--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_alignment_mafft.xml	Wed Jul 17 03:05:17 2019 -0400
@@ -0,0 +1,56 @@
+<?xml version="1.0" ?>
+<tool id="qiime_alignment_mafft" name="qiime alignment mafft" version="2019.4">
+	<description> - De novo multiple sequence alignment with MAFFT</description>
+	<requirements>
+		<requirement type="package" version="2019.4">qiime2</requirement>
+	</requirements>
+	<command><![CDATA[
+qiime alignment mafft
+
+--i-sequences=$isequences
+--o-alignment=oalignment
+
+#set $pnthreads = '${GALAXY_SLOTS:-4}'
+
+#if str($pnthreads):
+ --p-n-threads="$pnthreads"
+#end if
+
+
+#if $pparttree:
+ --p-parttree
+#end if
+;
+cp oalignment.qza $oalignment
+	]]></command>
+	<inputs>
+		<param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The sequences to be aligned.              [required]" name="isequences" optional="False" type="data"/>
+		<param label="--p-parttree: --p-no-parttree This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default                             [default: False]" name="pparttree" selected="False" type="boolean"/>
+	</inputs>
+	<outputs>
+		<data format="qza" label="${tool.name} on ${on_string}: alignment.qza" name="oalignment"/>
+	</outputs>
+	<help><![CDATA[
+De novo multiple sequence alignment with MAFFT
+##############################################
+
+Perform de novo multiple sequence alignment using MAFFT.
+
+Parameters
+----------
+sequences : FeatureData[Sequence]
+    The sequences to be aligned.
+parttree : Bool, optional
+    This flag is required if the number of sequences being aligned are
+    larger than 1000000. Disabled by default
+
+Returns
+-------
+alignment : FeatureData[AlignedSequence]
+    The aligned sequences.
+	]]></help>
+<macros>
+    <import>qiime_citation.xml</import>
+</macros>
+<expand macro="qiime_citation"/>
+</tool>