# HG changeset patch # User peterjc # Date 1364397665 14400 # Node ID 09ff180d1615727913089901daadaabddbfb686c # Parent e52220a9ddada323daa22eb866198f62952bec02 Uploaded v0.1.3 with missing HMM file for RXLR tool included. diff -r e52220a9ddad -r 09ff180d1615 tools/protein_analysis/README --- a/tools/protein_analysis/README Fri Jan 25 06:08:31 2013 -0500 +++ b/tools/protein_analysis/README Wed Mar 27 11:21:05 2013 -0400 @@ -129,6 +129,7 @@ v0.1.1 - Fixed an error in the header of the tabular output from Promoter v0.1.2 - Use the new settings in the XML wrappers to catch errors - Use SGE style $NSLOTS for thread count (otherwise default to 4) +v0.1.3 - Added missing file whisson_et_al_rxlr_eer_cropped.hmm to Tool Shed Developers @@ -143,7 +144,7 @@ For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use the following command from the Galaxy root folder: -tar -czf ~/tmhmm_signalp_etc.tar.gz tools/protein_analysis/LICENSE tools/protein_analysis/README tools/protein_analysis/suite_config.xml tools/protein_analysis/seq_analysis_utils.py tools/protein_analysis/signalp3.xml tools/protein_analysis/signalp3.py tools/protein_analysis/tmhmm2.xml tools/protein_analysis/tmhmm2.py tools/protein_analysis/promoter2.xml tools/protein_analysis/promoter2.py tools/protein_analysis/wolf_psort.xml tools/protein_analysis/wolf_psort.py tools/protein_analysis/rxlr_motifs.xml tools/protein_analysis/rxlr_motifs.py test-data/four_human_proteins.* test-data/empty.fasta test-data/empty_tmhmm2.tabular test-data/empty_signalp3.tabular +tar -czf ~/tmhmm_signalp_etc.tar.gz tools/protein_analysis/LICENSE tools/protein_analysis/README tools/protein_analysis/suite_config.xml tools/protein_analysis/seq_analysis_utils.py tools/protein_analysis/signalp3.xml tools/protein_analysis/signalp3.py tools/protein_analysis/tmhmm2.xml tools/protein_analysis/tmhmm2.py tools/protein_analysis/promoter2.xml tools/protein_analysis/promoter2.py tools/protein_analysis/wolf_psort.xml tools/protein_analysis/wolf_psort.py tools/protein_analysis/rxlr_motifs.xml tools/protein_analysis/rxlr_motifs.py tools/protein_analysis/whisson_et_al_rxlr_eer_cropped.hmm test-data/four_human_proteins.* test-data/empty.fasta test-data/empty_tmhmm2.tabular test-data/empty_signalp3.tabular Check this worked: @@ -162,6 +163,7 @@ tools/protein_analysis/wolf_psort.py tools/protein_analysis/rxlr_motifs.xml tools/protein_analysis/rxrl_motifs.py +tools/protein_analysis/whisson_et_al_rxlr_eer_cropped.hmm test-data/four_human_proteins.fasta test-data/four_human_proteins.signalp3.tabular test-data/four_human_proteins.tmhmm2.tabular diff -r e52220a9ddad -r 09ff180d1615 tools/protein_analysis/whisson_et_al_rxlr_eer_cropped.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/protein_analysis/whisson_et_al_rxlr_eer_cropped.hmm Wed Mar 27 11:21:05 2013 -0400 @@ -0,0 +1,135 @@ +HMMER2.0 [2.3.2] +NAME cropped +LENG 39 +ALPH Amino +RF no +CS no +MAP yes +COM hmmbuild --amino consistency/cropped.hmm cropped.fas +NSEQ 39 +DATE Mon Dec 4 09:31:34 2006 +CKSUM 7487 +XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 +NULT -4 -8455 +NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 +HMM A C D E F G H I K L M N P Q R S T V W Y + m->m m->i m->d i->m i->i d->m d->d b->m m->e + -40 * -5177 + 1 -255 -3924 1452 -518 -4241 -1227 1132 -986 195 -3938 -3014 1281 153 -1634 -2181 93 1473 691 -4109 -192 5 + - 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