diff qiime2/qiime_taxa_barplot.xml @ 6:de4c22a52df4 draft

Fixes
author florianbegusch
date Tue, 13 Aug 2019 07:46:48 -0400
parents 914fa4daf16a
children f190567fe3f6
line wrap: on
line diff
--- a/qiime2/qiime_taxa_barplot.xml	Mon Aug 05 01:29:30 2019 -0400
+++ b/qiime2/qiime_taxa_barplot.xml	Tue Aug 13 07:46:48 2019 -0400
@@ -7,8 +7,17 @@
 	<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=$itable
---i-taxonomy=$itaxonomy
 
 #if $input_files_mmetadatafile:
 #def list_dict_to_string(list_dict):
@@ -28,11 +37,27 @@
 && mv '$ovisualization.files_path/index.html' '$ovisualization';
 	]]></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="True" 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" />
+		<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>
+
+
+		<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>
 
 	</inputs>