/var/lib/mobyle/programs/xpound.xml is in mobyle-programs 5.1.1-1.
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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 | <?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>xpound</name>
<doc>
<title>Xpound</title>
<description>
<text lang="en">Software for exon trapping</text>
</description>
<authors>Thomas and Skolnick</authors>
<reference>A probabilistic model for detecting coding regions in DNA sequences. Alun Thomas and Mark H Skolnick, IMA Journal of Mathematics Applied in Medicine and Biology, 1994, 11, 149-160.</reference>
</doc>
<category>sequence:nucleic:gene_finding</category>
<command>xpound</command>
</head>
<parameters>
<parameter ismandatory="1" issimple="1">
<name>seq</name>
<prompt lang="en">DNA sequence File</prompt>
<type>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>RAW</dataFormat>
<card>1,1</card>
</type>
<format>
<code proglang="perl">" <$value"</code>
<code proglang="python">" <"+str(value)</code>
</format>
<argpos>2</argpos>
<comment>
<text lang="en">Everything after a % on a line in the input
file is ignored. Other than comment xpound expects only white
space, which is also ignored, or IUPAC characters:</text>
<text lang="en">A C M G R S V T W Y H K D B N</text>
<text lang="en">in upper or lower case. Characters which do
not uniquely determine a base, such as N, B, S and so on, are
all interpreted as a C.</text>
<text lang="en">Xpound will not accept the IUPAC character -,
all occurences of which should be stripped from the input file
beforehand.</text>
</comment>
</parameter>
<parameter isstdout="1">
<name>outfile</name>
<prompt lang="en">Output file</prompt>
<type>
<datatype>
<class>XpoundReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<filenames>
<code proglang="perl">"xpound.out"</code>
<code proglang="python">"xpound.out"</code>
</filenames>
</parameter>
<paragraph>
<name>report_options</name>
<prompt lang="en">Report options</prompt>
<parameters>
<parameter>
<name>report</name>
<prompt lang="en">Reports regions of bases for which the probability of coding is high (xreport)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">($value) ? " ; xreport <xpound.out " : ""</code>
<code proglang="python">( "" , " ; xreport <xpound.out " )[ value ]</code>
</format>
<argpos>20</argpos>
</parameter>
<parameter>
<name>cut_off</name>
<prompt lang="en">Cut off value for report</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">$report</code>
<code proglang="python">report</code>
</precond>
<vdef>
<value>0.75</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " $value " : ""</code>
<code proglang="python">( "" , " " + str(value) )[ value is not None and value != vdef]</code>
</format>
<argpos>21</argpos>
</parameter>
<parameter>
<name>min_length</name>
<prompt lang="en">Minimum length value for report</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">$report</code>
<code proglang="python">report</code>
</precond>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " $value " : ""</code>
<code proglang="python">( "" , " " + str(value) )[ value is not None and value != vdef]</code>
</format>
<argpos>22</argpos>
</parameter>
<parameter isout="1">
<name>report_file</name>
<prompt lang="en">Report file</prompt>
<type>
<datatype>
<class>XreportReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$report</code>
<code proglang="python">report</code>
</precond>
<format>
<code proglang="perl">" >xreport.out "</code>
<code proglang="python">">xreport.out "</code>
</format>
<argpos>25</argpos>
<filenames>
<code proglang="perl">"xreport.out"</code>
<code proglang="python">"xreport.out"</code>
</filenames>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>postscript_options</name>
<prompt lang="en">Postscript options</prompt>
<parameters>
<parameter>
<name>postscript</name>
<prompt lang="en">Produces a file of graphs in PostScript format (xpscript)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">($value) ? "; xpscript xpound.out" : ""</code>
<code proglang="python">( "" , "; xpscript xpound.out" )[ value ]</code>
</format>
<argpos>30</argpos>
</parameter>
<parameter>
<name>orientation</name>
<prompt lang="en">Orientation (-l)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<precond>
<code proglang="perl">$postscript</code>
<code proglang="python">postscript</code>
</precond>
<vdef>
<value>portrait</value>
</vdef>
<vlist>
<velem>
<value>portrait</value>
<label>Portrait</label>
</velem>
<velem>
<value>lanscape</value>
<label>Lanscape</label>
</velem>
</vlist>
<format>
<code proglang="perl">($value eq "lanscape") ? " -l " : ""</code>
<code proglang="python">( "" , " -l " )[ value == "lanscape" ]</code>
</format>
<argpos>31</argpos>
</parameter>
<parameter>
<name>rows</name>
<prompt lang="en">Rows of plots per page (-r)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">$postscript</code>
<code proglang="python">postscript</code>
</precond>
<vdef>
<value>5</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -r $value " : ""</code>
<code proglang="python">( "" , " -r " + str(value) )[ value is not None and value != vdef]</code>
</format>
<argpos>32</argpos>
</parameter>
<parameter>
<name>columns</name>
<prompt lang="en">Columns of plots per page (-c)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<precond>
<code proglang="perl">$postscript</code>
<code proglang="python">postscript</code>
</precond>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -c $value " : ""</code>
<code proglang="python">( "" , " -c " + str(value) )[ value is not None and value != vdef]</code>
</format>
<argpos>32</argpos>
</parameter>
<parameter>
<name>high</name>
<prompt lang="en">Draw a line at this level (-hi)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">$postscript</code>
<code proglang="python">postscript</code>
</precond>
<vdef>
<value>0.75</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -hi $value " : ""</code>
<code proglang="python">( "" , " -hi " + str(value) )[ value is not None and value != vdef]</code>
</format>
<argpos>33</argpos>
</parameter>
<parameter>
<name>low</name>
<prompt lang="en">Draw a line at this level (-lo)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">$postscript</code>
<code proglang="python">postscript</code>
</precond>
<vdef>
<value>0.5</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -lo $value " : ""</code>
<code proglang="python">( "" , " -lo " + str(value) )[ value is not None and value != vdef]</code>
</format>
<argpos>34</argpos>
</parameter>
<parameter isout="1">
<name>psfile</name>
<prompt lang="en">PostScript file</prompt>
<type>
<datatype>
<class>PostScript</class>
<superclass>Binary</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$postscript</code>
<code proglang="python">postscript</code>
</precond>
<format>
<code proglang="perl">" >xpound.ps"</code>
<code proglang="python">" >xpound.ps"</code>
</format>
<argpos>100</argpos>
<filenames>
<code proglang="perl">"xpound.ps"</code>
<code proglang="python">"xpound.ps"</code>
</filenames>
</parameter>
</parameters>
</paragraph>
</parameters>
</program>
|