Mercurial > repos > florianbegusch > qiime2_suite

diff qiime2/qiime_taxa_filter-table.xml @ 14:a0a8d77a991c draft

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Uploaded
author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
parents f190567fe3f6
children
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line diff
--- a/qiime2/qiime_taxa_filter-table.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_taxa_filter-table.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,77 +1,63 @@
 <?xml version="1.0" ?>
-<tool id="qiime_taxa_filter-table" name="qiime taxa filter-table" version="2019.7">
-	<description> - Taxonomy-based feature table filter.</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<tool id="qiime_taxa_filter-table" name="qiime taxa filter-table"
+      version="2020.8">
+  <description>Taxonomy-based feature table filter.</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
 qiime taxa filter-table
 
-
-#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=$itaxonomy
+
 #if str($pinclude):
- --p-include="$pinclude"
-#end if
-
-#if str($pexclude):
- --p-exclude="$pexclude"
+  --p-include=$pinclude
 #end if
-
-#if str($pquerydelimiter):
- --p-query-delimiter="$pquerydelimiter"
+#if str($pexclude):
+  --p-exclude=$pexclude
 #end if
-
+#if str($pquerydelimiter):
+  --p-query-delimiter=$pquerydelimiter
+#end if
 #if str($pmode) != 'None':
- --p-mode=$pmode
+--p-mode=$pmode
 #end if
 
 --o-filtered-table=ofilteredtable
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
 ;
 cp ofilteredtable.qza $ofilteredtable
-	]]></command>
-	<inputs>
-		<param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table to be filtered.              [required]" name="itable" optional="False" type="data"/>
 
-		<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 be filtered.              [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 for features that are not present in the feature table will be ignored.             [required]" name="itaxonomy" optional="False" type="data" />
+    <param label="--p-include: TEXT       One or more search terms that indicate which taxa should be included in the resulting table. If providing more than one term, terms should be delimited by the query-delimiter character. By default, all taxa will be included.        [optional]" name="pinclude" optional="False" type="text" />
+    <param label="--p-exclude: TEXT       One or more search terms that indicate which taxa should be excluded from the resulting table. If providing more than one term, terms should be delimited by the query-delimiter character. By default, no taxa will be excluded.         [optional]" name="pexclude" optional="False" type="text" />
+    <param label="--p-query-delimiter: TEXT The string used to delimit multiple search terms provided to include or exclude. This parameter should only need to be modified if the default delimiter (a comma) is used in the provided taxonomic annotations. [default: \',\']" name="pquerydelimiter" optional="False" type="text" value="\',\'" />
+    <param label="--p-mode: " name="pmode" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="exact">exact</option>
+      <option value="contains">contains</option>
+    </param>
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
 
-		<param label="--p-include: TEXT       One or more search terms that indicate which taxa should be included in the resulting table. If providing more than one term, terms should be delimited by the query-delimiter character. By default, all taxa will be included.        [optional]" name="pinclude" optional="True" type="text"/>
-		<param label="--p-exclude: TEXT       One or more search terms that indicate which taxa should be excluded from the resulting table. If providing more than one term, terms should be delimited by the query-delimiter character. By default, no taxa will be excluded.         [optional]" name="pexclude" optional="True" type="text"/>
-		<param label="--p-query-delimiter: TEXT The string used to delimit multiple search terms provided to include or exclude. This parameter should only need to be modified if the default delimiter (a comma) is used in the provided taxonomic annotations. [default: ',']" name="pquerydelimiter" optional="True" type="text" value=","/>
-		<param label="--p-mode: " name="pmode" optional="True" type="select">
-			<option selected="True" value="None">Selection is Optional</option>
-			<option value="exact">exact</option>
-			<option value="contains">contains</option>
-		</param>
-	</inputs>
-	<outputs>
-		<data format="qza" label="${tool.name} on ${on_string}: filteredtable.qza" name="ofilteredtable"/>
-	</outputs>
-	<help><![CDATA[
+  <outputs>
+    <data format="qza" label="${tool.name} on ${on_string}: filteredtable.qza" name="ofilteredtable" />
+    
+  </outputs>
+
+  <help><![CDATA[
 Taxonomy-based feature table filter.
-####################################
+###############################################################
 
 This method filters features from a table based on their taxonomic
 annotations. Features can be retained in the resulting table by specifying
@@ -115,9 +101,9 @@
 -------
 filtered_table : FeatureTable[Frequency]
     The taxonomy-filtered feature table.
-	]]></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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