diff qiime2/qiime_feature-table_summarize.xml @ 14:a0a8d77a991c draft

Uploaded

--- a/qiime2/qiime_feature-table_summarize.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_feature-table_summarize.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,46 +1,58 @@
 <?xml version="1.0" ?>
-<tool id="qiime_feature-table_summarize" name="qiime feature-table summarize" version="2019.7">
-	<description> - Summarize table</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<tool id="qiime_feature-table_summarize" name="qiime feature-table summarize"
+      version="2020.8">
+  <description>Summarize table</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
 qiime feature-table summarize
 
 --i-table=$itable
-
-
-#if $m_sample_metadatafile:
-#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-sample-metadata-file=' + d['additional_input'].__getattr__('file_name')
-#end for
-#return $file_list
-#end def
---m-sample-metadata-file=$list_dict_to_string($m_sample_metadatafile)
-#end if
-
+# 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 + ' --m-sample-metadata-file=' + 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
 
 --o-visualization=ovisualization
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
 ;
-qiime tools export --input-path ovisualization.qzv --output-path out   && mkdir -p '$ovisualization.files_path'
+cp osampledtable.qza $osampledtable
+
+;
+qiime tools export  ovisualization.qzv --output-path out
+&& mkdir -p '$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 | RelativeFrequency | PresenceAbsence]   The feature table to be summarized.          [required]" name="itable" optional="False" type="data"/>
 
-		<repeat name="m_sample_metadatafile" optional="False" title="--m-metadata-file">
-			<param label="--m-sample-metadata-file: (multiple arguments will be merged)  The sample metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
-		</repeat>
-	</inputs>
-	<outputs>
-		<data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
-	</outputs>
-	<help><![CDATA[
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]   The feature table to be summarized.          [required]" name="itable" optional="False" type="data" />
+    <repeat name="input_files_msamplemetadatafile" optional="True" title="--m-sample-metadata-file">
+      <param format="tabular,qza,no_unzip.zip" label="--m-sample-metadata-file: METADATA... (multiple          The sample metadata. arguments will be merged)                                                     [optional]" name="additional_input" optional="True" type="data" />
+    </repeat>
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
+    
+  </outputs>
+
+  <help><![CDATA[
 Summarize table
-###############
+###############################################################
 
 Generate visual and tabular summaries of a feature table.
 
@@ -54,9 +66,9 @@
 Returns
 -------
 visualization : Visualization
-	]]></help>
-<macros>
+  ]]></help>
+  <macros>
     <import>qiime_citation.xml</import>
-</macros>
-<expand macro="qiime_citation"/>
-</tool>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
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