annotate train.xml @ 2:8b77643cf479 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 13abac83068b126399ec415141007a48c2efaa84
author iuc
date Fri, 10 Nov 2023 20:49:30 +0000
parents 43df7a4c33a2
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
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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 #if $mode.input_fasta.ext.endswith(".gz")
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15 gunzip -c '$mode.input_fasta' > 'contigs.fasta' &&
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16 #else
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17 ln -s '$mode.input_fasta' 'contigs.fasta' &&
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18 #end if
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19 #else
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20 #for $e in $mode.input_fasta
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21 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($e.element_identifier))
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22 #if $e.ext.endswith(".gz")
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23 gunzip -c '$e' > '${identifier}.fasta' &&
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24 #else
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25 ln -s '$e' '${identifier}.fasta' &&
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26 #end if
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27 #end for
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28 #end if
2
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29 SemiBin2 train_semi
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30 #if $mode.select == 'single'
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31 --input-fasta 'contigs.fasta'
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32 --data '$mode.data'
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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
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37 #for $e in $mode.input_fasta
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38 --input-fasta '${e.element_identifier}.fasta'
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39 #end for
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40 #for $e in $mode.data
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41 --data '$e'
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42 #end for
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43 #for $e in $mode.data_split
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44 --data-split '$e'
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45 #end for
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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"/>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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86 </inputs>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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87 <outputs>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
88 <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
89 </outputs>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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90 <tests>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
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91 <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
92 <conditional name="mode">
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
93 <param name="select" value="single"/>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
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diff changeset
94 <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
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diff changeset
95 <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
96 <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
97 <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:
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98 </conditional>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
99 <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
100 <param name="method" value="min-len"/>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
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diff changeset
101 <param name="min_len" value="2500" />
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
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102 </conditional>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
103 <param name="orf_finder" value="prodigal"/>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
104 <param name="random-seed" value="0"/>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
105 <param name="epoches" value="1"/>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
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106 <param name="batch_size" value="2048"/>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
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107 <output name="model" ftype="h5">
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
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108 <assert_contents>
1
43df7a4c33a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
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parents: 0
diff changeset
109 <has_size value="3119000" delta="2000" />
0
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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110 </assert_contents>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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111 </output>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
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diff changeset
112 </test>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
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113 <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
114 <conditional name="mode">
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
115 <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
116 <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
117 <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
118 <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
119 <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"
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120 </conditional>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
121 <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
122 <param name="method" value="ratio"/>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
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diff changeset
123 <param name="ratio" value="0.05" />
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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124 </conditional>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
125 <param name="orf_finder" value="prodigal"/>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
126 <param name="random-seed" value="0"/>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
127 <param name="epoches" value="20"/>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
128 <param name="batch_size" value="2048"/>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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diff changeset
129 <output name="model" ftype="h5">
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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130 <assert_contents>
1
43df7a4c33a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
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parents: 0
diff changeset
131 <has_size value="3119000" delta="2000" />
0
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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132 </assert_contents>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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133 </output>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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diff changeset
134 </test>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
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diff changeset
135 </tests>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
136 <help><![CDATA[
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
137 @HELP_HEADER@
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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138
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
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139 This tool trains 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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140
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
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diff changeset
141 Inputs
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
142 ======
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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143
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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parents:
diff changeset
144 @HELP_INPUT_FASTA@
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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diff changeset
145 @HELP_CANNOT@
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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parents:
diff changeset
146 @HELP_DATA@
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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147
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
148 Outputs
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
149 =======
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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diff changeset
150
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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parents:
diff changeset
151 @HELP_MODEL@
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
iuc
parents:
diff changeset
152 ]]></help>
08cc1cd58f38 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit aa9bfb2fb62547ee8bac34f0de5b3beaa0bfd1a4"
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diff changeset
153 <expand macro="citations"/>
1
43df7a4c33a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 59a7b7a334fd2c3aca6163c2ff11d18ef654ab9d
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parents: 0
diff changeset
154 </tool>