diff qiime2/qiime_feature-table_summarize.xml @ 0:51b9b6b57732 draft

Uploaded
author florianbegusch
date Thu, 24 May 2018 05:21:07 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_feature-table_summarize.xml	Thu May 24 05:21:07 2018 -0400
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+<?xml version="1.0" ?>
+<tool id="qiime_feature-table_summarize" name="qiime feature-table summarize" version="2018.4">
+	<description> - Summarize table</description>
+	<requirements>
+		<requirement type="package" version="2018.4">qiime2</requirement>
+	</requirements>
+	<command>
+	<![CDATA[
+	qiime feature-table summarize --i-table=$itable
+
+	#if $input_files_msamplemetadatafile:
+
+	#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 + ',' + d['additional_input'].__getattr__('file_name')
+		#end for
+		#return $file_list
+	#end def
+	 --m-sample-metadata-file=$list_dict_to_string($input_files_msamplemetadatafile)
+	#end if
+
+	#if str($cmdconfig) != 'None':
+	 --cmd-config=$cmdconfig
+	#end if
+	 --o-visualization=ovisualization;
+
+	qiime tools export ovisualization.qzv --output-dir out   && mkdir -p '$ovisualization.files_path'
+	&& cp -r out/* '$ovisualization.files_path'
+	&& mv '$ovisualization.files_path/index.html' '$ovisualization'
+		]]>
+	</command>
+	<inputs>
+		<param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Frequency | PresenceAbsence | RelativeFrequency] The feature table to be summarized. [required]" name="itable" optional="False" type="data"/>
+		<repeat name="input_files_msamplemetadatafile" optional="True" title="--m-sample-metadata-file">
+			<param label="--m-sample-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. The sample metadata.  [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
+		</repeat>
+		<param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
+	</inputs>
+	<outputs>
+		<data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
+	</outputs>
+	<help>
+		<![CDATA[
+Summarize table
+----------------
+
+Generate visual and tabular summaries of a feature table.
+
+Parameters
+----------
+table : FeatureTable[Frequency | PresenceAbsence | RelativeFrequency]
+    The feature table to be summarized.
+sample_metadata : Metadata, optional
+    The sample metadata.
+
+Returns
+-------
+visualization : Visualization
+		\
+		]]>
+	</help>
+<macros>
+	<import>qiime_citation.xml</import>
+</macros>
+<expand macro="qiime_citation" />
+</tool>