Daniel Blankenberg 7d4b23e1d9 Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

..

emboss_antigenic.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_backtranseq.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_banana.pl

2007-12-11 16:19:53 +00:00

emboss_banana.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_biosed.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_btwisted.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_cai_custom.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_cai.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_chaos.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_charge.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_checktrans.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_chips.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_cirdna.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_codcmp.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_coderet.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_compseq.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_cpgplot_wrapper.pl

Fix for EMBOSS 5 cpgplot tool.

2008-04-25 19:05:56 +00:00

emboss_cpgplot.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_cpgreport.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_cusp.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_cutseq.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_dan.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_degapseq.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_descseq.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_diffseq.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_digest.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_dotmatcher.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_dotpath.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_dottup.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_dreg.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_einverted.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_epestfind.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_equicktandem.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_est2genome.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_etandem.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_extractfeat.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_extractseq.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_format_corrector.py

Fix most of the db flushes to be compatibel with sqlalchemy 05. Add the _monkeypatch_query_method() back into assignmapper due to a single object.get() method in the MetadataCollection class since Metadata has no current hook into mapping.context ( the sqlalchemy session ). There a 4 flushes in metadata,py and 20 flushes in model.__init__.py that still use the _monkeypatch_session_method in assignmapper due to the same issue, but all other flushes are fixed.

2009-11-11 15:59:41 -05:00

emboss_freak.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_fuzznuc.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_fuzzpro.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_fuzztran.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_garnier.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_geecee.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_getorf.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_helixturnhelix.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_hmoment.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_iep.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_infoseq_wrapper.pl

Adding EMBOSS tools version 5.0 for helixturnhelix, hmoment, iep infoseq lindna and associated test files

2007-12-17 14:10:03 +00:00

emboss_infoseq.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_isochore.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_lindna.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_marscan.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_maskfeat.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_maskseq.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_matcher.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_megamerger.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_merger.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_msbar.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_multiple_outputfile_wrapper.pl

Committing EMBOSS v5.0 tools marscan maskfeat maskseq matcher megamerger merger and associated test files.

2007-12-17 14:16:37 +00:00

emboss_needle.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_newcpgreport.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_newcpgseek.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_newseq.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_noreturn.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_notseq.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_nthseq.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_octanol.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_oddcomp.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_palindrome.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_pasteseq.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_patmatdb.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_pepcoil.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_pepinfo.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_pepnet.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_pepstats.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_pepwheel.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_pepwindow.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_pepwindowall.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_plotcon.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_plotorf.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_polydot.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_preg.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_prettyplot.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_prettyseq.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_primersearch.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_revseq.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_seqmatchall.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_seqret.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_showfeat.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_shuffleseq.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_sigcleave.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_single_outputfile_wrapper.pl

Adding EMBOSS v5.0 tools seqret showfeat shuffleseq sigcleave sixpack skipseq supermatcher syco

2007-12-17 14:35:58 +00:00

emboss_sirna.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_sixpack.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_skipseq.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_splitter.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_supermatcher.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_syco.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_tcode.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_textsearch.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_tmap.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_tranalign.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_transeq.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_trimest.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_trimseq.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_twofeat.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_union.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_vectorstrip.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_water.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_wobble.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_wordcount.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00

emboss_wordmatch.xml

Update EMBOSS tools to use quotes to escape user specified parameters during commandline substitution. Resolves #610.

2011-12-08 10:44:42 -05:00