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

Uploaded
author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
parents
children 51025741f326
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_metadata_tabulate.xml	Wed Jul 17 03:05:17 2019 -0400
@@ -0,0 +1,64 @@
+<?xml version="1.0" ?>
+<tool id="qiime_metadata_tabulate" name="qiime metadata tabulate" version="2019.4">
+	<description> - Interactively explore Metadata in an HTML table</description>
+	<requirements>
+		<requirement type="package" version="2019.4">qiime2</requirement>
+	</requirements>
+	<command><![CDATA[
+qiime metadata tabulate
+
+
+#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-input-file=' + d['additional_input'].__getattr__('file_name')
+#end for
+#return $file_list
+#end def
+--m-input-file=$list_dict_to_string($input_files_minputfile)
+
+
+#if $ppagesize:
+ --p-page-size=$ppagesize
+#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 label="--p-page-size: INTEGER  The maximum number of Metadata records to display per page                               [default: 100]" name="ppagesize" optional="True" type="integer" value="100"/>
+
+		<repeat name="input_files_minputfile" optional="False" title="--m-input-file">
+			<param label="--m-input-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. The metadata to tabulate.  [required]" 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[
+Interactively explore Metadata in an HTML table
+###############################################
+
+Generate a tabular view of Metadata. The output visualization supports
+interactive filtering, sorting, and exporting to common file formats.
+
+Parameters
+----------
+input : Metadata
+    The metadata to tabulate.
+page_size : Int, optional
+    The maximum number of Metadata records to display per page
+
+Returns
+-------
+visualization : Visualization
+	]]></help>
+<macros>
+    <import>qiime_citation.xml</import>
+</macros>
+<expand macro="qiime_citation"/>
+</tool>