# HG changeset patch
# User p.lucas
# Date 1556790001 14400
# Node ID a56bda3448b185798f4eea9abaa74cb8f29fdb5a

Uploaded

diff -r 000000000000 -r a56bda3448b1 mafft.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mafft.xml	Thu May 02 05:40:01 2019 -0400
@@ -0,0 +1,42 @@
+<tool id="rbc_mafft" name="MAFFT" version="7.221.3">
+    <description>Multiple alignment program for amino acid or nucleotide sequences</description>
+    <requirements>
+        <requirement type="package" version="7.221">mafft</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
+        <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />
+    </stdio>
+    <version_command>
+    <![CDATA[
+        mafft --version
+    ]]>
+    </version_command>
+    <command>
+    <![CDATA[
+        mafft --thread \${GALAXY_SLOTS:-1} --add $seqtoadd --reorder $existingalignment > $outputAlignment
+    ]]>
+    </command>
+    <inputs>
+        <param name="seqtoadd" type="data" format="fasta" label="Sequences to add" help="Sequences to add in FASTA format."/>
+        <param name="existingalignment" type="data" format="fasta" label="Alignment already done" help="Multi-alignment in FASTA format."/>
+    </inputs>
+    <outputs>
+        <data format="fasta" name="outputAlignment" label="${tool.name} on ${on_string}"/>
+    </outputs>
+    <help>
+    <![CDATA[
+**What it does**
+
+MAFFT is a multiple sequence alignment program for unix-like operating systems.  
+It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), 
+FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc.
+
+Using only to add new sequence in alignment already done.
+
+    ]]>
+    </help>
+    <citations>
+        <citation type="doi">10.1093/molbev/mst010</citation>
+    </citations>
+</tool>