Mercurial > repos > iuc > semibin_train

annotate train.xml @ 2:35c4a1990ba2 draft

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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
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fe0ba89f385f 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@">
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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2 <description>
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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3 the semi-supervised deep learning model
fe0ba89f385f 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>
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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6 <import>macros.xml</import>
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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7 </macros>
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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8 <expand macro="biotools"/>
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9 <expand macro="requirements"/>
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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10 <expand macro="version"/>
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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11 <command detect_errors="exit_code"><![CDATA[
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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12 #import re
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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13 #if $mode.select == 'single'
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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14 #if $mode.input_fasta.ext.endswith(".gz")
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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15 gunzip -c '$mode.input_fasta' > 'contigs.fasta' &&
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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16 #else
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17 ln -s '$mode.input_fasta' 'contigs.fasta' &&
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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18 #end if
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19 #else
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20 #for $e in $mode.input_fasta
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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21 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($e.element_identifier))
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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22 #if $e.ext.endswith(".gz")
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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23 gunzip -c '$e' > '${identifier}.fasta' &&
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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24 #else
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25 ln -s '$e' '${identifier}.fasta' &&
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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26 #end if
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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27 #end for
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28 #end if
2
35c4a1990ba2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
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29 SemiBin2 train_semi
0
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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30 #if $mode.select == 'single'
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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31 --input-fasta 'contigs.fasta'
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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32 --data '$mode.data'
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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33 --data-split '$mode.data_split'
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34 --cannot-link '$mode.cannot_link'
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35 #else
2
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36 --train-from-many
0
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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37 #for $e in $mode.input_fasta
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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38 --input-fasta '${e.element_identifier}.fasta'
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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39 #end for
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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40 #for $e in $mode.data
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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41 --data '$e'
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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42 #end for
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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43 #for $e in $mode.data_split
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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44 --data-split '$e'
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45 #end for
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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46 #for $e in $mode.cannot_link
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47 --cannot-link '$e'
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48 #end for
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49 #end if
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50 --output 'output'
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51 --threads \${GALAXY_SLOTS:-1}
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52 --epoches $epoches
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53 --batch-size $batch_size
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54 --random-seed $random_seed
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55 #if $min_len.method == 'min-len'
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56 --min-len $min_len.min_len
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57 #else if $min_len.method == 'ratio'
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58 --ratio $min_len.ratio
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59 #end if
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60 --orf-finder '$orf_finder'
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61 ]]></command>
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62 <inputs>
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63 <conditional name="mode">
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64 <param argument="select" type="select" label="Mode to train the models">
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65 <option value="single" selected="true">From one sample</option>
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66 <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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67 </param>
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68 <when value="single">
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69 <param argument="--input-fasta" type="data" format="fasta,fasta.gz" label="Contig sequences"/>
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70 <param argument="--data" type="data" format="csv" label="Train data"/>
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71 <param argument="--data-split" type="data" format="csv" label="Split train data"/>
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72 <param argument="--cannot-link" type="data" format="txt" label="Cannot-link constraints"/>
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73 </when>
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74 <when value="several">
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75 <param argument="--input-fasta" type="data" multiple="true" format="fasta,fasta.gz" label="Contig sequences"/>
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76 <param argument="--data" type="data" format="csv" multiple="true" label="Train data"/>
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77 <param argument="--data-split" type="data" format="csv" multiple="true" label="Split train data"/>
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78 <param argument="--cannot-link" type="data" format="txt" multiple="true" label="Cannot-link constraints"/>
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79 </when>
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80 </conditional>
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81 <expand macro="min_len"/>
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82 <expand macro="orf-finder"/>
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83 <expand macro="random-seed"/>
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84 <expand macro="epoches"/>
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85 <expand macro="batch-size"/>
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86 </inputs>
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87 <outputs>
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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88 <expand macro="train_output"/>
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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89 </outputs>
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90 <tests>
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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91 <test expect_num_outputs="1">
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92 <conditional name="mode">
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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93 <param name="select" value="single"/>
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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94 <param name="input_fasta" ftype="fasta" value="input_single.fasta"/>
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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95 <param name="data" ftype="csv" value="data.csv"/>
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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96 <param name="data_split" ftype="csv" value="data_split.csv"/>
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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97 <param name="cannot_link" ftype="txt" value="cannot.txt"/>
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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98 </conditional>
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99 <conditional name="min_len">
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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100 <param name="method" value="min-len"/>
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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101 <param name="min_len" value="2500" />
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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102 </conditional>
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103 <param name="orf_finder" value="prodigal"/>
2
35c4a1990ba2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
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104 <param name="random_seed" value="0"/>
0
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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105 <param name="epoches" value="1"/>
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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106 <param name="batch_size" value="2048"/>
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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107 <output name="model" ftype="h5">
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108 <assert_contents>
1
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109 <has_size value="3119000" delta="2000" />
0
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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110 </assert_contents>
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111 </output>
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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112 </test>
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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113 <test expect_num_outputs="1">
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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114 <conditional name="mode">
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115 <param name="select" value="several"/>
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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116 <param name="input_fasta" ftype="fasta" value="input_single.fasta,input_single_2.fasta,input_single_3.fasta"/>
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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117 <param name="data" ftype="csv" value="data.csv,data.csv,data.csv"/>
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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118 <param name="data_split" ftype="csv" value="data_split.csv,data_split.csv,data_split.csv"/>
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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119 <param name="cannot_link" ftype="txt" value="cannot.txt,cannot.txt,cannot.txt"/>
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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120 </conditional>
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121 <conditional name="min_len">
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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122 <param name="method" value="ratio"/>
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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123 <param name="ratio" value="0.05" />
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124 </conditional>
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125 <param name="orf_finder" value="prodigal"/>
2
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126 <param name="random_seed" value="0"/>
0
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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127 <param name="epoches" value="20"/>
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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128 <param name="batch_size" value="2048"/>
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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129 <output name="model" ftype="h5">
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130 <assert_contents>
1
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131 <has_size value="3119000" delta="2000" />
0
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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132 </assert_contents>
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133 </output>
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134 </test>
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135 </tests>
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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136 <help><![CDATA[
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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137 @HELP_HEADER@
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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138
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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139 This tool trains the semi-supervised deep learning model
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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140
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141 Inputs
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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142 ======
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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143
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144 @HELP_INPUT_FASTA@
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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145 @HELP_CANNOT@
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146 @HELP_DATA@
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147
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148 Outputs
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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149 =======
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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150
fe0ba89f385f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4
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151 @HELP_MODEL@
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152 ]]></help>
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153 <expand macro="citations"/>
1
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154 </tool>