Mercurial > repos > florianbegusch > qiime2_suite
diff qiime2-2020.8/qiime_feature-table_core-features.xml @ 20:d93d8888f0b0 draft
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author | florianbegusch |
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date | Fri, 04 Sep 2020 12:44:24 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2-2020.8/qiime_feature-table_core-features.xml Fri Sep 04 12:44:24 2020 +0000 @@ -0,0 +1,82 @@ +<?xml version="1.0" ?> +<tool id="qiime_feature-table_core-features" name="qiime feature-table core-features" + version="2020.8"> + <description>Identify core features in table</description> + <requirements> + <requirement type="package" version="2020.8">qiime2</requirement> + </requirements> + <command><![CDATA[ +qiime feature-table core-features + +--i-table=$itable + +--p-min-fraction=$pminfraction + +--p-max-fraction=$pmaxfraction + +--p-steps=$psteps + +--o-visualization=ovisualization + +#if str($examples) != 'None': +--examples=$examples +#end if + +; +cp oclassifier.qza $oclassifier + +; +qiime tools export ovisualization.qzv --output-path out +&& mkdir -p '$ovisualization.files_path' +&& cp -r out/* '$ovisualization.files_path' +&& mv '$ovisualization.files_path/index.html' '$ovisualization' + + ]]></command> + <inputs> + <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table to use in core features calculations. [required]" name="itable" optional="False" type="data" /> + <param exclude_min="True" label="--p-min-fraction: PROPORTION Range(0.0, 1.0, inclusive_start=False) The minimum fraction of samples that a feature must be observed in for that feature to be considered a core feature. [default: 0.5]" max="1.0" min="0.0" name="pminfraction" optional="True" type="float" value="0.5" /> + <param exclude_max="False" label="--p-max-fraction: PROPORTION Range(0.0, 1.0, inclusive_end=True) The maximum fraction of samples that a feature must be observed in for that feature to be considered a core feature. [default: 1.0]" max="1.0" min="0.0" name="pmaxfraction" optional="True" type="float" value="1.0" /> + <param label="--p-steps: INTEGER The number of steps to take between `min-fraction` and Range(2, None) `max-fraction` for core features calculations. This parameter has no effect if `min-fraction` and `max-fraction` are the same value. [default: 11]" min="2" name="psteps" optional="True" type="integer" value="11" /> + <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" /> + + </inputs> + + <outputs> + <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" /> + + </outputs> + + <help><![CDATA[ +Identify core features in table +############################################################### + +Identify "core" features, which are features observed in a user-defined +fraction of the samples. Since the core features are a function of the +fraction of samples that the feature must be observed in to be considered +core, this is computed over a range of fractions defined by the +`min_fraction`, `max_fraction`, and `steps` parameters. + +Parameters +---------- +table : FeatureTable[Frequency] + The feature table to use in core features calculations. +min_fraction : Float % Range(0.0, 1.0, inclusive_start=False), optional + The minimum fraction of samples that a feature must be observed in for + that feature to be considered a core feature. +max_fraction : Float % Range(0.0, 1.0, inclusive_end=True), optional + The maximum fraction of samples that a feature must be observed in for + that feature to be considered a core feature. +steps : Int % Range(2, None), optional + 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. + +Returns +------- +visualization : Visualization + ]]></help> + <macros> + <import>qiime_citation.xml</import> + </macros> + <expand macro="qiime_citation"/> +</tool> \ No newline at end of file