diff qiime2-2020.8/qiime_feature-table_tabulate-seqs.xml @ 20:d93d8888f0b0 draft

Uploaded
author florianbegusch
date Fri, 04 Sep 2020 12:44:24 +0000
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+++ b/qiime2-2020.8/qiime_feature-table_tabulate-seqs.xml	Fri Sep 04 12:44:24 2020 +0000
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+<?xml version="1.0" ?>
+<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
+# 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
+
+;
+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' '$ovisualization'
+
+  ]]></command>
+  <inputs>
+    <repeat name="input_files_idata" optional="False" title="--i-data">
+      <param format="qza,no_unzip.zip" label="--i-data: ARTIFACT FeatureData[Sequence | AlignedSequence] The feature sequences to be tabulated.       [required]" name="additional_input" optional="False" type="data" />
+    </repeat>
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="html" label="${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 | AlignedSequence]
+    The feature sequences to be tabulated.
+
+Returns
+-------
+visualization : Visualization
+  ]]></help>
+  <macros>
+    <import>qiime_citation.xml</import>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
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