File: ktreedist.xml

package info (click to toggle)
mobyle-programs 4.0-1
  • links: PTS, VCS
  • area: main
  • in suites: wheezy
  • size: 5,508 kB
  • sloc: xml: 128,440; sh: 20; makefile: 4
file content (261 lines) | stat: -rw-r--r-- 9,975 bytes parent folder | download
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
<?xml version='1.0' encoding='UTF-8'?>
<!-- XML Authors: Sandrine Larroude,             -->
<!-- 'Biological Software and Databases' Group, Institut Pasteur, Paris.         -->
<!-- Distributed under LGPLv2 License. Please refer to the COPYING.LIB document. -->
<program>
  <head>
    <name>ktreedist</name>
    <version>Version 1.0</version>
    <doc>
      <title>Ktreedist</title>
      <description>
        <text lang="en">Calculation of the minimum branch length distance (K tree score) between phylogenetic trees</text>
      </description>
      <authors>Victor Soria-Carrasco, Jose Castresana</authors>
      <reference>Soria-Carrasco, V., Talavera, G., Igea, J., and Castresana, J. (2007). The K tree score: quantification of differences 
      		in the relative branch length and topology of phylogenetic trees. Bioinformatics 23, 2954-2956.</reference>
      <doclink>http://bioweb2.pasteur.fr/docs/ktreedist/</doclink>
      <homepagelink>http://molevol.cmima.csic.es/castresana/Ktreedist.html</homepagelink>
      <sourcelink>http://molevol.cmima.csic.es/castresana/Ktreedist.html</sourcelink>
    </doc>
    <category>phylogeny:tree_analyser</category>
    <command>ktreedist</command>
  </head>
  <parameters>
    <paragraph>
      <name>input</name>
      <prompt lang="en">Input</prompt>
      <comment>
        <text lang="en">The program is supposed to run with one reference tree and one or several comparison trees. If the reference file contains more than one tree, only the first one will be used.</text>
      </comment>
      <parameters>
        <parameter ismandatory="1" issimple="1">
          <name>ref_tree</name>
          <prompt lang="en">Reference Tree</prompt>
          <type>
            <datatype>
              <class>Tree</class>
            </datatype>
            <dataFormat>NEWICK</dataFormat>
            <dataFormat>NEXUS</dataFormat>
          </type>
          <format>
            <code proglang="perl">"-rt $value"</code>
            <code proglang="python">" -rt "+str(value)</code>
          </format>
          <argpos>2</argpos>
          <comment>
            <text lang="en">This is the file that contains the tree to which you want to compare the comparison tree/s.</text>
            <text lang="en"> Only NEWICK or NEXUS tree format are accepted by ktreedist.</text>
            <text lang="en">The input tree must be write in one line. for nexus tree the tree itself must be write in one line</text>
          </comment>
          <example>
#NEXUS
begin trees;
tree 'name' =(1:0.212481,8:0.297838,(9:0.222729,((6:0.201563,7:0.194547):0.282035,(4:1.146091,(3:1.008881,(10:0.384105,(2:0.235682,5:0.353432):0.323680):0.103875):0.413540):0.254687):0.095341):0.079254):0.000000;
end;
          </example>
        </parameter>
        <parameter ismandatory="1" issimple="1">
          <name>comp_tree</name>
          <prompt lang="en">Comparison Tree</prompt>
          <type>
            <datatype>
              <class>Tree</class>
            </datatype>
            <dataFormat>NEWICK</dataFormat>
            <dataFormat>NEXUS</dataFormat>
          </type>
          <format>
            <code proglang="perl">"-ct $value "</code>
            <code proglang="python">" -ct "+str(value)+" "</code>
          </format>
          <comment>
            <text lang="en">This is the file that contains the tree or the set of trees you want to compare to the reference tree. They will be scaled to match as much as possible the reference tree.</text>
            <text lang="en">Only NEWICK or NEXUS tree format are accepted by ktreedist.</text>
            <text lang="en">The input tree must be write in one line. for nexus tree the tree itself must be write in one line</text>
          </comment>
          <example>
(1:0.212481,8:0.297838,(9:0.222729,((6:0.201563,7:0.194547):0.282035,(4:1.146091,(3:1.008881,(10:0.384105,(2:0.235682,5:0.353432):0.323680):0.103875):0.413540):0.254687):0.095341):0.079254):0.000000;          
          </example>
          <argpos>3</argpos>
        </parameter>
      </parameters>
    </paragraph>
    <paragraph>
      <name>options</name>
      <prompt lang="en">Options</prompt>
      <argpos>4</argpos>
      <parameters>
        <parameter>
          <name>output_res</name>
          <prompt lang="en">Output file for table of results (-t)</prompt>
          <type>
            <datatype>
              <class>Boolean</class>
            </datatype>
          </type>
          <vdef>
            <value>0</value>
          </vdef>
          <format>
            <code proglang="perl">($value) ? " -t"</code>
            <code proglang="python">("", " -t")[ value ]</code>
          </format>
          <comment>
            <text lang="en"> A file containing a table of results is generated.</text>
          </comment>
        </parameter>
        <parameter>
          <name>output_part</name>
          <prompt lang="en">Output file for table of partitions (-p)</prompt>
          <type>
            <datatype>
              <class>Boolean</class>
            </datatype>
          </type>
          <vdef>
            <value>0</value>
          </vdef>
          <format>
            <code proglang="perl">($value) ? " -p"</code>
            <code proglang="python">("", " -p")[ value ]</code>
          </format>
          <comment>
            <text lang="en"> A file containing a table of partitions for each comparison tree is generated.</text>
          </comment>
        </parameter>
        <parameter>
          <name>output_comp</name>
          <prompt lang="en">Output file for comparison tree/s after scaling (-s)</prompt>
          <type>
            <datatype>
              <class>Boolean</class>
            </datatype>
          </type>
          <vdef>
            <value>0</value>
          </vdef>
          <format>
            <code proglang="perl">($value) ? " -s"</code>
            <code proglang="python">("", " -s")[ value ]</code>
          </format>
          <comment>
            <text lang="en">A file containing the scaled comparison tree/s is generated.</text>
          </comment>
        </parameter>
        <parameter>
          <name>output_rf</name>
          <prompt lang="en">Output symmetric difference (Robinson-Foulds) (-r)</prompt>
          <type>
            <datatype>
              <class>Boolean</class>
            </datatype>
          </type>
          <vdef>
            <value>0</value>
          </vdef>
          <format>
            <code proglang="perl">($value) ? " -r"</code>
            <code proglang="python">("", " -r")[ value ]</code>
          </format>
          <comment>
            <text lang="en">The symmetric difference is defined as the number of partitions that are not shared between two trees, 
						that is, the number of partitions of the first tree that are not present in the second tree plus the number of partitions 
						of the second tree that are not present in the first tree.</text>
          </comment>
        </parameter>
        <parameter>
          <name>output_nbpf</name>
          <prompt lang="en">Output number of partitions in the comparison tree/s (-n)</prompt>
          <type>
            <datatype>
              <class>Boolean</class>
            </datatype>
          </type>
          <vdef>
            <value>0</value>
          </vdef>
          <format>
            <code proglang="perl">($value) ? " -n"</code>
            <code proglang="python">("", " -n")[ value ]</code>
          </format>
          <comment>
            <text lang="en">The knowledge of the number of partitions may be useful to detect trees with polytomies.</text>
          </comment>
        </parameter>
        <parameter>
          <name>output_all</name>
          <prompt lang="en">Equivalent to all options (-a)</prompt>
          <type>
            <datatype>
              <class>Boolean</class>
            </datatype>
          </type>
          <vdef>
            <value>0</value>
          </vdef>
          <format>
            <code proglang="perl">($value) ? " -a"</code>
            <code proglang="python">("", " -a")[ value ]</code>
          </format>
          <comment>
            <text lang="en">Equivalent to all options.</text>
          </comment>
        </parameter>
      </parameters>
    </paragraph>
    <parameter isout="1">
      <name>output_res_f</name>
      <prompt lang="en">Output file for table of results</prompt>
      <type>
        <datatype>
          <class>Text</class>
        </datatype>
      </type>
      <precond>
        <code proglang="perl">$output_res or $output_all</code>
        <code proglang="python">output_res or output_all</code>
      </precond>
      <filenames>
        <code proglang="perl">"*.tab"</code>
        <code proglang="python">"*.tab"</code>
      </filenames>
    </parameter>
    <parameter isout="1">
      <name>output_part_f</name>
      <prompt lang="en">Output file for table of partitions</prompt>
      <type>
        <datatype>
          <class>Text</class>
        </datatype>
      </type>
      <precond>
        <code proglang="perl">$output_part or $output_all</code>
        <code proglang="python">output_part or output_all</code>
      </precond>
      <filenames>
        <code proglang="perl">"*.part"</code>
        <code proglang="python">"*.part"</code>
      </filenames>
    </parameter>
    <parameter isout="1">
      <name>output_comp_f</name>
      <prompt lang="en">Output file for comparison tree/s after scaling</prompt>
      <type>
        <datatype>
          <class>Tree</class>
        </datatype>
      </type>
      <precond>
        <code proglang="perl">$output_comp or $output_all</code>
        <code proglang="python">output_comp or output_all</code>
      </precond>
      <filenames>
        <code proglang="perl">"*.scaled"</code>
        <code proglang="python">"*.scaled"</code>
      </filenames>
    </parameter>
  </parameters>
</program>