# HG changeset patch
# User edward-kirton
# Date 1310695856 14400
# Node ID 38a28f5f9449e5aa5a03682dc85b8037ea6d0ed8

Uploaded

diff -r 000000000000 -r 38a28f5f9449 muscle.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/muscle.xml	Thu Jul 14 22:10:56 2011 -0400
@@ -0,0 +1,102 @@
+<tool id="muscle" name="Muscle" version="1.0.0">
+<description>Multiple sequence alignment</description>
+<command>muscle
+-quiet
+#if $input.select == '1':
+-in $input.file
+#else:
+-profile
+-in1 $input.file1
+-in2 $input.file2
+#end if
+#if $usetree.select == 'yes':
+-usetree_nowarn $usetree.file
+#end if
+$refine
+-out $output
+$diags
+-maxiters $maxiters
+-maxhours $maxhours
+#if $advanced.select == 'yes':
+-maxtrees $advanced.maxtrees
+-anchorspacing $advanced.anchorspacing
+-diagbreak $advanced.diagbreak
+-diaglength $advanced.diaglength
+-diagmargin $advanced.diagmargin
+-smoothwindow $advanced.smoothwindow
+$advanced.brenner
+$advanced.dimer
+#end if
+</command>
+<inputs>
+<conditional name="input">
+    <param name="select" type="select" label="Mode">
+        <option value="1" selected="true">Single file</option>
+        <option value="2">Profile-profile alignment</option>
+    </param>
+    <when value="1">
+        <param name="file" type="data" format="fasta" label="Unaligned sequences" />
+    </when>
+    <when value="2">
+        <param name="file1" type="data" format="fasta" label="Aligned sequences #1" />
+        <param name="file2" type="data" format="fasta" label="Aligned sequences #2" />
+    </when>
+</conditional>
+<conditional name="usetree">
+    <param name="select" type="select" label="Use guide tree" help="NB: The best guide tree for multiple alignment is not in general the correct evolutionary tree">
+      <option value="no" selected="True">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <when value="no">
+        <param name="file" type="hidden" value="" /> 
+    </when>
+    <when value="yes">
+        <param name="file" type="data" format="phylip" label="Guide tree in Newick/Phylip format" />
+    </when>
+</conditional>
+<param name="refine" type="boolean" truevalue="-refine" falsevalue="" label="Refine an existing alignment" />
+<param name="diags" type="boolean" truevalue="-diags" falsevalue="" label="Find diagonals" help="Faster for similar sequences" />
+<param name="maxiters" label="Maximum number of iterations" type="integer" value="16" help="Use small number for very large files (as low as 1 or 2)." />
+<param name="maxhours" label="Maximum hours" type="float" value="24.0" help="If this time is exceeded, muscle will write out current alignment and stop." />
+<conditional name="advanced">
+    <param name="select" type="select" label="Show advanced options">
+      <option value="no" selected="True">No</option>
+      <option value="yes">Yes</option>
+    </param>
+    <when value="no">
+    </when>
+    <when value="yes">
+        <param name="maxtrees" label="Maximum number of new trees to create in iteration 2" type="integer" value="1" />
+        <param name="anchorspacing" label="Minimum spacing between anchor columns" type="integer" value="32" />
+        <param name="diagbreak" label="Maximum distance between two diagonals that allows them to merge into one diagonal" type="integer" value="1" />
+        <param name="diaglength" label="Minimum length of diagonal" type="integer" value="24" />
+        <param name="diagmargin" label="Discard this many positions at ends of diagonal" type="integer" value="5" />
+        <param name="smoothwindow" label="Window used for anchor column smoothing" type="integer" value="7" />
+        <!-- flags -->
+        <param name="brenner" label="Use Steven Brenner's method for computing the root alignment" type="boolean" truevalue="-brenner" falsevalue="" selected="false" />
+        <param name="dimer" label="Use dimer approximation for the SP score" help="Faster, slightly less accurate" type="boolean" truevalue="-dimer" falsevalue="" selected="false" />
+    </when>
+</conditional>
+</inputs>
+<outputs>
+<data format="fasta" name="output" />
+</outputs>
+<help>
+**What it does**
+
+Perform multiple sequence alignment.
+
+**Documentation**
+
+http://www.drive5.com/muscle/muscle_userguide3.8.pdf
+
+**Author**
+
+Robert C. Edgar
+
+**Citation**
+
+Edgar, R.C. Nucleic Acids Res 32(5), 1792-97.
+
+</help>
+</tool>