Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2/qiime_feature-table_core-features.xml @ 0:370e0b6e9826 draft
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| author | florianbegusch |
|---|---|
| date | Wed, 17 Jul 2019 03:05:17 -0400 |
| parents | |
| children | 914fa4daf16a |
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| -1:000000000000 | 0:370e0b6e9826 |
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| 1 <?xml version="1.0" ?> | |
| 2 <tool id="qiime_feature-table_core-features" name="qiime feature-table core-features" version="2019.4"> | |
| 3 <description> - Identify core features in table</description> | |
| 4 <requirements> | |
| 5 <requirement type="package" version="2019.4">qiime2</requirement> | |
| 6 </requirements> | |
| 7 <command><![CDATA[ | |
| 8 qiime feature-table core-features | |
| 9 | |
| 10 --i-table=$itable | |
| 11 | |
| 12 #if $pminfraction: | |
| 13 --p-min-fraction=$pminfraction | |
| 14 #end if | |
| 15 | |
| 16 #if $pmaxfraction: | |
| 17 --p-max-fraction=$pmaxfraction | |
| 18 #end if | |
| 19 | |
| 20 #if $psteps: | |
| 21 --p-steps=$psteps | |
| 22 #end if | |
| 23 | |
| 24 --o-visualization=ovisualization | |
| 25 ; | |
| 26 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path' | |
| 27 && cp -r out/* '$ovisualization.files_path' | |
| 28 && mv '$ovisualization.files_path/index.html' '$ovisualization'; | |
| 29 ]]></command> | |
| 30 <inputs> | |
| 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"/> | |
| 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"/> | |
| 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"/> | |
| 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"/> | |
| 35 </inputs> | |
| 36 <outputs> | |
| 37 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/> | |
| 38 </outputs> | |
| 39 <help><![CDATA[ | |
| 40 Train an almost arbitrary scikit-learn classifier | |
| 41 ################################################# | |
| 42 | |
| 43 Train a scikit-learn classifier to classify reads. | |
| 44 | |
| 45 Parameters | |
| 46 ---------- | |
| 47 reference_reads : FeatureData[Sequence] | |
| 48 \ | |
| 49 | |
| 50 reference_taxonomy : FeatureData[Taxonomy] | |
| 51 \ | |
| 52 | |
| 53 classifier_specification : Str | |
| 54 \ | |
| 55 | |
| 56 class_weight : FeatureTable[RelativeFrequency], optional | |
| 57 \ | |
| 58 | |
| 59 Returns | |
| 60 ------- | |
| 61 classifier : TaxonomicClassifier | |
| 62 \ | |
| 63 | |
| 64 ]]></help> | |
| 65 <macros> | |
| 66 <import>qiime_citation.xml</import> | |
| 67 </macros> | |
| 68 <expand macro="qiime_citation"/> | |
| 69 </tool> |