Mercurial > repos > yating-l > gbtofasta
changeset 2:cabe1df9d31a draft
planemo upload commit 56d60a9f66cc04ee92cbc568dd40b4353dab8b62-dirty
| author | yating-l |
|---|---|
| date | Fri, 03 Feb 2017 13:21:33 -0500 |
| parents | da5fba0ed4fc |
| children | 894d96efad6d |
| files | README.rst gbToFasta.xml |
| diffstat | 2 files changed, 34 insertions(+), 1 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Fri Feb 03 13:21:33 2017 -0500 @@ -0,0 +1,33 @@ +gbToFasta +========================================================== +Galaxy wrapper for UCSC tools gbToFasta and raToTab. Convert GenBank records to fasta and create table with coding regions information for each mRNA record. + +gbToFasta +--------- + +gbToFaRa - Convert GenBank flat format file to an fa file containing +the sequence data, an ra file containing other relevant info and +a ta file containing summary statistics. + +usage: + gbToFaRa filterFile faFile raFile taFile genBankFile(s) + where filterFile is definition of which records and fields + use /dev/null if you want no filtering. + + $ gbToFaRa /dev/null gbfile.fa gbfile.ra gbfile.ta gbfile + +raToTab +-------- +raToTab - Create table with coding regions information for each mRNA record + +usage: + raToTab -cols=acc,cds gbfile.ra gbfile.cds + +Source code: +============ + +http://hgdownload.cse.ucsc.edu/admin/exe/ + +Licence +------- +Please note that commercial download and installation of the Blat and In-Silico PCR software may be licensed through Kent Informatics (http://www.kentinformatics.com).
--- a/gbToFasta.xml Fri Feb 03 11:30:42 2017 -0500 +++ b/gbToFasta.xml Fri Feb 03 13:21:33 2017 -0500 @@ -28,7 +28,7 @@ </inputs> <outputs> <data format="fasta" name="outputfa" label="${tool.name} on ${on_string}:fasta"></data> - <data format="fasta" name="outputcds" label="${tool.name} on ${on_string}:cds"> + <data format="tabular" name="outputcds" label="${tool.name} on ${on_string}:cds"> <filter>cds == "yes"</filter> </data> </outputs>