# HG changeset patch # User bgruening # Date 1377950632 14400 # Node ID 26ef7e66c39bbc20f1599e43cd5272a3c898c53a # Parent 3d17c3197be52cf2d3709b573be76b7c3a6a057c Uploaded diff -r 3d17c3197be5 -r 26ef7e66c39b cmsearch.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cmsearch.xml Sat Aug 31 08:03:52 2013 -0400 @@ -0,0 +1,211 @@ + + against a sequence database (cmsearch) + + infernal + + + cmsearch --tblout + --cpu 12 + -o /dev/null + --tformat $seqdb.ext #target format: fasta, embl, genbank, ddbj, stockholm, pfam, a2m, afa, clustal, and phylip + $bottomonly + $toponly + $cyk + $notrunc + $max + $nohmm + $mid + $bitscore_thresholds + --tblout $outfile + $g + #if $A: + $A $multiple_alignment_output + #end if + + + #if $inclusion_thresholds_opts.inclusion_thresholds_selector == "--incE": + --incE $inclusion_thresholds_opts.incE + #else: + --incT $inclusion_thresholds_opts.incT + #end if + + #if $reporting_thresholds_opts.reporting_thresholds_selector == "-E": + -E $inclusion_thresholds_opts.E + #else: + -T $inclusion_thresholds_opts.T + #end if + + #if $cm_opts.cm_opts_selector == "db": + $cm_opts.database.fields.path + #else: + $cm_opts.cmfile + #end if + + $seqdb + + + 2>&1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A is True + + + + + + + +**What it does** + +Options for model-specific score thresholding +--------------------------------------------- + + + - GA thresholds are generally considered to be the reliable curated thresholds defining family membership; for example, in Rfam, these thresholds define what gets included in Rfam Full alignments based on searches with Rfam Seed models. + - NC thresholds are generally considered to be the score of the highest-scoring known false positive. + - TC thresholds are generally considered to be the score of the lowest-scoring known true positive that is above all known false positives. + + +-g Turn on the glocal alignment algorithm, global with respect to the query model and local with +respect to the target database. By default, the local alignment algorithm is used which is +local with respect to both the target sequence and the model. In local mode, the alignment to +span two or more subsequences if necessary (e.g. if the structures of the query model and +target sequence are only partially shared), allowing certain large insertions and deletions +in the structure to be penalized differently than normal indels. Local mode performs better +on empirical benchmarks and is significantly more sensitive for remote homology detection. +Empirically, glocal searches return many fewer hits than local searches, so glocal may be +desired for some applications. With -g, all models must be calibrated, even those with zero +basepairs. + + + + + + diff -r 3d17c3197be5 -r 26ef7e66c39b infernal.tar.xz Binary file infernal.tar.xz has changed diff -r 3d17c3197be5 -r 26ef7e66c39b readme.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.rst Sat Aug 31 08:03:52 2013 -0400 @@ -0,0 +1,62 @@ +================================================ +Galaxy wrapper for Infernal prediction tools +================================================ + +Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases +for RNA structure and sequence similarities. It is an implementation of a special +case of profile stochastic context-free grammars called covariance models (CMs). +A CM is like a sequence profile, but it scores a combination of sequence consensus +and RNA secondary structure consensus, so in many cases, it is more capable of +identifying RNA homologs that conserve their secondary structure more than their +primary sequence. + +This wrapper is copyright 2013 by: + * Bjoern Gruening + + +This prepository contains wrapper for the Infernal_ command line tool. + +.. _Infernal: http://infernal.janelia.org/ + + +E. P. Nawrocki, D. L. Kolbe, and S. R. Eddy, Infernal 1.0: Inference of RNA alignments , Bioinformatics 25:1335-1337 (2009), . + + +============ +Installation +============ + +Please download install Infernal and the tool wrappers with the Galaxy Tool Shed: + + +======= +History +======= + +interproscan: + + - v1.1.0: Initial public release + + +=============================== +Wrapper Licence (MIT/BSD style) +=============================== + +Permission to use, copy, modify, and distribute this software and its +documentation with or without modifications and for any purpose and +without fee is hereby granted, provided that any copyright notices +appear in all copies and that both those copyright notices and this +permission notice appear in supporting documentation, and that the +names of the contributors or copyright holders not be used in +advertising or publicity pertaining to distribution of the software +without specific prior permission. + +THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL +WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE +CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT +OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS +OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE +OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE +OR PERFORMANCE OF THIS SOFTWARE. + diff -r 3d17c3197be5 -r 26ef7e66c39b tool-data/infernal.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/infernal.loc.sample Sat Aug 31 08:03:52 2013 -0400 @@ -0,0 +1,17 @@ +#This is a sample file distributed with Galaxy that is used to define a +#list of infernal covariance models, using three columns tab separated +#(longer whitespace are TAB characters): +# +#The entries are as follows: +# +# +# +#Your homer.loc file should include an entry per line for each "base name" +#you have stored. For example: +# +#rfam01 RFAM 4.2 08 Aug 2013 /data/0/galaxy_data/infernal/08_08_2013/rfam.cm +# +#...etc... +# + + diff -r 3d17c3197be5 -r 26ef7e66c39b tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Sat Aug 31 08:03:52 2013 -0400 @@ -0,0 +1,6 @@ + + + + + +