comparison cmbuild.xml @ 3:2c2c5e5e495b draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 9eeedfaf35c069d75014c5fb2e42046106bf813c-dirty
author bgruening
date Fri, 04 Mar 2016 07:24:53 -0500
parents fac157e22e1b
children c47a7c52ac4f
comparison
equal deleted inserted replaced
2:fac157e22e1b 3:2c2c5e5e495b
69 <param name="model_construction_opts_selector" type="select" label="These options control how consensus columns are defined in an alignment" help=""> 69 <param name="model_construction_opts_selector" type="select" label="These options control how consensus columns are defined in an alignment" help="">
70 <option value="--fast" selected="true">automatic (--fast)</option> 70 <option value="--fast" selected="true">automatic (--fast)</option>
71 <option value="--hand">user defined (--hand)</option> 71 <option value="--hand">user defined (--hand)</option>
72 </param> 72 </param>
73 <when value="--fast"> 73 <when value="--fast">
74 <param name="symfrac" type="float" value="0.5" size="5" 74 <param name="symfrac" type="float" value="0.5"
75 label="Define the residue fraction threshold necessary to define a consensus (--symfrac)" help=""/> 75 label="Define the residue fraction threshold necessary to define a consensus (--symfrac)" help=""/>
76 </when> 76 </when>
77 <when value="--hand"/> 77 <when value="--hand"/>
78 </conditional> 78 </conditional>
79 79
91 <when value="--wpb"/> 91 <when value="--wpb"/>
92 <when value="--wgsc"/> 92 <when value="--wgsc"/>
93 <when value="--wnone"/> 93 <when value="--wnone"/>
94 <when value="--wgiven"/> 94 <when value="--wgiven"/>
95 <when value="--wblosum"> 95 <when value="--wblosum">
96 <param name="wid" type="float" value="0.5" size="5" 96 <param name="wid" type="float" value="0.5"
97 label="Percent identity for clustering the alignment (--wid)" help=""/> 97 label="Percent identity for clustering the alignment (--wid)" help=""/>
98 </when> 98 </when>
99 </conditional> 99 </conditional>
100 100
101 101
104 <option value="--eent" selected="true">entropy weighting strategy (--eent)</option> 104 <option value="--eent" selected="true">entropy weighting strategy (--eent)</option>
105 <option value="--enone">Turn off the entropy weighting strategy (--enone)</option> 105 <option value="--enone">Turn off the entropy weighting strategy (--enone)</option>
106 </param> 106 </param>
107 <when value="--enone"/> 107 <when value="--enone"/>
108 <when value="--eent"> 108 <when value="--eent">
109 <param name="ere" type="float" value="0.59" size="5" 109 <param name="ere" type="float" value="0.59"
110 label="Set the target mean match state relative entropy (--ere)" help=""/> 110 label="Set the target mean match state relative entropy (--ere)" help=""/>
111 111
112 <param name="eminseq" type="integer" value="" size="5" 112 <param name="eminseq" type="integer" value=""
113 label="Define the minimum allowed effective sequence number (--eminseq)" help=""/> 113 label="Define the minimum allowed effective sequence number (--eminseq)" help=""/>
114 114
115 <param name="ehmmre" type="float" value="" size="5" 115 <param name="ehmmre" type="float" value=""
116 label="Set the target HMM mean match state relative entropy (--ehmmre)" help=""/> 116 label="Set the target HMM mean match state relative entropy (--ehmmre)" help=""/>
117 117
118 <param name="eset" type="integer" value="" size="5" 118 <param name="eset" type="integer" value=""
119 label="Set the effective sequence number for entropy weighting (--eset)" help=""/> 119 label="Set the effective sequence number for entropy weighting (--eset)" help=""/>
120 </when> 120 </when>
121 </conditional> 121 </conditional>
122 122
123 123
184 <![CDATA[ 184 <![CDATA[
185 185
186 186
187 **What it does** 187 **What it does**
188 188
189 For each multiple sequence alignment build a covariance model. 189 cmbuild belongs to the INFERNAL software package that allows you to make consensus RNA secondary structure profiles, and use them to search nucleic acid sequence databases for homologous RNAs, or to create new structure-based multiple sequence alignments.
190 The alignment file must be in Stockholm or SELEX format, and must contain consensus secondary structure annotation. 190
191 cm build builds a covariance model of an RNA multiple alignment. cmbuild uses the consensus structure to determine the architecture of the CM.
192
193
194 **Input**
195
196 Input file is a multiple sequence alignment file in Stockholm or SELEX format, and must contain consensus secondary structure annotation.
191 cmbuild uses the consensus structure to determine the architecture of the CM. 197 cmbuild uses the consensus structure to determine the architecture of the CM.
192 198
193 In addition to writing CM(s) to CMFILE_OUT, cmbuild also outputs a single line for each model created to stdout. Each 199 Example: simple example of a multiple RNA sequence alignment with secondary structure annotation
194 line has the following fields: ”aln”: the index of the alignment used to build the CM; ”idx”: the index of the CM in the 200
195 CMFILE_OUT; ”name”: the name of the CM; ”nseq”: the number of sequences in the alignment used to build the CM; 201 # STOCKHOLM 1.0
196 ”eff nseq”: the effective number of sequences used to build the model; ”alen”: the length of the alignment used to build 202 tRNA1 GCGGAUUUAGCUCAGUUGGG.AGAGCGCCAGACUGAAGAUCUGGAGGUCC
197 the CM; ”clen”: the number of columns from the alignment defined as consensus (match) columns; ”bps”: the number 203 tRNA2 UCCGAUAUAGUGUAAC.GGCUAUCACAUCACGCUUUCACCGUGGAGA.CC
198 of basepairs in the CM; ”bifs”: the number of bifurcations in the CM; ”rel entropy: CM”: the total relative entropy of the 204 tRNA3 UCCGUGAUAGUUUAAU.GGUCAGAAUGGGCGCUUGUCGCGUGCCAGA.UC
199 model divided by the number of consensus columns; ”rel entropy: HMM”: the total relative entropy of the model ignoring 205 tRNA4 GCUCGUAUGGCGCAGU.GGU.AGCGCAGCAGAUUGCAAAUCUGUUGGUCC
200 secondary structure divided by the number of consensus columns. ”description”: description of the model/alignment. 206 tRNA5 GGGCACAUGGCGCAGUUGGU.AGCGCGCUUCCCUUGCAAGGAAGAGGUCA
201 207 #=GC SS_cons <<<<<<<..<<<<.........>>>>.<<<<<.......>>>>>.....<
202 208
203 Options controlling model construction 209
204 -------------------------------------- 210 **Output**
211
212 The output of cmbuild contains information about the size of your input alignment (in aligned columns
213 and # of sequences), and about the size of the resulting model.
214
215 In addition to writing CM(s) to the output file, cmbuild also outputs a single line for each model created to stdout.
216 Each line has the following fields:
217 - aln: the index of the alignment used to build the CM
218 - idx: the index of the CM in the output file
219 - name: the name of the CM
220 - nseq: the number of sequences in the alignment used to build the CM
221 - eff nseq: the effective number of sequences used to build the model
222 - alen: the length of the alignment used to build the CM
223 - clen: the number of columns from the alignment defined as consensus (match) columns
224 - bps: the number of basepairs in the CM
225 - bifs: the number of bifurcations in the CM
226 - rel entropy: CM: the total relative entropy of the model divided by the number of consensus columns
227 - rel entropy: HMM: the total relative entropy of the model ignoring secondary structure divided by the number of consensus columns
228 - description: description of the model/alignment.
229
230
231 **Options controlling model construction**
232
205 233
206 These options control how consensus columns are defined in an alignment. 234 These options control how consensus columns are defined in an alignment.
207 235
208 * --fast Define consensus columns automatically as those that have a fraction >= symfrac of residues as opposed to gaps. (See below for the --symfrac option.) This is the default. 236 - *--fast*: Define consensus columns automatically as those that have a fraction >= symfrac of residues as opposed to gaps. (See below for the --symfrac option.) This is the default.
209 * --hand Use reference coordinate annotation (#=GC RF line, in Stockholm) to determine which columns are consensus, and which are inserts. Any non-gap character indicates a consensus column. (For example, mark consensus columns with ”x”, and insert columns with ”.”.) 237 - *--hand*: Use reference coordinate annotation (#=GC RF line, in Stockholm) to determine which columns are consensus, and which are inserts. Any non-gap character indicates a consensus column. (For example, mark consensus columns with ”x”, and insert columns with ”.”.)
210 * --symfrac Define the residue fraction threshold necessary to define a consensus column when not using --hand. The default is 0.5. The symbol fraction in each column is calculated after taking relative sequence weighting into account. Setting this to 0.0 means that every alignment column will be assigned as consensus, which may be useful in some cases. Setting it to 1.0 means that only columns that include 0 gaps will be assigned as consensus. 238 - *--symfrac*: Define the residue fraction threshold necessary to define a consensus column when not using --hand. The default is 0.5. The symbol fraction in each column is calculated after taking relative sequence weighting into account. Setting this to 0.0 means that every alignment column will be assigned as consensus, which may be useful in some cases. Setting it to 1.0 means that only columns that include 0 gaps will be assigned as consensus.
211 * --noss Ignore the secondary structure annotation, if any, in MSA-Infile and build a CM with zero basepairs. This model will be similar to a profile HMM and the cmsearch and cmscan programs will use HMM algorithms which are faster than CM ones for this model. Additionally, a zero basepair model need not be calibrated with cmcalibrate prior to running cmsearch with it. The --noss option must be used if there is no secondary structure annotation in MSA-Infile. 239 - *--noss*: Ignore the secondary structure annotation, if any, in MSA-Infile and build a CM with zero basepairs. This model will be similar to a profile HMM and the cmsearch and cmscan programs will use HMM algorithms which are faster than CM ones for this model. Additionally, a zero basepair model need not be calibrated with cmcalibrate prior to running cmsearch with it. The --noss option must be used if there is no secondary structure annotation in MSA-Infile.
212 240
213 241
214 Options controlling relative weights 242 **Options controlling relative weights**
215 ------------------------------------ 243
216 244
217 cmbuild uses an ad hoc sequence weighting algorithm to downweight closely related sequences and upweight distantly 245 cmbuild uses an ad hoc sequence weighting algorithm to downweight closely related sequences and upweight distantly related ones. This has the effect of making models less biased by uneven phylogenetic representation. For example, two identical sequences would typically each receive half the weight that one sequence would. These options control which algorithm gets used.
218 related ones. This has the effect of making models less biased by uneven phylogenetic representation. For example, 246
219 two identical sequences would typically each receive half the weight that one sequence would. These options control 247 - *--wgb*: Use the Henikoff position-based sequence weighting scheme ([Henikoff and Henikoff](http://zhanglab.ccmb.med.umich.edu/literature/henikoff_weight_1994.pdf), J. Mol. Biol. 243:574, 1994). This is the default.
220 which algorithm gets used. 248 - *--wgsc*: Use the Gerstein/Sonnhammer/Chothia weighting algorithm ([Gerstein et al.](http://ac.els-cdn.com/0022283694900124/1-s2.0-0022283694900124-main.pdf?_tid=6ed29974-3044-11e5-8949-00000aacb35f&acdnat=1437550798_aaa62caa2c812bb81013f967e7b119ee), J. Mol. Biol. 236:1067, 1994).
221 249 - *--wnone*: Turn sequence weighting off; e.g. explicitly set all sequence weights to 1.0.
222 * --wpb Use the Henikoff position-based sequence weighting scheme [Henikoff and Henikoff, J. Mol. Biol. 243:574, 1994]. This is the default. 250 - *--wgiven*: Use sequence weights as given in annotation in the input alignment file. If no weights were given, assume they are all 1.0. The default is to determine new sequence weights by the Gerstein/Sonnhammer/Chothia algorithm, ignoring any annotated weights.
223 * --wgsc Use the Gerstein/Sonnhammer/Chothia weighting algorithm [Gerstein et al, J. Mol. Biol. 235:1067, 1994]. 251 - *--wblosum*: Use the BLOSUM filtering algorithm to weight the sequences, instead of the default GSC weighting. Cluster the sequences at a given percentage identity (see --wid); assign each cluster a total weight of 1.0, distributed equally amongst the members of that cluster.
224 * --wnone Turn sequence weighting off; e.g. explicitly set all sequence weights to 1.0. 252
225 * --wgiven Use sequence weights as given in annotation in the input alignment file. If no weights were given, assume they are all 1.0. The default is to determine new sequence weights by the Gerstein/Sonnhammer/Chothia algorithm, ignoring any annotated weights. 253
226 * --wblosum Use the BLOSUM filtering algorithm to weight the sequences, instead of the default GSC weighting. Cluster the sequences at a given percentage identity (see --wid); assign each cluster a total weight of 1.0, distributed equally amongst the members of that cluster. 254 **Options controlling effective sequence number**
227 * --wid Controls the behavior of the --wblosum weighting option by setting the percent identity for clustering the alignment. 255
228 256
229 257 After relative weights are determined, they are normalized to sum to a total effective sequence number, eff nseq. This number may be the actual number of sequences in the alignment, but it is almost always smaller than that. The default entropy weighting method (--eent) reduces the effective sequence number to reduce the information content (relative entropy, or average expected score on true homologs) per consensus position. The target relative entropy is controlled by a two-parameter function, where the two parameters are settable with --ere and --esigma.
230 Options controlling effective sequence number 258
231 --------------------------------------------- 259 - *--eent*: Use the entropy weighting strategy to determine the effective sequence number that gives a target mean match state relative entropy. This option is the default, and can be turned off with --enone. The default target mean match state relative entropy is 0.59 bits for models with at least 1 basepair and 0.38 bits for models with zero basepairs, but changed with --ere. The default of 0.59 or 0.38 bits is automatically changed if the total relative entropy of the model (summed match state relative entropy) is less than a cutoff, which is is 6.0 bits by default, but can be changed with the expert, undocumented --eX option. If you really want to play with that option, consult the source code.
232 260 - *--enone*: Turn off the entropy weighting strategy. The effective sequence number is just the number of sequences in the alignment.
233 After relative weights are determined, they are normalized to sum to a total effective sequence number, eff nseq. This 261 - *--ere*: Set the target mean match state relative entropy. By default the target relative entropy per match position is 0.59 bits for models with at least 1 basepair and 0.38 for models with zero basepairs.
234 number may be the actual number of sequences in the alignment, but it is almost always smaller than that. The default 262 - *--eminseq*: Define the minimum allowed effective sequence number.
235 entropy weighting method (--eent) reduces the effective sequence number to reduce the information content (relative 263 - *--ehmmre*: Set the target HMM mean match state relative entropy. Entropy for basepairing match states is calculated using marginalized basepair emission probabilities.
236 entropy, or average expected score on true homologs) per consensus position. The target relative entropy is controlled 264 - *--eset*: Set the effective sequence number for entropy weighting.
237 by a two-parameter function, where the two parameters are settable with --ere and --esigma. 265
238 266
239 * --eent Use the entropy weighting strategy to determine the effective sequence number that gives a target mean match state relative entropy. This option is the default, and can be turned off with --enone. The default target mean match state relative entropy is 0.59 bits for models with at least 1 basepair and 0.38 bits for models with zero basepairs, but changed with --ere. The default of 0.59 or 0.38 bits is automatically changed if the total relative entropy of the model (summed match state relative entropy) is less than a cutoff, which is is 6.0 bits by default, but can be changed with the expert, undocumented --eX option. If you really want to play with that option, consult the source code. 267
240 * --enone Turn off the entropy weighting strategy. The effective sequence number is just the number of sequences in the alignment. 268 **Options for refining the input alignment**
241 * --ere Set the target mean match state relative entropy. By default the target relative entropy per match position is 0.59 bits for models with at least 1 basepair and 0.38 for models with zero basepairs. 269
242 * --eminseq Define the minimum allowed effective sequence number. 270 - *--refine*: Attempt to refine the alignment before building the CM using expectation-maximization (EM). A CM is first built from the initial alignment as usual. Then, the sequences in the alignment are realigned optimally (with the HMM banded CYK algorithm, optimal means optimal given the bands) to the CM, and a new CM is built from the resulting alignment. The sequences are then realigned to the new CM, and a new CM is built from that alignment. This is continued until convergence, specifically when the alignments for two successive iterations are not significantly different (the summed bit scores of all the sequences in the alignment changes less than 1% between two successive iterations).
243 * --ehmmre Set the target HMM mean match state relative entropy. Entropy for basepairing match states is calculated using marginalized basepair emission probabilities. 271 - *Turn on the local alignment algorithm*: allows 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. The default is to globally align the query model to the target sequences.
244 * --eset Set the effective sequence number for entropy weighting. 272 - *--gibbs sampling*: Modifies the behavior of --refine so Gibbs sampling is used instead of EM. The difference is that during the alignment stage the alignment is not necessarily optimal, instead an alignment (parsetree) for each sequences is sampled from the posterior distribution of alignments as determined by the Inside algorithm. Due to this sampling step --gibbs is non- deterministic, so different runs with the same alignment may yield different results. This is not true when --refine is used without the --gibbs option, in which case the final alignment and CM will always be the same. When --gibbs is enabled, the --seed "number" option can be used to seed the random number generator predictably, making the results reproducible. The goal of the --gibbs option is to help expert RNA alignment curators refine structural alignments by allowing them to observe alternative high scoring alignments.
245 273 - *--Random seed*: Seed the random number generator with an integer >= 0. This option can only be used in combination with --gibbs. If the given number is nonzero, stochastic sampling of alignments will be reproducible; the same command will give the same results. If the given number is 0, the random number generator is seeded arbitrarily, and stochastic samplings may vary from run to run of the same command. The default seed is 0.
246 274 - *--Turn off the truncated alignment algorithm*: With --refine, turn off the truncated alignment algorithm. There is more information on this in the cmalign manual page.
247 275 - *--cyk algorithm*: With --refine, align with the CYK algorithm. By default the optimal accuracy algorithm is used. There is more information on this in the cmalign manual page.
248 Options for refining the input alignment 276
249 ---------------------------------------- 277
250
251 * --refine Attempt to refine the alignment before building the CM using expectation-maximization (EM). A CM is first built from the initial alignment as usual. Then, the sequences in the alignment are realigned optimally (with the HMM banded CYK algorithm, optimal means optimal given the bands) to the CM, and a new CM is built from the resulting alignment. The sequences are then realigned to the new CM, and a new CM is built from that alignment. This is continued until convergence, specifically when the alignments for two successive iterations are not significantly different (the summed bit scores of all the sequences in the alignment changes less than 1% between two successive iterations).
252 * -l Turn on the local alignment algorithm, which allows 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. The default is to globally align the query model to the target sequences.
253 * --gibbs Modifies the behavior of --refine so Gibbs sampling is used instead of EM. The difference is that during the alignment stage the alignment is not necessarily optimal, instead an alignment (parsetree) for each sequences is sampled from the posterior distribution of alignments as determined by the Inside algorithm. Due to this sampling step --gibbs is non- deterministic, so different runs with the same alignment may yield different results. This is not true when --refine is used without the --gibbs option, in which case the final alignment and CM will always be the same. When --gibbs is enabled, the --seed "number" option can be used to seed the random number generator predictably, making the results reproducible. The goal of the --gibbs option is to help expert RNA alignment curators refine structural alignments by allowing them to observe alternative high scoring alignments.
254 * --seed Seed the random number generator with an integer >= 0. This option can only be used in combination with --gibbs. If the given number is nonzero, stochastic sampling of alignments will be reproducible; the same command will give the same results. If the given number is 0, the random number generator is seeded arbitrarily, and stochastic samplings may vary from run to run of the same command. The default seed is 0.
255 * --cyk With --refine, align with the CYK algorithm. By default the optimal accuracy algorithm is used. There is more information on this in the cmalign manual page.
256 * --notrunc With --refine, turn off the truncated alignment algorithm. There is more information on this in the cmalign manual page.
257
258 278
259 For further questions please refere to the Infernal Userguide_. 279 For further questions please refere to the Infernal Userguide_.
260 280
261 .. _Userguide: http://selab.janelia.org/software/infernal/Userguide.pdf 281 .. _Userguide: http://selab.janelia.org/software/infernal/Userguide.pdf
262 282
263
264 How do I cite Infernal?
265 -----------------------
266
267 The recommended citation for using Infernal 1.1 is E. P. Nawrocki and S. R. Eddy, Infernal 1.1: 100-fold faster RNA homology searches , Bioinformatics 29:2933-2935 (2013).
268
269 **Galaxy Wrapper Author**::
270
271 * Bjoern Gruening, University of Freiburg
272 283
273 ]]> 284 ]]>
274 </help> 285 </help>
286
287 <citations>
288 <citation type="doi">10.1093/bioinformatics/btt509</citation>
289 <citation type="bibtex">
290 @ARTICLE{bgruening_galaxytools,
291 Author = {Björn Grüning, Cameron Smith, Torsten Houwaart, Nicola Soranzo, Eric Rasche},
292 keywords = {bioinformatics, ngs, galaxy, cheminformatics, rna},
293 title = {{Galaxy Tools - A collection of bioinformatics and cheminformatics tools for the Galaxy environment}},
294 url = {https://github.com/bgruening/galaxytools}
295 }
296 </citation>
297 </citations>
298
275 </tool> 299 </tool>