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1 <?xml version="1.0" ?>
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2 <tool id="qiime_feature-table_core-features" name="qiime feature-table core-features"
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3 version="2020.8">
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4 <description>Identify core features in table</description>
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5 <requirements>
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6 <requirement type="package" version="2020.8">qiime2</requirement>
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7 </requirements>
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8 <command><![CDATA[
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9 qiime feature-table core-features
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10
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11 --i-table=$itable
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12
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13 --p-min-fraction=$pminfraction
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14
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15 --p-max-fraction=$pmaxfraction
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16
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17 --p-steps=$psteps
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18
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19 --o-visualization=ovisualization
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20
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21 #if str($examples) != 'None':
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22 --examples=$examples
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23 #end if
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24
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25 ;
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26 cp oclassifier.qza $oclassifier
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27
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28 ;
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29 qiime tools export ovisualization.qzv --output-path out
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30 && mkdir -p '$ovisualization.files_path'
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31 && cp -r out/* '$ovisualization.files_path'
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32 && mv '$ovisualization.files_path/index.html' '$ovisualization'
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33
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34 ]]></command>
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35 <inputs>
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36 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table to use in core features calculations. [required]" name="itable" optional="False" type="data" />
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37 <param exclude_min="True" label="--p-min-fraction: PROPORTION Range(0.0, 1.0, inclusive_start=False) The minimum fraction of samples that a feature must be observed in for that feature to be considered a core feature. [default: 0.5]" max="1.0" min="0.0" name="pminfraction" optional="True" type="float" value="0.5" />
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38 <param exclude_max="False" label="--p-max-fraction: PROPORTION Range(0.0, 1.0, inclusive_end=True) The maximum fraction of samples that a feature must be observed in for that feature to be considered a core feature. [default: 1.0]" max="1.0" min="0.0" name="pmaxfraction" optional="True" type="float" value="1.0" />
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39 <param label="--p-steps: INTEGER The number of steps to take between `min-fraction` and Range(2, None) `max-fraction` for core features calculations. This parameter has no effect if `min-fraction` and `max-fraction` are the same value. [default: 11]" min="2" name="psteps" optional="True" type="integer" value="11" />
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40 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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41
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42 </inputs>
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43
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44 <outputs>
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45 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
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46
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47 </outputs>
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48
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49 <help><![CDATA[
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50 Identify core features in table
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51 ###############################################################
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52
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53 Identify "core" features, which are features observed in a user-defined
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54 fraction of the samples. Since the core features are a function of the
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55 fraction of samples that the feature must be observed in to be considered
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56 core, this is computed over a range of fractions defined by the
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57 `min_fraction`, `max_fraction`, and `steps` parameters.
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58
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59 Parameters
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60 ----------
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61 table : FeatureTable[Frequency]
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62 The feature table to use in core features calculations.
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63 min_fraction : Float % Range(0.0, 1.0, inclusive_start=False), optional
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64 The minimum fraction of samples that a feature must be observed in for
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65 that feature to be considered a core feature.
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66 max_fraction : Float % Range(0.0, 1.0, inclusive_end=True), optional
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67 The maximum fraction of samples that a feature must be observed in for
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68 that feature to be considered a core feature.
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69 steps : Int % Range(2, None), optional
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70 The number of steps to take between `min_fraction` and `max_fraction`
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71 for core features calculations. This parameter has no effect if
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72 `min_fraction` and `max_fraction` are the same value.
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73
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74 Returns
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75 -------
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76 visualization : Visualization
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77 ]]></help>
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78 <macros>
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79 <import>qiime_citation.xml</import>
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80 </macros>
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81 <expand macro="qiime_citation"/>
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82 </tool> |
