/var/lib/mobyle/programs/comalign.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 | <?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>comalign</name>
<doc>
<title>ComAlign</title>
<description>
<text lang="en">is a program, that given a number of sequences generates a number of heuristic alignments and combines these best possible.</text>
</description>
<authors>O. Caprani, K. Bucka-Lassen</authors>
<homepagelink>http://www.daimi.au.dk/~ocaprani/ComAlign/ComAlign.html</homepagelink>
<sourcelink>http://www.daimi.au.dk/~ocaprani/ComAlign/programs/</sourcelink>
<doclink>http://www.daimi.au.dk/~ocaprani/ComAlign/HowTo.html</doclink>
</doc>
<category>alignment:multiple</category>
<command>ComAlign</command>
</head>
<parameters>
<parameter ismandatory="1" issimple="1">
<name>seq</name>
<prompt lang="en">Sequences File (-f)</prompt>
<type>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>GenAl</dataFormat>
</type>
<format>
<code proglang="perl">" -f$value"</code>
<code proglang="python">" -f" + str(value)</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">the sequences must be in the GenAl format</text>
</comment>
<example>
>Test1
ATGAAA
*
*
>Test2
ATCAAA
*
*
</example>
</parameter>
<parameter>
<name>seed</name>
<prompt lang="en">Random seed number (-s)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -s$value" : ""</code>
<code proglang="python">( "" , " -s" + str(value) )[ value is not None and value != vdef]</code>
</format>
<argpos>1</argpos>
</parameter>
<parameter>
<name>seqnb</name>
<prompt lang="en">Number of sequences that are to be aligned (-n)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>2</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>
</parameter>
<parameter>
<name>iterations</name>
<prompt lang="en">Number of iterations (-i)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>10</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " -i$value" : ""</code>
<code proglang="python">( "" , " -i" + str(value) )[ value is not None and value != vdef]</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">On each iteration a new alignment is added to the pool of alignments ComAlign is working on</text>
</comment>
</parameter>
<parameter>
<name>score</name>
<prompt lang="en">Score: ComAlign records the time it took to find a solution as good as this score (-l)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -l$value" : ""</code>
<code proglang="python">( "" , " -l" + str(value) )[ value is not None]</code>
</format>
<argpos>1</argpos>
</parameter>
<parameter>
<name>time</name>
<prompt lang="en">ComAlign marks the best solution found after this number of 1/100 seconds (-t)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " -t$value" : ""</code>
<code proglang="python">( "" , " -t" + str(value) )[ value is not None ]</code>
</format>
<argpos>1</argpos>
</parameter>
<parameter>
<name>last_iterations</name>
<prompt lang="en">Makes ComAlign terminate if the score hasn't changed within the last this number of iterations (-c)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>20</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>1</argpos>
</parameter>
<parameter>
<name>print_best</name>
<prompt lang="en">Print the best found alignment on termination (-a)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">($value) ? " -a" : ""</code>
<code proglang="python">( "" , " -a" )[ value ]</code>
</format>
<argpos>1</argpos>
</parameter>
</parameters>
</program>
|