diff qiime2/qiime_feature-table_presence-absence.xml @ 14:a0a8d77a991c draft

Uploaded

--- a/qiime2/qiime_feature-table_presence-absence.xml	Thu Sep 03 09:46:00 2020 +0000
+++ b/qiime2/qiime_feature-table_presence-absence.xml	Thu Sep 03 09:51:29 2020 +0000
@@ -1,27 +1,43 @@
 <?xml version="1.0" ?>
-<tool id="qiime_feature-table_presence-absence" name="qiime feature-table presence-absence" version="2019.7">
-	<description> - Convert to presence/absence</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<tool id="qiime_feature-table_presence-absence" name="qiime feature-table presence-absence"
+      version="2020.8">
+  <description>Convert to presence/absence</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
 qiime feature-table presence-absence
 
---i-table=$itable
+#if $itable:
+ --i-table
+#end if
 
---o-presence-absence-table=opresenceabsencetable
+#if $opresenceabsencetable:
+ --o-presence-absence-table
+#end if
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
 ;
-cp opresenceabsencetable.qza $opresenceabsencetable
-	]]></command>
-	<inputs>
-		<param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency | RelativeFrequency] The feature table to be converted into presence/absence abundances.                 [required]" name="itable" optional="False" type="data"/>
-	</inputs>
-	<outputs>
-		<data format="qza" label="${tool.name} on ${on_string}: presenceabsencetable.qza" name="opresenceabsencetable"/>
-	</outputs>
-	<help><![CDATA[
+cp omergeddata.qza $omergeddata
+
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-table: --i-table: ARTIFACT FeatureTable[Frequency | RelativeFrequency] The feature table to be converted into presence/absence abundances.                 [required]" name="itable" selected="False" type="boolean" />
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <param label="--o-presence-absence-table: --o-presence-absence-table: ARTIFACT FeatureTable[PresenceAbsence] The resulting presence/absence feature table. [required]" name="opresenceabsencetable" selected="False" type="boolean" />
+    
+  </outputs>
+
+  <help><![CDATA[
 Convert to presence/absence
-###########################
+###############################################################
 
 Convert frequencies to binary values indicating presence or absence of a
 feature in a sample.
@@ -35,9 +51,9 @@
 -------
 presence_absence_table : FeatureTable[PresenceAbsence]
     The resulting presence/absence feature table.
-	]]></help>
-<macros>
+  ]]></help>
+  <macros>
     <import>qiime_citation.xml</import>
-</macros>
-<expand macro="qiime_citation"/>
-</tool>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
\ No newline at end of file