diff qiime2-2020.8/qiime_taxa_collapse.xml @ 20:d93d8888f0b0 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2-2020.8/qiime_taxa_collapse.xml	Fri Sep 04 12:44:24 2020 +0000
@@ -0,0 +1,72 @@
+<?xml version="1.0" ?>
+<tool id="qiime_taxa_collapse" name="qiime taxa collapse"
+      version="2020.8">
+  <description>Collapse features by their taxonomy at the specified level</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
+qiime taxa collapse
+
+--i-table=$itable
+
+--i-taxonomy=$itaxonomy
+
+--p-level=$plevel
+
+--o-collapsed-table=ocollapsedtable
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
+;
+cp ocollapsedtable.qza $ocollapsedtable
+
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table to be collapsed.             [required]" name="itable" optional="False" type="data" />
+    <param format="qza,no_unzip.zip" label="--i-taxonomy: ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored.                           [required]" name="itaxonomy" optional="False" type="data" />
+    <param label="--p-level: INTEGER      The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation.       [required]" name="plevel" optional="False" type="text" />
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="qza" label="${tool.name} on ${on_string}: collapsedtable.qza" name="ocollapsedtable" />
+    
+  </outputs>
+
+  <help><![CDATA[
+Collapse features by their taxonomy at the specified level
+###############################################################
+
+Collapse groups of features that have the same taxonomic assignment through
+the specified level. The frequencies of all features will be summed when
+they are collapsed.
+
+Parameters
+----------
+table : FeatureTable[Frequency]
+    Feature table to be collapsed.
+taxonomy : FeatureData[Taxonomy]
+    Taxonomic annotations for features in the provided feature table. All
+    features in the feature table must have a corresponding taxonomic
+    annotation. Taxonomic annotations that are not present in the feature
+    table will be ignored.
+level : Int
+    The taxonomic level at which the features should be collapsed. All
+    ouput features will have exactly this many levels of taxonomic
+    annotation.
+
+Returns
+-------
+collapsed_table : FeatureTable[Frequency]
+    The resulting feature table, where all features are now taxonomic
+    annotations with the user-specified number of levels.
+  ]]></help>
+  <macros>
+    <import>qiime_citation.xml</import>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
\ No newline at end of file