diff qiime2/qiime_taxa_barplot.xml @ 14:a0a8d77a991c draft

Uploaded

--- a/qiime2/qiime_taxa_barplot.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_taxa_barplot.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,72 +1,67 @@
 <?xml version="1.0" ?>
-<tool id="qiime_taxa_barplot" name="qiime taxa barplot" version="2019.7">
-	<description> - Visualize taxonomy with an interactive bar plot</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<tool id="qiime_taxa_barplot" name="qiime taxa barplot"
+      version="2020.8">
+  <description>Visualize taxonomy with an interactive bar plot</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
 qiime taxa barplot
 
-
-#if str( $id_to_taxonomy_fp.selector ) == 'history'
-	#set $tax = $id_to_taxonomy_fp.taxonomy_fp
-	--i-taxonomy '$tax'
-#else:
-	#set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path
-	--i-taxonomy '$tax'
-#end if
-
-
 --i-table=$itable
 
-#if $input_files_mmetadatafile:
-#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-metadata-file=' + d['additional_input'].__getattr__('file_name')
-	#end for
-	#return $file_list
-#end def
- --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
-#end if
+--i-taxonomy=$itaxonomy
+# if $input_files_mmetadatafile:
+  # 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-metadata-file=' + d['additional_input'].__getattr__('file_name')
+    # end for
+    # return $file_list
+  # end def
+--m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
+# 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 otesttable.qza $otesttable
+
+;
+qiime tools export  ovisualization.qzv --output-path out
+&& mkdir -p '$ovisualization.files_path'
 && cp -r out/* '$ovisualization.files_path'
-&& mv '$ovisualization.files_path/index.html' '$ovisualization';
-	]]></command>
-	<inputs>
+&& mv '$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'
 
-		<conditional name="id_to_taxonomy_fp" optional="True">
-		   <param name="selector" type="select" label="Reference taxonomy to query">
-			  <option value="cached">Public databases</option>
-			  <option value="history">Databases from your history</option>
-		   </param>
-		   <when value="cached">
-			  <param argument="--taxonomy_fp" label="Reference taxonomy" type="select" optional="True">
-				 <options from_data_table="qiime_taxonomy" />
-			  </param>
-		   </when>
-		   <when value="history">
-			  <param argument="--taxonomy_fp" type="data" format="qza,no_unzip.zip" label="Reference databases" optional="True" />
-		   </when>
-		</conditional>
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table to visualize at various taxonomic levels.                                    [required]" name="itable" optional="False" type="data" />
+    <param format="qza,no_unzip.zip" label="--i-taxonomy: ARTIFACT FeatureData[Taxonomy] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored.                           [required]" name="itaxonomy" optional="False" type="data" />
+    <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
+      <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA... (multiple            The sample metadata. arguments will be merged)                                                        [required]" name="additional_input" optional="False" type="data" />
+    </repeat>
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
 
-
-		<param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table to visualize at various taxonomic levels.                                    [required]" name="itable" optional="False" type="data"/>
-
-		<repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file  [required]">
-			<param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" optional="False" />
-		</repeat>
+  <outputs>
+    <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
+    
+  </outputs>
 
-	</inputs>
-	<outputs>
-		<data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
-	</outputs>
-	<help><![CDATA[
+  <help><![CDATA[
 Visualize taxonomy with an interactive bar plot
-###############################################
+###############################################################
 
 This visualizer produces an interactive barplot visualization of
 taxonomies. Interactive features include multi-level sorting, plot
@@ -87,9 +82,9 @@
 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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