diff qiime2/qiime_taxa_barplot.xml @ 0:370e0b6e9826 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_taxa_barplot.xml	Wed Jul 17 03:05:17 2019 -0400
@@ -0,0 +1,70 @@
+<?xml version="1.0" ?>
+<tool id="qiime_taxa_barplot" name="qiime taxa barplot" version="2019.4">
+	<description> - Visualize taxonomy with an interactive bar plot</description>
+	<requirements>
+		<requirement type="package" version="2019.4">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($input_files_mmetadatafile)
+#end if
+
+--o-visualization=ovisualization
+;
+qiime tools export --input-path ovisualization.qzv --output-path out   && mkdir -p '$ovisualization.files_path'
+&& cp -r out/* '$ovisualization.files_path'
+&& mv '$ovisualization.files_path/index.html' '$ovisualization';
+	]]></command>
+	<inputs>
+		<param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table to visualize at various taxonomic levels.                                    [required]" name="itable" optional="False" type="data"/>
+		<param format="qza,no_unzip.zip" label="--i-taxonomy: ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored.                           [required]" name="itaxonomy" optional="False" type="data"/>
+
+		<repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
+			<param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
+		</repeat>
+
+	</inputs>
+	<outputs>
+		<data format="html" label="${tool.name} on ${on_string}: visualization.qzv" 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>