diff qiime2/qiime_fragment-insertion_classify-otus-experimental.xml @ 14:a0a8d77a991c draft

Uploaded

--- a/qiime2/qiime_fragment-insertion_classify-otus-experimental.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_fragment-insertion_classify-otus-experimental.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,54 +1,46 @@
 <?xml version="1.0" ?>
-<tool id="qiime_fragment-insertion_classify-otus-experimental" name="qiime fragment-insertion classify-otus-experimental" version="2019.7">
-	<description> - Experimental: Obtain taxonomic lineages, by finding closest OTU in reference phylogeny.</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<tool id="qiime_fragment-insertion_classify-otus-experimental" name="qiime fragment-insertion classify-otus-experimental"
+      version="2020.8">
+  <description>Experimental: Obtain taxonomic lineages, by finding closest OTU in reference phylogeny.</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
 qiime fragment-insertion classify-otus-experimental
 
 --i-representative-sequences=$irepresentativesequences
---i-tree=$itree --o-classification=oclassification
 
+--i-tree=$itree
+
+--i-reference-taxonomy=$ireferencetaxonomy
 
-#if str( $id_to_taxonomy_fp.selector ) == 'history'
-#set $tax = $id_to_taxonomy_fp.taxonomy_fp
---i-reference-taxonomy '$tax'
-#else:
-#set $tax = $id_to_taxonomy_fp.taxonomy_fp.fields.path
---i-reference-taxonomy '$tax'
+--o-classification=oclassification
+
+#if str($examples) != 'None':
+--examples=$examples
 #end if
 
-
 ;
 cp oclassification.qza $oclassification
-	]]></command>
-	<inputs>
-		<param format="qza,no_unzip.zip" label="--i-representative-sequences: ARTIFACT FeatureData[Sequence] The sequences used for a 'sepp' run to produce the 'tree'.                                      [required]" name="irepresentativesequences" optional="False" type="data"/>
-		<param format="qza,no_unzip.zip" label="--i-tree: ARTIFACT    The tree resulting from inserting fragments into a Phylogeny[Rooted]  reference phylogeny, i.e. the output of function 'sepp' [required]" name="itree" optional="False" type="data"/>
+
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-representative-sequences: ARTIFACT FeatureData[Sequence] The sequences used for a \'sepp\' run to produce the \'tree\'.                                      [required]" name="irepresentativesequences" optional="False" type="data" />
+    <param format="qza,no_unzip.zip" label="--i-tree: ARTIFACT    The tree resulting from inserting fragments into a Phylogeny[Rooted]  reference phylogeny, i.e. the output of function \'sepp\' [required]" name="itree" optional="False" type="data" />
+    <param format="qza,no_unzip.zip" label="--i-reference-taxonomy: ARTIFACT FeatureData[Taxonomy] Reference taxonomic table that maps every OTU-ID into a taxonomic lineage string.                  [required]" name="ireferencetaxonomy" optional="False" type="data" />
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
 
-		<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>
+  <outputs>
+    <data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification" />
+    
+  </outputs>
 
-	</inputs>
-	<outputs>
-		<data format="qza" label="${tool.name} on ${on_string}: classification.qza" name="oclassification"/>
-	</outputs>
-	<help><![CDATA[
+  <help><![CDATA[
 Experimental: Obtain taxonomic lineages, by finding closest OTU in reference phylogeny.
-#######################################################################################
+###############################################################
+
 
 Experimental: Use the resulting tree from 'sepp' and find closest OTU-ID
 for every inserted fragment. Then, look up the reference lineage string in
@@ -61,7 +53,7 @@
 tree : Phylogeny[Rooted]
     The tree resulting from inserting fragments into a reference phylogeny,
     i.e. the output of function 'sepp'
-reference_taxonomy : FeatureData[Taxonomy], optional
+reference_taxonomy : FeatureData[Taxonomy]
     Reference taxonomic table that maps every OTU-ID into a taxonomic
     lineage string.
 
@@ -69,9 +61,9 @@
 -------
 classification : FeatureData[Taxonomy]
     Taxonomic lineages for inserted fragments.
-	]]></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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