mobyle-programs 5.1.1-1 / var / lib / mobyle / programs / xxr.xml

This file is indexed.

/var/lib/mobyle/programs/xxr.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
<?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>xxr</name>
    <version>3.02</version>
    <doc>
      <title>xxr</title>
      <description>
        <text lang="en">Integrons Analysis and Cassette Identification</text>
      </description>
      <authors>P. Bouige</authors>
      <reference>Rowe-Magnus D.A., Guerout A.M., Biskri L., Bouige P., Mazel D. Comparative analysis of superintegrons: Engineering extensive genetic diversity in the Vibrionaceae. Genome Res. 2003;13:428-442.</reference>
      <comment>
        <text lang="en">This software is able to extract putative cassette structures that fulfill the criteria established from analysis of previously known cassettes from integrons and superintegrons.</text>
      </comment>
    </doc>
    <category>sequence:nucleic:prediction</category>
    <category>sequence:nucleic:gene_finding</category>
  </head>
  <parameters>
    <parameter iscommand="1" ishidden="1">
      <name>xxr</name>
      <type>
        <datatype>
          <class>String</class>
        </datatype>
      </type>
      <format>
        <code proglang="perl">"xxr &lt;xxr.params"</code>
        <code proglang="python">"xxr &lt;xxr.params"</code>
      </format>
    </parameter>
    <parameter ismandatory="1" issimple="1">
      <name>input</name>
      <prompt lang="en">Input sequence</prompt>
      <type>
        <biotype>DNA</biotype>
        <datatype>
          <class>Sequence</class>
        </datatype>
        <dataFormat>FASTA</dataFormat>
      </type>
      <format>
        <code proglang="perl">"$value\\n.\\n"</code>
        <code proglang="python">str( value )+"\n.\n"</code>
      </format>
      <paramfile>xxr.params</paramfile>
    </parameter>
    <paragraph>
      <name>input_opt</name>
      <prompt>Options</prompt>
      <parameters>
        <parameter>
          <name>outsuffix</name>
          <prompt lang="en">Extension to add to files</prompt>
          <type>
            <datatype>
              <class>String</class>
            </datatype>
          </type>
          <format>
            <code proglang="perl">(defined $value) ? "$value\\n" : "\\n"</code>
            <code proglang="python">( "\n" , str( value ) + "\n" )[value is not None]</code>
          </format>
          <paramfile>xxr.params</paramfile>
        </parameter>
        <parameter>
          <name>minsize</name>
          <prompt lang="en">Minimal core size</prompt>
          <type>
            <datatype>
              <class>Integer</class>
            </datatype>
          </type>
          <vdef>
            <value>4</value>
          </vdef>
          <format>
            <code proglang="perl">($value != $vdef) ? "$value\\n" : "\\n"</code>
            <code proglang="python">( "\n" , str( value ) + "\n" )[value != vdef]</code>
          </format>
          <paramfile>xxr.params</paramfile>
        </parameter>
        <parameter>
          <name>maxsize</name>
          <prompt lang="en">Maximal core size</prompt>
          <type>
            <datatype>
              <class>Integer</class>
            </datatype>
          </type>
          <vdef>
            <value>10</value>
          </vdef>
          <format>
            <code proglang="perl">($value != $vdef) ? "$value\\n" : "\\n"</code>
            <code proglang="python">( "\n" , str( value ) + "\n" )[value != vdef]</code>
          </format>
          <paramfile>xxr.params</paramfile>
        </parameter>
        <parameter>
          <name>maxxxr</name>
          <prompt lang="en">Maximal XXR size</prompt>
          <type>
            <datatype>
              <class>Integer</class>
            </datatype>
          </type>
          <vdef>
            <value>200</value>
          </vdef>
          <format>
            <code proglang="perl">($value != $vdef) ? "$value\\n" : "\\n"</code>
            <code proglang="python">( "\n" , str( value ) + "\n" )[value != vdef]</code>
          </format>
          <paramfile>xxr.params</paramfile>
        </parameter>
        <parameter>
          <name>maxgene</name>
          <prompt lang="en">Maximal gene size</prompt>
          <type>
            <datatype>
              <class>Integer</class>
            </datatype>
          </type>
          <vdef>
            <value>2800</value>
          </vdef>
          <format>
            <code proglang="perl">($value != $vdef) ? "$value\\n" : "\\n"</code>
            <code proglang="python">( "\n" , str( value ) + "\n" )[value != vdef]</code>
          </format>
          <paramfile>xxr.params</paramfile>
        </parameter>
        <parameter>
          <name>cs</name>
          <prompt>Core Site (CS) - Variable site part upstream GTT</prompt>
          <type>
            <datatype>
              <class>String</class>
            </datatype>
          </type>
          <vdef>
            <value>GC</value>
          </vdef>
          <format>
            <code proglang="perl">($value ne $vdef) ? "$value\\n" : "\\n"</code>
            <code proglang="python">( "\n" , str( value ) + "\n" )[value != vdef]</code>
          </format>
          <comment>
            <text lang="en">By default, Core Site is GCGTT.</text>
          </comment>
          <paramfile>xxr.params</paramfile>
        </parameter>
        <parameter>
          <name>ICS</name>
          <prompt>Inverted Core Site (ICS) - Variable site part downstream AAC</prompt>
          <type>
            <datatype>
              <class>String</class>
            </datatype>
          </type>
          <vdef>
            <value>AAA</value>
          </vdef>
          <format>
            <code proglang="perl">($value ne $vdef) ? "$value\\n" : "\\n"</code>
            <code proglang="python">( "\n" , str( value ) + "\n" )[value != vdef]</code>
          </format>
          <comment>
            <text lang="en">By default, Inverted Core Site is AACAAA.</text>
          </comment>
          <paramfile>xxr.params</paramfile>
        </parameter>
      </parameters>
    </paragraph>
    <parameter isout="1">
      <name>res</name>
      <prompt lang="en">XXR results report</prompt>
      <type>
        <datatype>
          <class>Text</class>
        </datatype>
      </type>
      <filenames>
        <code proglang="perl">"Resultat_*"</code>
        <code proglang="python">"Resultat_*"</code>
      </filenames>
    </parameter>
    <parameter isout="1">
      <name>sk7</name>
      <prompt lang="en">Cassette gene files</prompt>
      <type>
        <datatype>
          <class>Text</class>
        </datatype>
      </type>
      <filenames>
        <code proglang="perl">"1_*_XXR_*"</code>
        <code proglang="perl">"2_*_XXR_*"</code>
        <code proglang="perl">"3_*_XXR_*"</code>
        <code proglang="python">"1_*_XXR_*"</code>
        <code proglang="python">"2_*_XXR_*"</code>
        <code proglang="python">"3_*_XXR_*"</code>
      </filenames>
      <comment>
        <text lang="en">If they exist, the 3th cassette gene files ONLY are displayed but you will find ALL of them in the job archive.</text>
      </comment>
    </parameter>
    <parameter isout="1">
      <name>xxrfasta</name>
      <prompt lang="en">XXR fasta</prompt>
      <type>
        <datatype>
          <class>Sequence</class>
        </datatype>
        <dataFormat>FASTA</dataFormat>
      </type>
      <filenames>
        <code proglang="perl">"XXR.fasta_*"</code>
        <code proglang="python">"XXR.fasta_*"</code>
      </filenames>
    </parameter>
    <parameter isout="1" ishidden="1">
      <name>hk7</name>
      <prompt lang="en">Cassette gene files</prompt>
      <type>
        <datatype>
          <class>Filename</class>
        </datatype>
      </type>
      <filenames>
        <code proglang="perl">"*_XXR_*"</code>
        <code proglang="python">"*_XXR_*"</code>
      </filenames>
    </parameter>
  </parameters>
</program>

APT Browse - Built by Thomas Orozco.