# HG changeset patch
# User lijing
# Date 1509640150 14400
# Node ID 5107c9510fe0b8e9ad396e4022896ee59b1fabeb

dnapars

diff -r 000000000000 -r 5107c9510fe0 dnapars.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dnapars.xml	Thu Nov 02 12:29:10 2017 -0400
@@ -0,0 +1,37 @@
+<tool id="dnapars" name="Phylip DNAPARS" version="0.1.0">
+    <description>carries out unrooted parsimony on DNA sequences</description>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <command><![CDATA[
+	cp $infasta infile;
+	echo $inoptions | sed 's/; /\n/g; s/;/\n/g'| /usr/lib/phylip/bin/dnapars infile;
+	cp outfile $outfile;
+	cp outtree $outtree
+    ]]></command>
+    <inputs>
+        <param type="data" name="infasta" format="txt" label="Aligned fasta sequences" />
+	<param type="text" value= "Y;" name="inoptions" format="txt" label="Keyboard responses separated by semicolon and space (see example below)" />
+    </inputs>
+    <outputs>
+        <data name="outfile" format="txt" label="${tool.name} on ${on_string}: Outfile" />
+	<data name="outtree" format="txt" label="${tool.name} on ${on_string}: Tree" />
+    </outputs>
+
+    <help><![CDATA[
+**What it does**        
+
+This program carries out unrooted parsimony (analogous to Wagner trees) (Eck and Dayhoff, 1966; Kluge and Farris, 1969) on DNA sequences. The method of Fitch (1971) is used to count the number of changes of base needed on a given tree.
+Reference: http://evolution.genetics.washington.edu/phylip/doc/dnapars.html
+
+**Prototyping keyboard response files**
+
+Making the proper files of keyboard responses for use with command files is most easily done if you prototype the process by simply running the program and keeping a careful record of the keyboard responses that you need to give to get the program to run properly. Then create a file in an editor and type those keyboard responses into it. Thus if the program requires that you answer a question about what to do with the output file with a keyboard response of R, then wants you to type a menu selection of U (to have it use a User tree), then wants you to answer Y to end the menu, and another R to tell it to replace the output file, you would have the file of keyboard responses be::
+
+  R; U; Y; R;
+
+Testing the keyboard responses with an interactive run will be essential to having batch runs succeed.
+
+    ]]></help>
+
+</tool>