Mercurial > repos > rnateam > mafft

changeset 2:d71e007323d4 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit ef7eb622ae8ea3a2a5aa5f5d2c9eaf41367bfef9-dirty
author rnateam
date Tue, 04 Aug 2015 04:01:23 -0400
parents 5e48c4621f9f
children a681631ccee6
files mafft.xml
diffstat 1 files changed, 9 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/mafft.xml	Fri Jul 31 19:02:11 2015 -0400
+++ b/mafft.xml	Tue Aug 04 04:01:23 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="rbc_mafft" name="MAFFT" version="7.221.0">
+<tool id="rbc_mafft" name="MAFFT" version="7.221.1">
     <description>Multiple alignment program for amino acid or nucleotide sequences</description>
     <requirements>
         <requirement type="package" version="7.221">mafft</requirement>
@@ -23,6 +23,8 @@
         
         ## specify threads to use
         --thread \${GALAXY_SLOTS:-1}
+      
+        $adjustdirection
         
         #if $outputFormat.value == 'clustalw'
             --clustalout
@@ -64,6 +66,10 @@
             <when value="mafft-qinsi"/>
             <when value="mafft-xinsi"/>
         </conditional>
+        <param name="adjustdirection" type="select" display="radio" label="Direction of nucleotide sequences" help="Generate reverse complement sequences, as necessary, and align them together with the remaining sequences">
+            <option value="--adjustdirection">adjust direction</option>
+            <option value=" " selected="true">do not adjust direction</option>
+            </param>
         <param name="outputFormat" type="select" label="Output format" help="Either FASTA or ClustalW">
             <option value="fasta" selected="true">FASTA</option>
             <option value="clustalw">ClustalW</option>
@@ -150,6 +156,8 @@
 
 --auto
     Automatically selects an appropriate strategy from L-INS-i, FFT-NS-i and FFT-NS-2, according to data size. Default: off (always FFT-NS-2)
+--adjustdirection
+    Generate reverse complement sequences, as necessary, and align them together with the remaining sequences. In the case of protein alignment, these options are just ignored.
     ]]>
     </help>
     <citations>