Mercurial > repos > florianbegusch > qiime2_suite
diff qiime2/qiime_feature-table_core-features.xml @ 0:370e0b6e9826 draft
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author | florianbegusch |
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date | Wed, 17 Jul 2019 03:05:17 -0400 |
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children | 914fa4daf16a |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_feature-table_core-features.xml Wed Jul 17 03:05:17 2019 -0400 @@ -0,0 +1,69 @@ +<?xml version="1.0" ?> +<tool id="qiime_feature-table_core-features" name="qiime feature-table core-features" version="2019.4"> + <description> - Identify core features in table</description> + <requirements> + <requirement type="package" version="2019.4">qiime2</requirement> + </requirements> + <command><![CDATA[ +qiime feature-table core-features + +--i-table=$itable + +#if $pminfraction: + --p-min-fraction=$pminfraction +#end if + +#if $pmaxfraction: + --p-max-fraction=$pmaxfraction +#end if + +#if $psteps: + --p-steps=$psteps +#end if + +--o-visualization=ovisualization +; +qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path' +&& cp -r out/* '$ovisualization.files_path' +&& mv '$ovisualization.files_path/index.html' '$ovisualization'; + ]]></command> + <inputs> + <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"/> + <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"/> + <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"/> + <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"/> + </inputs> + <outputs> + <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/> + </outputs> + <help><![CDATA[ +Train an almost arbitrary scikit-learn classifier +################################################# + +Train a scikit-learn classifier to classify reads. + +Parameters +---------- +reference_reads : FeatureData[Sequence] + \ + +reference_taxonomy : FeatureData[Taxonomy] + \ + +classifier_specification : Str + \ + +class_weight : FeatureTable[RelativeFrequency], optional + \ + +Returns +------- +classifier : TaxonomicClassifier + \ + + ]]></help> +<macros> + <import>qiime_citation.xml</import> +</macros> +<expand macro="qiime_citation"/> +</tool>