Mercurial > repos > lijing > bubio
changeset 1:d54f08ba3264 draft
seqboot
| author | lijing |
|---|---|
| date | Thu, 02 Nov 2017 12:32:01 -0400 |
| parents | 5107c9510fe0 |
| children | 706c69f2cec3 |
| files | dnapars.xml seqboot.xml |
| diffstat | 2 files changed, 35 insertions(+), 37 deletions(-) [+] |
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--- a/dnapars.xml Thu Nov 02 12:29:10 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,37 +0,0 @@ -<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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/seqboot.xml Thu Nov 02 12:32:01 2017 -0400 @@ -0,0 +1,35 @@ +<tool id="seqboot" name="Phylip Seqboot" version="0.1.0"> + <description>Bootstrap, Jackknife, or Permutation Resampling of Molecular Sequence, Restriction Site, Gene Frequency or Character Data</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/seqboot; + cp outfile $outfile + ]]></command> + <inputs> + <param type="data" name="infasta" format="txt" label="Txt format: aligned fasta sequences or other data types" /> + <param type="text" value= "Y;" name="inoptions" format="txt" label="Keyboard responses separated by semicolon and space (see example below)" /> + </inputs> + <outputs> + <data name="outfile" format="txt" label="${tool.name} on ${on_string}: Outfile" /> + </outputs> + + <help><![CDATA[ +**What it does** + +Reference: http://evolution.genetics.washington.edu/phylip/doc/seqboot.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>