Mercurial > repos > lijing > bubio
changeset 0:5107c9510fe0 draft
dnapars
| author | lijing |
|---|---|
| date | Thu, 02 Nov 2017 12:29:10 -0400 |
| parents | |
| children | d54f08ba3264 |
| files | dnapars.xml |
| diffstat | 1 files changed, 37 insertions(+), 0 deletions(-) [+] |
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--- /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>