Add all needed infrastructure for MSAprobs and GLprobs

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

diff --git a/conf/settings/GLprobsParameters.xml b/conf/settings/GLprobsParameters.xml
new file mode 100644 (file)
index 0000000..ee18617
--- /dev/null
+++ b/conf/settings/GLprobsParameters.xml
@@ -0,0 +1,73 @@
+<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
+<runnerConfig>\r
+    <runnerClassName>compbio.runner.msa.GLprobs</runnerClassName>\r
+\r
+    <options isRequired="true">\r
+        <name>CLUSTAL format for output alignment</name>\r
+        <description>\r
+            CLUSTAL output format is used instead of the FASTA format\r
+        </description>\r
+        <optionNames>-clustalw</optionNames>\r
+        <furtherDetails>prog_docs/glprobs.txt</furtherDetails>\r
+    </options>\r
+\r
+    <options isRequired="true">\r
+        <name>Another order of sequence in output alignment</name>\r
+        <description>\r
+            print sequences in alignment order rather than input order\r
+        </description>\r
+        <optionNames>-a</optionNames>\r
+        <optionNames>--alignment-order</optionNames>\r
+        <furtherDetails>prog_docs/glprobs.txt</furtherDetails>\r
+    </options>\r
+\r
+    <prmSeparator> </prmSeparator>\r
+\r
+    <parameters isRequired="false">\r
+        <name>passes of consistency transformation</name>\r
+        <description>\r
+            passes of consistency transformation\r
+        </description>\r
+        <optionNames>-c</optionNames>\r
+        <optionNames>--consistency</optionNames>\r
+        <furtherDetails>prog_docs/glprobs.txt</furtherDetails>\r
+        <defaultValue>2</defaultValue>\r
+        <validValue>\r
+            <type>Integer</type>\r
+            <min>0</min>\r
+            <max>5</max>\r
+        </validValue>\r
+     </parameters>\r
+\r
+    <parameters isRequired="false">\r
+        <name>passes of consistency transformation</name>\r
+        <description>\r
+            number of passes of iterative-refinement\r
+        </description>\r
+        <optionNames>-ir</optionNames>\r
+        <optionNames>--iterative-refinement</optionNames>\r
+        <furtherDetails>prog_docs/glprobs.txt</furtherDetails>\r
+        <defaultValue>100</defaultValue>\r
+        <validValue>\r
+            <type>Integer</type>\r
+            <min>0</min>\r
+            <max>1000</max>\r
+        </validValue>\r
+     </parameters>\r
+\r
+     <parameters isRequired="false">\r
+        <name>Number of CPUs</name>\r
+        <description>\r
+            Number of CPU used by msaprobs. \r
+            My default the number is equal to the total number of CPU on the system.\r
+        </description>\r
+        <optionNames>-num_threads</optionNames>\r
+        <furtherDetails>prog_docs/glprobs.txt</furtherDetails>\r
+        <defaultValue>1</defaultValue>\r
+        <validValue>\r
+            <type>Integer</type>\r
+            <min>1</min>\r
+        </validValue>\r
+    </parameters>\r
+\r
+</runnerConfig>\r