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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2-2020.8/qiime_taxa_barplot.xml	Fri Sep 04 12:44:24 2020 +0000
@@ -0,0 +1,90 @@
+<?xml version="1.0" ?>
+<tool id="qiime_taxa_barplot" name="qiime taxa barplot"
+      version="2020.8">
+  <description>Visualize taxonomy with an interactive bar plot</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
+qiime taxa barplot
+
+--i-table=$itable
+
+--i-taxonomy=$itaxonomy
+# if $input_files_mmetadatafile:
+  # def list_dict_to_string(list_dict):
+    # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
+    # for d in list_dict[1:]:
+      # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
+    # end for
+    # return $file_list
+  # end def
+--m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
+# end if
+
+--o-visualization=ovisualization
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
+;
+cp otesttable.qza $otesttable
+
+;
+qiime tools export  ovisualization.qzv --output-path out
+&& mkdir -p '$ovisualization.files_path'
+&& cp -r out/* '$ovisualization.files_path'
+&& mv '$ovisualization.files_path/index.html' '$ovisualization'
+
+;
+qiime tools export  ovisualization.qzv --output-path out
+&& mkdir -p '$ovisualization.files_path'
+&& cp -r out/* '$ovisualization.files_path'
+&& mv '$ovisualization.files_path/index.html' '$ovisualization'
+
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table to visualize at various taxonomic levels.                                    [required]" name="itable" optional="False" type="data" />
+    <param format="qza,no_unzip.zip" label="--i-taxonomy: ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored.                           [required]" name="itaxonomy" optional="False" type="data" />
+    <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
+      <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple            The sample metadata. arguments will be merged)                                                        [required]" name="additional_input" optional="False" type="data" />
+    </repeat>
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
+    
+  </outputs>
+
+  <help><![CDATA[
+Visualize taxonomy with an interactive bar plot
+###############################################################
+
+This visualizer produces an interactive barplot visualization of
+taxonomies. Interactive features include multi-level sorting, plot
+recoloring, sample relabeling, and SVG figure export.
+
+Parameters
+----------
+table : FeatureTable[Frequency]
+    Feature table to visualize at various taxonomic levels.
+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.
+metadata : Metadata
+    The sample metadata.
+
+Returns
+-------
+visualization : Visualization
+  ]]></help>
+  <macros>
+    <import>qiime_citation.xml</import>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
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