comparison qiime2/qiime_feature-table_core-features.xml @ 14:a0a8d77a991c draft

Uploaded

13:887cd4ad8e16

<?xml version="1.0" ?>
<tool id="qiime_feature-table_core-features" name="qiime feature-table core-features" version="2019.7">
	<description> - Identify core features in table</description>
	<requirements>
		<requirement type="package" version="2019.7">qiime2</requirement>
	</requirements>
	<command><![CDATA[
qiime feature-table core-features

--i-table=$itable

#if str($pminfraction):
 --p-min-fraction=$pminfraction
#end if

#if str($pmaxfraction):
 --p-max-fraction=$pmaxfraction
#end if

#if str($psteps):
 --p-steps=$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>

14:a0a8d77a991c

<?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>