# HG changeset patch
# User lijing
# Date 1509723235 14400
# Node ID 9929063b59f953a20d0a25dfc114480b5a01568f
# Parent  19d3ec5664711a5de35389c4d1d2627462e81a04
Phylip tools update

diff -r 19d3ec566471 -r 9929063b59f9 ._consense.xml
Binary file ._consense.xml has changed
diff -r 19d3ec566471 -r 9929063b59f9 ._dnapars.xml
Binary file ._dnapars.xml has changed
diff -r 19d3ec566471 -r 9929063b59f9 ._interleave-fastqgz-MITOBIM.py
Binary file ._interleave-fastqgz-MITOBIM.py has changed
diff -r 19d3ec566471 -r 9929063b59f9 ._interleave.xml
Binary file ._interleave.xml has changed
diff -r 19d3ec566471 -r 9929063b59f9 ._mitobim.xml
Binary file ._mitobim.xml has changed
diff -r 19d3ec566471 -r 9929063b59f9 ._seqboot.xml
Binary file ._seqboot.xml has changed
diff -r 19d3ec566471 -r 9929063b59f9 consense.xml
--- a/consense.xml	Thu Nov 02 12:49:05 2017 -0400
+++ b/consense.xml	Fri Nov 03 11:33:55 2017 -0400
@@ -4,14 +4,14 @@
         <exit_code range="1:" />
     </stdio>
     <command><![CDATA[
-	cp $infasta intree;
-	echo $inoptions | sed 's/; /\n/g; s/;/\n/g' | /usr/lib/phylip/bin/consense;
+	cp $intree intree;
+	echo $inoptions | sed 's/$/\n/' | sed 's/, /\n/g; s/,/\n/g' | /usr/lib/phylip/bin/consense;
 	cp outfile $outfile;
 	cp outtree $outtree
     ]]></command>
     <inputs>
         <param type="data" name="intree" format="txt" label="A series of trees in the Newick standard form" />
-	<param type="text" value= "Y;" name="inoptions" format="txt" label="Keyboard responses separated by semicolon and space (see example below)" />
+	<param type="text" value= "Y" name="inoptions" format="txt" label="Keyboard responses separated by comma and space (see example below)" />
     </inputs>
     <outputs>
         <data name="outfile" format="txt" label="${tool.name} on ${on_string}: Outfile" />
@@ -23,11 +23,11 @@
 
 Reference: http://evolution.genetics.washington.edu/phylip/doc/consense.html
 
-**Prototyping keyboard response files**
+**Prototyping keyboard response**
 
 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.
 
diff -r 19d3ec566471 -r 9929063b59f9 dnapars.xml
--- 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.
 
diff -r 19d3ec566471 -r 9929063b59f9 seqboot.xml
--- a/seqboot.xml	Thu Nov 02 12:49:05 2017 -0400
+++ b/seqboot.xml	Fri Nov 03 11:33:55 2017 -0400
@@ -5,12 +5,12 @@
     </stdio>
     <command><![CDATA[
 	cp $infasta infile;
-	echo $inoptions | sed 's/; /\n/g; s/;/\n/g' | /usr/lib/phylip/bin/seqboot;
+	echo $inoptions | sed 's/$/\n/' | sed 's/, /\n/g; s/,/\n/g' | /usr/lib/phylip/bin/seqboot;
 	cp outfile $outfile
     ]]></command>
     <inputs>
         <param type="data" name="infasta" format="txt" label="Txt format: aligned fasta sequences or other data types" />
-	<param type="text" value= "Y;" name="inoptions" format="txt" label="Keyboard responses separated by semicolon and space (see example below)" />
+	<param type="text" value= "Y, 123" name="inoptions" format="txt" label="Keyboard responses separated by comma and space (see example below)" />
     </inputs>
     <outputs>
         <data name="outfile" format="txt" label="${tool.name} on ${on_string}: Outfile" />
@@ -25,7 +25,7 @@
 
 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.