# HG changeset patch
# User florianbegusch
# Date 1599126360 0
# Node ID 887cd4ad8e163ea6f18eb1799f87f16fed37015a
# Parent  33e7a34700468971aa6b1b233df55d862e321e33
Uploaded

diff -r 33e7a3470046 -r 887cd4ad8e16 qiime2/qiime_alignment_mafft.xml
--- a/qiime2/qiime_alignment_mafft.xml	Thu Sep 03 09:44:28 2020 +0000
+++ b/qiime2/qiime_alignment_mafft.xml	Thu Sep 03 09:46:00 2020 +0000
@@ -1,38 +1,53 @@
 <?xml version="1.0" ?>
-<tool id="qiime_alignment_mafft" name="qiime alignment mafft" version="2019.7">
-	<description> - De novo multiple sequence alignment with MAFFT</description>
-	<requirements>
-		<requirement type="package" version="2019.7">qiime2</requirement>
-	</requirements>
-	<command><![CDATA[
+<tool id="qiime_alignment_mafft" name="qiime alignment mafft"
+      version="2020.8">
+  <description>De novo multiple sequence alignment with MAFFT</description>
+  <requirements>
+    <requirement type="package" version="2020.8">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"
+#if str($pnthreads) != 'None':
+--p-n-threads=$pnthreads
 #end if
 
-
 #if $pparttree:
  --p-parttree
 #end if
+
+--o-alignment=oalignment
+
+#if str($examples) != 'None':
+--examples=$examples
+#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 ${on_string}: alignment.qza" name="oalignment"/>
-	</outputs>
-	<help><![CDATA[
+
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The sequences to be aligned.              [required]" name="isequences" optional="False" type="data" />
+    <param label="--p-n-threads: " name="pnthreads" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="Int % Range(1">Int % Range(1</option>
+      <option value="None">None</option>
+    </param>
+    <param label="--p-parttree: --p-parttree: / --p-no-parttree This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default                             [default: False]" name="pparttree" selected="False" type="boolean" />
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="qza" label="${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.
 
@@ -40,6 +55,9 @@
 ----------
 sequences : FeatureData[Sequence]
     The sequences to be aligned.
+n_threads : Int % Range(1, None) | Str % Choices('auto'), optional
+    The number of threads. (Use `auto` to automatically use all available
+    cores)
 parttree : Bool, optional
     This flag is required if the number of sequences being aligned are
     larger than 1000000. Disabled by default
@@ -48,9 +66,9 @@
 -------
 alignment : FeatureData[AlignedSequence]
     The aligned sequences.
-	]]></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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