Mercurial > repos > lijing > bubio

changeset 3:85a6e3a77554 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
consense
author lijing
date Thu, 02 Nov 2017 12:34:10 -0400
parents 706c69f2cec3
children 7f94bf630447
files consense.xml
diffstat 1 files changed, 36 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/consense.xml	Thu Nov 02 12:34:10 2017 -0400
@@ -0,0 +1,36 @@
+<tool id="consense" name="Phylip Consense" version="0.1.0">
+    <description>Consense reads a file of computer-readable trees and prints out (and may also write out onto a file) a consensus tree</description>
+    <stdio>
+        <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 outfile $outfile;
+	cp outtree $outtree
+    ]]></command>
+    <inputs>
+        <param type="data" name="intree" format="txt" label="A series of trees in the Newick standard form" />
+	<param type="text" value= "Y;" name="inoptions" format="txt" label="Keyboard responses separated by semicolon and space (see example below)" />
+    </inputs>
+    <outputs>
+        <data name="outfile" format="txt" label="${tool.name} on ${on_string}: Outfile" />
+	<data name="outtree" format="txt" label="${tool.name} on ${on_string}: Tree" />
+    </outputs>
+
+    <help><![CDATA[
+**What it does**        
+
+Reference: http://evolution.genetics.washington.edu/phylip/doc/consense.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>