/var/lib/mobyle/programs/combat.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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 | <?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>combat</name>
<version>1.0</version>
<doc>
<title>COMBAT</title>
<description>
<text lang="en">Comparison of coding DNA</text>
</description>
<authors>Pedersen, Lyngso,Hein</authors>
<reference>Christian N. S. Pedersen, Rune B. Lyngso and Jotun Hein. Comparison of coding DNA in Proceedings of the 9th Annual Symposium of Combinatorial Pattern Matching (CPM), 1998.</reference>
<homepagelink>http://www.daimi.au.dk/~cstorm/combat/</homepagelink>
<sourcelink>http://www.daimi.au.dk/~cstorm/combat/</sourcelink>
</doc>
<category>alignment:pairwise</category>
</head>
<parameters xmlns:xi="http://www.w3.org/2001/XInclude">
<parameter iscommand="1" ishidden="1">
<name>combat</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<precond>
<code proglang="perl">defined $sequence1 and defined $sequence2</code>
<code proglang="python">sequence1 is not None and sequence2 is not None</code>
</precond>
<format>
<code proglang="perl">"cat $sequence1 $sequence2 >> sequence && combat combat.params >distance.out && combine sequence combat.aln"</code>
<code proglang="python">"cat " + str(sequence2) + " " + str(sequence1) + " >> sequence.data && combat combat.params > distance.out && combine sequence.data combat.aln"</code>
</format>
<argpos>0</argpos>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>sequence1</name>
<prompt lang="en">First Sequence</prompt>
<type>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>FASTA</dataFormat>
</type>
<format>
<code proglang="perl">">inputfile\n\"sequence.data\"\n"</code>
<code proglang="python">'>inputfile\n"sequence.data"\n'</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">Sequences must describe an integer number of codon, i.e. the length of sequence must be a multiple of three.</text>
</comment>
<paramfile>combat.params</paramfile>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>sequence2</name>
<prompt lang="en">Second Sequence</prompt>
<type>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>FASTA</dataFormat>
</type>
<comment>
<text lang="en">Sequences must describe an integer number of codon, i.e. the length of sequence must be a multiple of three.</text>
</comment>
</parameter>
<parameter isout="1">
<name>output_aln</name>
<prompt lang="en">Output file</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<format>
<code proglang="perl">">outputfile\n\"combat.aln\"\n"</code>
<code proglang="python">'>outputfile\n"combat.aln"\n'</code>
</format>
<argpos>2</argpos>
<paramfile>combat.params</paramfile>
<filenames>
<code proglang="perl">"combat.aln"</code>
<code proglang="python">"combat.aln"</code>
</filenames>
</parameter>
<parameter ismandatory="1">
<name>protein_distance_matrix</name>
<prompt lang="en">Amino-acid distance matrix</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>Blosum62_distance.m</value>
</vdef>
<vlist>
<velem>
<value>PAM60_distance.m</value>
<label>PAM60</label>
</velem>
<velem>
<value>PAM120_distance.m</value>
<label>PAM120</label>
</velem>
<velem>
<value>PAM250_distance.m.m</value>
<label>PAM250</label>
</velem>
<velem>
<value>PAM350_distance.m</value>
<label>PAM350</label>
</velem>
<velem>
<value>Blosum30_distance.m</value>
<label>Blosum30</label>
</velem>
<velem>
<value>Blosum62_distance.m</value>
<label>Blosum62</label>
</velem>
<velem>
<value>Blosum90_distance.m</value>
<label>Blosum90</label>
</velem>
</vlist>
<format>
<code proglang="perl">">distance matrix\n\"<xi:include href="../../Local/Services/Programs/Env/combat_data.xml" xpointer="xpointer(/matrix/text())" />$value\"\n"</code>
<code proglang="python">">distance matrix\n\"<xi:include href="../../Local/Services/Programs/Env/combat_data.xml" xpointer="xpointer(/matrix/text())" />" + str(value) + '"\n'</code>
</format>
<argpos>3</argpos>
<paramfile>combat.params</paramfile>
</parameter>
<parameter ismandatory="1">
<name>nucleotide_distance_matrix</name>
<prompt lang="en">Nucleotid distance matrix</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>nucleotide_distance1.m</value>
</vdef>
<vlist>
<velem>
<value>nucleotide_distance1.m</value>
<label>Matrix 1</label>
</velem>
<velem>
<value>nucleotide_distance2.m</value>
<label>Matrix 2</label>
</velem>
<velem>
<value>nucleotide_distance3.m</value>
<label>Matrix 3</label>
</velem>
</vlist>
<format>
<code proglang="perl">">nucleotide matrix\n\"<xi:include href="../../Local/Services/Programs/Env/combat_data.xml" xpointer="xpointer(/matrix/text())" />$value\"\n"</code>
<code proglang="python">">nucleotide matrix\n\"<xi:include href="../../Local/Services/Programs/Env/combat_data.xml" xpointer="xpointer(/matrix/text())" />" + str(value) + '"\n'</code>
</format>
<argpos>4</argpos>
<paramfile>combat.params</paramfile>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>protein_gap_open</name>
<prompt lang="en">Gap open cost for protein</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>20</value>
</vdef>
<format>
<code proglang="perl">">gap functions\\nprotein: $value"</code>
<code proglang="python">">gap functions\nprotein: " + str(value)</code>
</format>
<argpos>5</argpos>
<paramfile>combat.params</paramfile>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>protein_gap_ext</name>
<prompt lang="en">Gap extension cost for protein</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>8</value>
</vdef>
<format>
<code proglang="perl">" + $value*k\\n"</code>
<code proglang="python">" + " + str(value) + "*k\n"</code>
</format>
<argpos>6</argpos>
<paramfile>combat.params</paramfile>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>dna_gap_open</name>
<prompt lang="en">Gap open cost for dna</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>8</value>
</vdef>
<format>
<code proglang="perl">"dna: $value"</code>
<code proglang="python">"dna: " + str(value)</code>
</format>
<argpos>7</argpos>
<paramfile>combat.params</paramfile>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>dna_gap_ext</name>
<prompt lang="en">Gap extension cost for dna</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>2</value>
</vdef>
<format>
<code proglang="perl">" + $value*k"</code>
<code proglang="python">" + " + str(value) + "*k"</code>
</format>
<argpos>8</argpos>
<paramfile>combat.params</paramfile>
</parameter>
<parameter isstdout="1">
<name>combat_out</name>
<prompt>Alignment file</prompt>
<type>
<datatype>
<class>Alignment</class>
</datatype>
<dataFormat>FASTA</dataFormat>
</type>
<filenames>
<code proglang="perl">"combat.out"</code>
<code proglang="python">"combat.out"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>distance_files</name>
<prompt>Distance file</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<filenames>
<code proglang="perl">"distance.out"</code>
<code proglang="python">"distance.out"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>ps_files</name>
<prompt>Postscript file</prompt>
<type>
<datatype>
<class>PostScript</class>
<superclass>Binary</superclass>
</datatype>
</type>
<filenames>
<code proglang="perl">"combat.ps"</code>
<code proglang="python">"combat.ps"</code>
</filenames>
</parameter>
<parameter ishidden="1">
<name>gnuplot_call</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">" && gnuplot <gnuplot.params"</code>
<code proglang="python">" && gnuplot <gnuplot.params"</code>
</format>
<argpos>100</argpos>
</parameter>
<parameter ishidden="1">
<name>gnuplot_commands</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">"set xtics 12,5.,1000\nset ytics 12,5.,1000\nset grid\nset terminal postscript\nset output \"combat.ps\"\nplot \"combat.aln\" with lines\n"</code>
<code proglang="python">'set xtics 12,5.,1000\nset ytics 12,5.,1000\nset grid\nset terminal postscript\nset output "combat.ps"\nplot "combat.aln" with lines\n'</code>
</format>
<argpos>1</argpos>
<paramfile>gnuplot.params</paramfile>
</parameter>
</parameters>
</program>
|