Mercurial > repos > lijing > bubio
changeset 10:9929063b59f9 draft
Phylip tools update
| author | lijing |
|---|---|
| date | Fri, 03 Nov 2017 11:33:55 -0400 |
| parents | 19d3ec566471 |
| children | b26a630d9448 |
| files | ._consense.xml ._dnapars.xml ._interleave-fastqgz-MITOBIM.py ._interleave.xml ._mitobim.xml ._seqboot.xml consense.xml dnapars.xml seqboot.xml |
| diffstat | 9 files changed, 11 insertions(+), 11 deletions(-) [+] |
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--- 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.
--- 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.
--- 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.