diff dnapars.xml @ 10:9929063b59f9 draft

Phylip tools update

--- a/dnapars.xml	Thu Nov 02 12:49:05 2017 -0400
+++ b/dnapars.xml	Fri Nov 03 11:33:55 2017 -0400
@@ -5,13 +5,13 @@
     </stdio>
     <command><![CDATA[
 	cp $infasta infile;
-	echo $inoptions | sed 's/; /\n/g; s/;/\n/g'| /usr/lib/phylip/bin/dnapars infile;
+	echo $inoptions | sed 's/$/\n/' | sed 's/, /\n/g; s/,/\n/g' | /usr/lib/phylip/bin/dnapars infile;
 	cp outfile $outfile;
 	cp outtree $outtree
     ]]></command>
     <inputs>
         <param type="data" name="infasta" format="txt" label="Aligned fasta sequences" />
-	<param type="text" value= "Y;" name="inoptions" format="txt" label="Keyboard responses separated by semicolon and space (see example below)" />
+	<param type="text" value= "Y" name="inoptions" format="txt" label="Keyboard responses separated by comma and space (see example below)" />
     </inputs>
     <outputs>
         <data name="outfile" format="txt" label="${tool.name} on ${on_string}: Outfile" />
@@ -28,7 +28,7 @@
 
 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;
+  R, U, Y, R
 
 Testing the keyboard responses with an interactive run will be essential to having batch runs succeed.