diff qiime2-2020.8/qiime_feature-table_core-features.xml @ 20:d93d8888f0b0 draft

Uploaded

--- /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>
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