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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="2019.4">
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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="2019.4">qiime2</requirement>
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6 </requirements>
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7 <command><![CDATA[
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8 qiime feature-table core-features
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9
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10 --i-table=$itable
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11
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4
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12 #if str($pminfraction):
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0
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13 --p-min-fraction=$pminfraction
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14 #end if
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15
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4
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16 #if str($pmaxfraction):
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0
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17 --p-max-fraction=$pmaxfraction
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18 #end if
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19
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4
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20 #if str($psteps):
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0
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21 --p-steps=$psteps
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22 #end if
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23
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24 --o-visualization=ovisualization
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25 ;
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26 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
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27 && cp -r out/* '$ovisualization.files_path'
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28 && mv '$ovisualization.files_path/index.html' '$ovisualization';
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29 ]]></command>
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30 <inputs>
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31 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table to use in core features calculations. [required]" name="itable" optional="False" type="data"/>
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32 <param label="--p-min-fraction: PROPORTION Range(0.0, 1.0, inclusive_start=False) The minimum fraction of samples that a feature must be observed in for that feature to be considered a core feature. [default: 0.5]" name="pminfraction" optional="True" type="float" value="0.5"/>
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33 <param label="--p-max-fraction: PROPORTION Range(0.0, 1.0, inclusive_end=True) The maximum fraction of samples that a feature must be observed in for that feature to be considered a core feature. [default: 1.0]" name="pmaxfraction" optional="True" type="float" value="1.0"/>
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34 <param label="--p-steps: INTEGER The number of steps to take between `min-fraction` and Range(2, None) `max-fraction` for core features calculations. This parameter has no effect if `min-fraction` and `max-fraction` are the same value. [default: 11]" name="psteps" optional="True" type="integer" value="11"/>
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35 </inputs>
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36 <outputs>
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37 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
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38 </outputs>
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39 <help><![CDATA[
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40 Train an almost arbitrary scikit-learn classifier
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41 #################################################
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42
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43 Train a scikit-learn classifier to classify reads.
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44
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45 Parameters
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46 ----------
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47 reference_reads : FeatureData[Sequence]
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48 \
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49
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50 reference_taxonomy : FeatureData[Taxonomy]
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51 \
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52
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53 classifier_specification : Str
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54 \
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55
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56 class_weight : FeatureTable[RelativeFrequency], optional
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57 \
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58
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59 Returns
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60 -------
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61 classifier : TaxonomicClassifier
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62 \
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63
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64 ]]></help>
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65 <macros>
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66 <import>qiime_citation.xml</import>
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67 </macros>
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68 <expand macro="qiime_citation"/>
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69 </tool>
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