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

Uploaded

--- a/qiime2/qiime_feature-table_tabulate-seqs.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_feature-table_tabulate-seqs.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,44 +1,76 @@
 <?xml version="1.0" ?>
-<tool id="qiime_feature-table_tabulate-seqs" name="qiime feature-table tabulate-seqs" version="2019.7">
-	<description> - View sequence associated with each feature</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<tool id="qiime_feature-table_tabulate-seqs" name="qiime feature-table tabulate-seqs"
+      version="2020.8">
+  <description>View sequence associated with each feature</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
 qiime feature-table tabulate-seqs
-
---i-data=$idata
+# if $input_files_idata:
+  # 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 + ' --i-data=' + d['additional_input'].__getattr__('file_name')
+    # end for
+    # return $file_list
+  # end def
+--i-data=$list_dict_to_string($input_files_idata)
+# 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' '$ovisualization'
+
+;
+qiime tools export  ovisualization.qzv --output-path out
+&& mkdir -p '$ovisualization.files_path'
 && cp -r out/* '$ovisualization.files_path'
-&& mv '$ovisualization.files_path/index.html' '$ovisualization';
-	]]></command>
-	<inputs>
-		<param format="qza,no_unzip.zip" label="--i-data: ARTIFACT FeatureData[Sequence] The feature sequences to be tabulated.       [required]" name="idata" optional="False" type="data"/>
-	</inputs>
-	<outputs>
-		<data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
-	</outputs>
-	<help><![CDATA[
+&& mv '$ovisualization.files_path/index.html' '$ovisualization'
+
+  ]]></command>
+  <inputs>
+    <repeat name="input_files_idata" optional="False" title="--i-data">
+      <param format="qza,no_unzip.zip" label="--i-data: ARTIFACT FeatureData[Sequence | AlignedSequence] The feature sequences to be tabulated.       [required]" name="additional_input" optional="False" type="data" />
+    </repeat>
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
+    
+  </outputs>
+
+  <help><![CDATA[
 View sequence associated with each feature
-##########################################
+###############################################################
 
 Generate tabular view of feature identifier to sequence mapping, including
 links to BLAST each sequence against the NCBI nt database.
 
 Parameters
 ----------
-data : FeatureData[Sequence]
+data : FeatureData[Sequence | AlignedSequence]
     The feature sequences to be tabulated.
 
 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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