Mercurial > repos > peterjc > align_back_trans
changeset 1:ec202446408a draft
Uploaded v0.0.4, fixed an error message.
| author | peterjc |
|---|---|
| date | Wed, 04 Jun 2014 08:42:23 -0400 |
| parents | 0c24e4e2177d |
| children | 9fbf29a8c12b |
| files | tools/align_back_trans/README.rst tools/align_back_trans/align_back_trans.py tools/align_back_trans/align_back_trans.xml |
| diffstat | 3 files changed, 11 insertions(+), 10 deletions(-) [+] |
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--- a/tools/align_back_trans/README.rst Thu Mar 06 08:58:13 2014 -0500 +++ b/tools/align_back_trans/README.rst Wed Jun 04 08:42:23 2014 -0400 @@ -14,6 +14,10 @@ * http://toolshed.g2.bx.psu.edu/view/peterjc/align_back_trans +The underlying Python script can also be used outside of Galaxy, for +details run:: + + $ python align_back_trans.py Automated Installation ====================== @@ -56,6 +60,9 @@ ------- ---------------------------------------------------------------------- v0.0.1 - Initial version, based on a previously written Python script v0.0.2 - Optionally check the translation is consistent +v0.0.3 - First official release +v0.0.4 - Simplified XML to apply input format to output data. + - Fixed error message when sequence length not a multiple of three. ======= ======================================================================
--- a/tools/align_back_trans/align_back_trans.py Thu Mar 06 08:58:13 2014 -0500 +++ b/tools/align_back_trans/align_back_trans.py Wed Jun 04 08:42:23 2014 -0400 @@ -28,7 +28,7 @@ from Bio.Data.CodonTable import ambiguous_generic_by_id if "-v" in sys.argv or "--version" in sys.argv: - print "v0.0.3" + print "v0.0.4" sys.exit(0) def stop_err(msg, error_level=1): @@ -40,7 +40,7 @@ """Returns nucleotide sequence if works (can remove trailing stop)""" if len(nuc) % 3: stop_err("Nucleotide sequence for %s is length %i (not a multiple of three)" - % (identifier, nuc)) + % (identifier, len(nuc))) p = str(prot).upper().replace("*", "X") t = str(nuc.translate(table)).upper().replace("*", "X")
--- a/tools/align_back_trans/align_back_trans.xml Thu Mar 06 08:58:13 2014 -0500 +++ b/tools/align_back_trans/align_back_trans.xml Wed Jun 04 08:42:23 2014 -0400 @@ -1,4 +1,4 @@ -<tool id="align_back_trans" name="Thread nucleotides onto a protein alignment (back-translation)" version="0.0.3"> +<tool id="align_back_trans" name="Thread nucleotides onto a protein alignment (back-translation)" version="0.0.4"> <description>Gives a codon aware alignment</description> <requirements> <requirement type="package" version="1.63">biopython</requirement> @@ -38,13 +38,7 @@ <param name="nuc_file" type="data" format="fasta" label="Unaligned nucleotide sequences" help="FASTA format, using same identifiers as your protein alignment" /> </inputs> <outputs> - <data name="out_nuc_align" format="fasta" label="${prot_align.name} (back-translated)"> - <!-- TODO - Replace this with format="input:prot_align" if/when that works --> - <change_format> - <when input_dataset="prot_align" attribute="extension" value="clustal" format="clustal" /> - <when input_dataset="prot_align" attribute="extension" value="phylip" format="phylip" /> - </change_format> - </data> + <data name="out_nuc_align" format="input" metadata_source="prot_align" label="${prot_align.name} (back-translated)"/> </outputs> <tests> <test>