mobyle-programs 5.1.2-1 / var / lib / mobyle / programs / extractseq.xml

This file is indexed.

/var/lib/mobyle/programs/extractseq.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
<?xml version="1.0" encoding="ISO-8859-1"?>

<!-- XML Authors: Corinne Maufrais and Nicolas Joly,                             -->
<!-- 'Biological Software and Databases' Group, Institut Pasteur, Paris.         -->
<!-- Distributed under LGPLv2 License. Please refer to the COPYING.LIB document. -->

<program>
  <head>
    <name>extractseq</name>
    <package>
      <name>EMBOSS</name>
      <version>6.3.1</version>
      <doc>
        <title>EMBOSS</title>
        <description>
          <text lang="en">European Molecular Biology Open Software Suite</text>
        </description>
        <authors>Rice,P. Longden,I. and Bleasby, A.</authors>
        <reference>EMBOSS: The European Molecular Biology Open Software Suite (2000)  Rice,P. Longden,I. and Bleasby, A. Trends in Genetics 16, (6) pp276--277</reference>
        <sourcelink>http://emboss.sourceforge.net/download</sourcelink>
        <homepagelink>http://emboss.sourceforge.net</homepagelink>
      </doc>
    </package>
    <doc>
      <title>extractseq</title>
      <description>
        <text lang="en">Extract regions from a sequence</text>
      </description>
      <doclink>http://bioweb2.pasteur.fr/docs/EMBOSS/extractseq.html</doclink>
      <doclink>http://emboss.sourceforge.net/docs/themes</doclink>
    </doc>
    <category>sequence:edit</category>
    <command>extractseq</command>
  </head>

  <parameters>

    <paragraph>
      <name>e_input</name>
      <prompt lang="en">Input section</prompt>

      <parameters>

        <parameter issimple="1" ismandatory="1">
          <name>e_sequence</name>
          <prompt lang="en">sequence option</prompt>
          <type>
            <datatype>
              <class>Sequence</class>
            </datatype>
            <dataFormat>EMBL</dataFormat>
            <dataFormat>FASTA</dataFormat>
            <dataFormat>GCG</dataFormat>
            <dataFormat>GENBANK</dataFormat>
            <dataFormat>NBRF</dataFormat>
            <dataFormat>CODATA</dataFormat>
            <dataFormat>RAW</dataFormat>
            <dataFormat>SWISSPROT</dataFormat>
            <dataFormat>GFF</dataFormat>
            <card>1,1</card>
          </type>
          <format>
            <code proglang="python">("", " -sequence=" + str(value))[value is not None]</code>
          </format>
          <argpos>1</argpos>
        </parameter>
      </parameters>
    </paragraph>

    <paragraph>
      <name>e_required</name>
      <prompt lang="en">Required section</prompt>

      <parameters>

        <parameter issimple="1" ismandatory="1">
          <name>e_regions</name>
          <prompt lang="en">Regions to extract (eg: 4-57,78-94)</prompt>
          <type>
            <datatype>
              <class>String</class>
            </datatype>
          </type>
          <format>
            <code proglang="python">("", " -regions=" + str(value))[value is not None]</code>
          </format>
          <argpos>2</argpos>
          <comment>
            <text lang="en">Regions to extract. 
 A set of regions is specified by a set of pairs of positions. 
  The positions are integers. 
  They are separated by any non-digit, non-alpha character. 
  Examples of region specifications are: 
  24-45, 56-78 
  1:45, 67=99;765..888 
  1,5,8,10,23,45,57,99</text>
          </comment>
        </parameter>
      </parameters>
    </paragraph>

    <paragraph>
      <name>e_additional</name>
      <prompt lang="en">Additional section</prompt>

      <parameters>

        <parameter>
          <name>e_separate</name>
          <prompt lang="en">Write regions to separate sequences</prompt>
          <type>
            <datatype>
              <class>Boolean</class>
            </datatype>
          </type>
          <vdef>
            <value>0</value>
          </vdef>
          <format>
            <code proglang="python">("", " -separate")[ bool(value) ]</code>
          </format>
          <argpos>3</argpos>
          <comment>
            <text lang="en">If this is set true then each specified region is written out as a separate sequence. The name of the sequence is created  from the name of the original sequence with the start and end  positions of the range appended with underscore characters between  them, eg: XYZ region 2 to 34 is written as: XYZ_2_34</text>
          </comment>
        </parameter>
      </parameters>
    </paragraph>

    <paragraph>
      <name>e_output</name>
      <prompt lang="en">Output section</prompt>

      <parameters>

        <parameter>
          <name>e_outseq</name>
          <prompt lang="en">Name of the output sequence file (e_outseq)</prompt>
          <type>
            <datatype>
              <class>Filename</class>
            </datatype>
          </type>
          <vdef>
            <value>extractseq.e_outseq</value>
          </vdef>
          <format>
            <code proglang="python">("" , " -outseq=" + str(value))[value is not None]</code>
          </format>
          <argpos>4</argpos>
        </parameter>

        <parameter>
          <name>e_osformat_outseq</name>
          <prompt lang="en">Choose the sequence output format</prompt>
          <type>
            <datatype>
              <class>Choice</class>
            </datatype>
          </type>
          <vdef>
            <value>FASTA</value>
          </vdef>
          <vlist>
            <velem>
              <value>EMBL</value>
              <label>Embl</label>
            </velem>
            <velem>
              <value>FASTA</value>
              <label>Fasta</label>
            </velem>
            <velem>
              <value>GCG</value>
              <label>Gcg</label>
            </velem>
            <velem>
              <value>GENBANK</value>
              <label>Genbank</label>
            </velem>
            <velem>
              <value>NBRF</value>
              <label>Nbrf</label>
            </velem>
            <velem>
              <value>CODATA</value>
              <label>Codata</label>
            </velem>
            <velem>
              <value>RAW</value>
              <label>Raw</label>
            </velem>
            <velem>
              <value>SWISSPROT</value>
              <label>Swissprot</label>
            </velem>
            <velem>
              <value>GFF</value>
              <label>Gff</label>
            </velem>
          </vlist>
          <format>
            <code proglang="python">("", " -osformat=" + str(value))[value is not None and value!=vdef]</code>
          </format>
          <argpos>5</argpos>
        </parameter>

        <parameter isout="1">
          <name>e_outseq_out</name>
          <prompt lang="en">outseq_out option</prompt>
          <type>
            <datatype>
              <class>Sequence</class>
            </datatype>
            <dataFormat>
              <ref param="e_osformat_outseq">
              </ref>
            </dataFormat>
          </type>
          <filenames>
            <code proglang="python">e_outseq</code>
          </filenames>
        </parameter>
      </parameters>
    </paragraph>

    <parameter ishidden="1">
      <name>auto</name>
      <prompt lang="en">Turn off any prompting</prompt>
      <type>
        <datatype>
          <class>String</class>
        </datatype>
      </type>
      <format>
        <code proglang="python">" -auto -stdout"</code>
      </format>
      <argpos>6</argpos>
    </parameter>
  </parameters>
</program>

APT Browse - Built by Thomas Orozco.