/var/lib/mobyle/programs/hmmemit.xml is in mobyle-programs 5.1.2-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 | <?xml version='1.0' encoding='UTF-8'?>
<!-- XML Authors: Corinne Maufrais, Nicolas Joly and Bertrand Neron, -->
<!-- 'Biological Software and Databases' Group, Institut Pasteur, Paris. -->
<!-- Distributed under LGPLv2 License. Please refer to the COPYING.LIB document. -->
<program>
<head>
<name>hmmemit</name>
<xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="Entities/hmmer_package.xml"/>
<doc>
<title>HMMEMIT</title>
<description>
<text lang="en">Generate sequences from a profile HMM</text>
</description>
<comment>
<text lang="en">hmmemit reads an HMM file from hmmfile and generates a number of sequences from it; or, if the -c option is selected, generate a single majority-rule consensus. This can be useful for various applications in which one needs a simulation of sequences consistent with a sequence family consensus.By default, hmmemit generates 10 sequences and outputs them in FASTA (unaligned) format.</text>
</comment>
</doc>
<category>hmm:building</category>
</head>
<parameters>
<parameter iscommand="1" ishidden="1">
<name>hmmcmd</name>
<prompt lang="en">HMM emit command</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">"hmmemit"</code>
<code proglang="python">"hmmemit"</code>
</format>
<argpos>0</argpos>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>hmmfile</name>
<prompt lang="en">HMM file</prompt>
<type>
<datatype>
<class>HmmProfile</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<format>
<code proglang="perl">" $hmmfile"</code>
<code proglang="python">" " + str(hmmfile)</code>
</format>
<argpos>2</argpos>
</parameter>
<parameter>
<name>outfile_name</name>
<prompt lang="en">Name of the synthetic sequences file (-o)</prompt>
<type>
<datatype>
<class>Filename</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -o $value" : ""</code>
<code proglang="python">( "" , " -o " + str(value) )[ value is not None ]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">Save the synthetic sequences to file rather than writing them to stdout.</text>
</comment>
</parameter>
<parameter isout="1">
<name>output_file</name>
<prompt lang="en">Output file</prompt>
<type>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>FASTA</dataFormat>
</type>
<precond>
<code proglang="perl">defined $outfile_name</code>
<code proglang="python">outfile_name is not None</code>
</precond>
<filenames>
<code proglang="perl">$outfile_name</code>
<code proglang="python">str(outfile_name)</code>
</filenames>
</parameter>
<parameter isstdout="1">
<name>out_file</name>
<prompt lang="en">Output file</prompt>
<type>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>FASTA</dataFormat>
</type>
<precond>
<code proglang="perl">not defined $outfile_name</code>
<code proglang="python">outfile_name is None</code>
</precond>
<filenames>
<code proglang="perl">"hmmemit.out"</code>
<code proglang="python">"hmmemit.out"</code>
</filenames>
</parameter>
<!--<parameter isout="1">
<name>output_align_name</name>
<prompt lang="en">Output align file</prompt>
<type>
<datatype>
<class>Alignment</class>
</datatype>
</type>
<precond>
<code proglang="perl">$outfile_name and defined $output_format</code>
<code proglang="python">outfile_name and output_format is not None</code>
</precond>
<filenames>
<code proglang="perl">$outfile_name</code>
<code proglang="python">str(outfile_name)</code>
</filenames>
</parameter>
-->
<parameter>
<name>consensus</name>
<prompt lang="en">Consensus sequence (-c)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<precond>
<code proglang="perl">$number == 1 and not sample</code>
<code proglang="python">number == 1 and not sample</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -c" : ""</code>
<code proglang="python">( "" , " -c" )[ value ]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">Emit a consensus sequence, instead of sampling a sequence from the profile
HMM's probability distribution. The consensus sequence is formed by selecting
the maximum probability residue at each match state.</text>
</comment>
</parameter>
<parameter>
<name>number</name>
<prompt lang="en">Number of sequences to sample (-N)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -N $value " : ""</code>
<code proglang="python">( "" , " -N " + str(value) )[ value is not None and value != vdef]</code>
</format>
<argpos>1</argpos>
<ctrl>
<message>
<text lang="en">Enter a value > 0</text>
</message>
<code proglang="perl">0 < $value</code>
<code proglang="python">0 < value</code>
</ctrl>
<comment>
<text lang="en">Sample x sequences, rather than just one.</text>
</comment>
</parameter>
<parameter>
<name>sample</name>
<prompt lang="en">Sample from profile, not core model (-p)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">( $value ) ? " -p " : ""</code>
<code proglang="python">( "" , " -p " )[ value ]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">Sample sequences from the implicit profile, not from the core model.
The core
model consists only of the homologous states (between the begin and end states
of a HMMER Plan7 model). The profile includes the nonhomologous N, C, and J
states, local/glocal and uni/multihit algorithm configuration, and the target length
model. Therefore sequences sampled from a profile may include nonhomologous
as well as homologous sequences, and may contain more than one homologous
sequence segment. By default, the profile is in multihit local mode, and the target
sequence length is configured for L=400. To change these defaults, see Options
Controlling Emission from Profiles, below.</text>
</comment>
</parameter>
<paragraph>
<name>controlP</name>
<prompt lang="en">Options controlling emission from profiles (with -p)</prompt>
<precond>
<code proglang="perl">define $sample</code>
<code proglang="python">sample</code>
</precond>
<parameters>
<parameter>
<name>len</name>
<prompt lang="en">Set expected length from profile (-L)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>400</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -L $value " : ""</code>
<code proglang="python">( "" , " -L " + str(value) )[ value is not None and value != vdef]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">Configure the profile's target sequence length model to generate a mean length of
approximately the value rather than the default of 400.</text>
</comment>
</parameter>
<parameter>
<name>local</name>
<prompt>Configure profile mode</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>null</value>
</vdef>
<vlist>
<velem undef="1">
<value>null</value>
<label/>
</velem>
<velem>
<value>local</value>
<label>local mode</label>
</velem>
<velem>
<value>unilocal</value>
<label>unilocal mode</label>
</velem>
<velem>
<value>glocal</value>
<label>glocal mode</label>
</velem>
<velem>
<value>uniglocal</value>
<label>uniglocal mode</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value) ? " --$value " : ""</code>
<code proglang="python">( "" , " --" + str(value) )[ value is not None ]</code>
</format>
</parameter>
</parameters>
</paragraph>
<parameter>
<name>seed</name>
<prompt lang="en">Seed number (--seed)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " --seed $value " : ""</code>
<code proglang="python">( "" , " --seed " + str(value) )[ value is not None and value !=vdef ]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">Seed the random number generator with the value, an integer >= 0. If the value is nonzero,
any stochastic simulations will be reproducible; the same command will give the
same results. If the value is 0, the random number generator is seeded arbitrarily, and
stochastic simulations will vary from run to run of the same command. The default
is 0: use an arbitrary seed, so different hmmemit runs will generate different
samples.</text>
</comment>
<ctrl>
<message>
<text lang="en">Enter a value >= 0</text>
</message>
<code proglang="perl">0 <= $value</code>
<code proglang="python">0 <= value</code>
</ctrl>
</parameter>
</parameters>
</program>
|