annotate consense.xml @ 13:9aa1ef328b2e draft default tip

add path to tool folder

<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 $intree intree;
	echo $inoptions | sed 's/$/\n/' | sed 's/, /\n/g; s/,/\n/g' | /usr/lib/phylip/bin/consense;
	cp outfile $outfile;
	cp outtree $outtree
    ]]></command>
    <inputs>
        <param type="data" name="intree" format="txt" label="A series of trees in the Newick standard form" />
	<param type="text" value= "Y" name="inoptions" format="txt" label="Keyboard responses separated by comma and space (see example below)" />
    </inputs>
    <outputs>
        <data name="outfile" format="txt" label="${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**

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>