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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" version="2018.4">
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3 <description> - Identify core features in table</description>
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4 <requirements>
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5 <requirement type="package" version="2018.4">qiime2</requirement>
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6 </requirements>
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7 <command>
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8 <![CDATA[
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9 qiime feature-table core-features --i-table=$itable
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10
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11 #if str($cmdconfig) != 'None':
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12 --cmd-config=$cmdconfig
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13 #end if
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14
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15 #if $pminfraction:
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16 --p-min-fraction=$pminfraction
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17 #end if
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18
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19 #if $pmaxfraction:
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20 --p-max-fraction=$pmaxfraction
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21 #end if
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22 --o-visualization=ovisualization
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23 #if $psteps:
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24 --p-steps=$psteps
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25 #end if
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26 ;
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27 qiime tools export ovisualization.qzv --output-dir out && mkdir -p '$ovisualization.files_path'
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28 && cp -r out/* '$ovisualization.files_path'
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29 && mv '$ovisualization.files_path/index.html' '$ovisualization';
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30 ]]></command>
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31 <inputs>
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32 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Frequency] The feature table to use in core features calculations. [required]" name="itable" optional="False" type="data"/>
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33
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34 <param label="--p-min-fraction: The minimum fraction of samples that a feature must be observed in for that feature to be considered a core feature. [default: 0.5]" name="pminfraction" optional="True" type="float" value="0.5"/>
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35 <param label="--p-max-fraction: The maximum fraction of samples that a feature must be observed in for that feature to be considered a core feature. [default: 1.0]" name="pmaxfraction" optional="True" type="float" value="1.0"/>
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36
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37 <param label="--p-steps: The number of steps to take between `min_fraction` and `max_fraction` for core features calculations. This parameter has no effect if `min_fraction` and `max_fraction` are the same value. [default: 11]" name="psteps" optional="True" type="integer" value="11"/>
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38
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39 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
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40 </inputs>
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41 <outputs>
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42 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
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43 </outputs>
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44 <help>
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45 <![CDATA[
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46 Identify core features in table
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47 --------------------------------
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48
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49 Identify "core" features, which are features observed in a user-defined
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50 fraction of the samples. Since the core features are a function of the
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51 fraction of samples that the feature must be observed in to be considered
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52 core, this is computed over a range of fractions defined by the
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53 `min_fraction`, `max_fraction`, and `steps` parameters.
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54
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55 Parameters
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56 ----------
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57 table : FeatureTable[Frequency]
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58 The feature table to use in core features calculations.
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59 min_fraction : Float % Range(0.0, 1.0, inclusive_start=False), optional
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60 The minimum fraction of samples that a feature must be observed in for
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61 that feature to be considered a core feature.
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62 max_fraction : Float % Range(0.0, 1.0, inclusive_end=True), optional
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63 The maximum fraction of samples that a feature must be observed in for
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64 that feature to be considered a core feature.
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65 steps : Int % Range(2, None), optional
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66 The number of steps to take between `min_fraction` and `max_fraction`
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67 for core features calculations. This parameter has no effect if
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68 `min_fraction` and `max_fraction` are the same value.
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69
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70 Returns
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71 -------
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72 visualization : Visualization
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73 \
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74 ]]>
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75 </help>
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76 </tool>
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