new version of muscle 3.8.31

[jabaws.git] / conf / settings / MuscleParameters.xml

diff --git a/conf/settings/MuscleParameters.xml b/conf/settings/MuscleParameters.xml
index 89ad920..08ff452 100644 (file)
--- a/conf/settings/MuscleParameters.xml
+++ b/conf/settings/MuscleParameters.xml
@@ -1,6 +1,8 @@
 <?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
 <runnerConfig>\r
  <runnerClassName>compbio.runner.muscle.Muscle</runnerClassName>\r
+    <!--\r
+    This is the only option possible so no point in having it  \r
     <options isRequired="false">\r
         <name>Group sequences</name>\r
         <description>Group sequences by similarity (this is the default) or preserve the input order</description>\r
@@ -8,6 +10,7 @@
         <furtherDetails>prog_docs/muscle.html</furtherDetails>\r
         <defaultValue>-group</defaultValue>\r
     </options>\r
+     -->\r
     <!-- optionNames>-stable</optionNames  this is commented out as it contain bug see muscle web site-->\r
     <options isRequired="false">\r
         <name>Anchor optimisation</name>\r
@@ -17,6 +20,15 @@
         <furtherDetails>prog_docs/muscle.html</furtherDetails>\r
         <defaultValue>-anchors</defaultValue>\r
     </options>\r
+    <!-- Programs failures often with this option \r
+    <options isRequired="false">\r
+        <name>Window refine</name>\r
+        <description>Refine an alignment by dividing it into non-overlapping windows and re-aligning each window. Typically used for whole-genome nucleotide alignments</description>\r
+        <optionNames>-refinew</optionNames>\r
+        <furtherDetails>prog_docs/muscle.html</furtherDetails>\r
+        <defaultValue>-refinew</defaultValue>\r
+    </options>\r
+     -->\r
     <options isRequired="false">\r
         <name>Root alignment computation method</name>\r
         <description>Use Steven Brenner's method for computing the root alignment.</description>\r
@@ -69,7 +81,8 @@
         <defaultValue>auto</defaultValue>\r
         <possibleValues>auto</possibleValues>\r
         <possibleValues>protein</possibleValues>\r
-        <possibleValues>nucleo</possibleValues>\r
+        <possibleValues>dna</possibleValues>\r
+        <possibleValues>rna</possibleValues>\r
     </parameters>\r
        <parameters isRequired="false">\r
         <name>Maxiters</name>\r
@@ -83,6 +96,68 @@
             <max>100</max>\r
         </validValue>\r
     </parameters>\r
+    <!-- disable as refinew is disabled \r
+    <parameters isRequired="false">\r
+        <name>Maxiters</name>\r
+        <description>Length of window for Window Refine (-refinew)</description>\r
+        <optionNames>-refinewindow</optionNames>\r
+        <furtherDetails>prog_docs/muscle.html</furtherDetails>\r
+        <defaultValue>200</defaultValue>\r
+        <validValue>\r
+               <type>Integer</type>\r
+            <min>1</min>\r
+            <max>1000</max>\r
+        </validValue>\r
+    </parameters>\r
+     -->\r
+    <parameters isRequired="false">\r
+        <name>Diagonal break</name>\r
+        <description>Maximum distance between two diagonals that allows them to merge into one diagonal</description>\r
+        <optionNames>-diagbreak</optionNames>\r
+        <furtherDetails>prog_docs/muscle.html</furtherDetails>\r
+        <defaultValue>1</defaultValue>\r
+        <validValue>\r
+               <type>Integer</type>\r
+            <min>1</min>\r
+            <max>100</max>\r
+        </validValue>\r
+    </parameters>\r
+    <parameters isRequired="false">\r
+        <name>Diagonal length</name>\r
+        <description>Minimum length of diagonal</description>\r
+        <optionNames>-diaglength</optionNames>\r
+        <furtherDetails>prog_docs/muscle.html</furtherDetails>\r
+        <defaultValue>24</defaultValue>\r
+        <validValue>\r
+               <type>Integer</type>\r
+            <min>2</min>\r
+            <max>100</max>\r
+        </validValue>\r
+    </parameters>\r
+    <parameters isRequired="false">\r
+        <name>Diagonal margin</name>\r
+        <description>Discard this many positions at ends of diagonal</description>\r
+        <optionNames>-diagmargin</optionNames>\r
+        <furtherDetails>prog_docs/muscle.html</furtherDetails>\r
+        <defaultValue>5</defaultValue>\r
+        <validValue>\r
+               <type>Integer</type>\r
+            <min>1</min>\r
+            <max>100</max>\r
+        </validValue>\r
+    </parameters>\r
+    <parameters isRequired="false">\r
+        <name>Anchor spacing</name>\r
+        <description>Minimum spacing between anchor columns</description>\r
+        <optionNames>-anchorspacing</optionNames>\r
+        <furtherDetails>prog_docs/muscle.html</furtherDetails>\r
+        <defaultValue>32</defaultValue>\r
+        <validValue>\r
+               <type>Integer</type>\r
+            <min>2</min>\r
+            <max>1000</max>\r
+        </validValue>\r
+    </parameters>\r
        <parameters isRequired="false">\r
         <name>Matrix</name>\r
         <description>Substitution Matrix to use</description>\r
@@ -222,6 +297,30 @@
             <max>10</max>\r
         </validValue>\r
     </parameters>\r
+     <parameters>\r
+        <name>Minimum anchor score</name>\r
+        <description>Minimum score a column must have to be an anchor (default depends on the profile scoring function!)</description>\r
+        <optionNames>-minbestcolscore</optionNames>\r
+        <furtherDetails>prog_docs/muscle.html</furtherDetails>\r
+        <defaultValue>1.2</defaultValue>\r
+        <validValue>\r
+               <type>Float</type>\r
+            <min>0</min>\r
+            <max>10</max>\r
+        </validValue>\r
+    </parameters>\r
+    <parameters>\r
+        <name>Minimum smoothed anchor score</name>\r
+        <description>Minimum smoothed score a column must have to be an anchor (default depends on the profile scoring function!)</description>\r
+        <optionNames>-minsmoothscore</optionNames>\r
+        <furtherDetails>prog_docs/muscle.html</furtherDetails>\r
+        <defaultValue>1.2</defaultValue>\r
+        <validValue>\r
+               <type>Float</type>\r
+            <min>0</min>\r
+            <max>10</max>\r
+        </validValue>\r
+    </parameters>\r
        <parameters isRequired="false">\r
         <name>cluster1</name>\r
         <description>Clustering method to use on the iteration 1</description>\r