype="csv" value="data.csv,data.csv,data.csv"/>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
159 <param name="data_split" ftype="csv" value="data_split.csv,data_split.csv,data_split.csv"/>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
160 <param name="cannot_link" ftype="txt" value="cannot.txt,cannot.txt,cannot.txt"/>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
161 </conditional>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
162 <conditional name="min_len">
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
163 <param name="method" value="ratio"/>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
164 <param name="ratio" value="0.05" />
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
165 </conditional>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
166 <param name="orf_finder" value="prodigal"/>
3
2344bc30a326 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
iuc
parents: 2
diff changeset
167 <param name="random_seed" value="0"/>
0
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
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168 <param name="epoches" value="20"/>
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169 <param name="batch_size" value="2048"/>
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170 <output name="model" ftype="h5">
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171 <assert_contents>
1
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172 <has_size value="3119000" delta="2000" />
0
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173 </assert_contents>
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174 </output>
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175 </test>
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176 </tests>
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177 <help><![CDATA[
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178 @HELP_HEADER@
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179
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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180 This tool trains the semi-supervised deep learning model
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181
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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182 Inputs
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183 ======
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184
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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185 @HELP_INPUT_FASTA@
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186 @HELP_CANNOT@
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187 @HELP_DATA@
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188
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189 Outputs
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190 =======
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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191
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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192 @HELP_MODEL@
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193 ]]></help>
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194 <expand macro="citations"/>
1
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195 </tool>