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

This file is indexed.

/var/lib/mobyle/programs/textsearch.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
312
313
314
315
316
<?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>textsearch</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>textsearch</title>
      <description>
        <text lang="en">Search the textual description of sequence(s)</text>
      </description>
      <doclink>http://bioweb2.pasteur.fr/docs/EMBOSS/textsearch.html</doclink>
      <doclink>http://emboss.sourceforge.net/docs/themes</doclink>
    </doc>
    <category>display:information</category>
    <command>textsearch</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,n</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_pattern</name>
          <prompt lang="en">Enter a pattern to search for</prompt>
          <type>
            <datatype>
              <class>String</class>
            </datatype>
          </type>
          <format>
            <code proglang="python">("", " -pattern=" + str(value))[value is not None]</code>
          </format>
          <argpos>2</argpos>
          <comment>
            <text lang="en">The search pattern is a regular expression. Use a | to indicate OR. 
  For example: 
  human|mouse 
  will find text with either 'human' OR 'mouse' in the text</text>
          </comment>
        </parameter>
      </parameters>
    </paragraph>

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

      <parameters>

        <parameter>
          <name>e_casesensitive</name>
          <prompt lang="en">Do a case-sensitive search</prompt>
          <type>
            <datatype>
              <class>Boolean</class>
            </datatype>
          </type>
          <vdef>
            <value>0</value>
          </vdef>
          <format>
            <code proglang="python">("", " -casesensitive")[ bool(value) ]</code>
          </format>
          <argpos>3</argpos>
        </parameter>
      </parameters>
    </paragraph>

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

      <parameters>

        <parameter>
          <name>e_html</name>
          <prompt lang="en">Format output as an html table</prompt>
          <type>
            <datatype>
              <class>Boolean</class>
            </datatype>
          </type>
          <vdef>
            <value>0</value>
          </vdef>
          <format>
            <code proglang="python">("", " -html")[ bool(value) ]</code>
          </format>
          <argpos>4</argpos>
        </parameter>

        <parameter>
          <name>e_only</name>
          <prompt lang="en">Display the specified columns</prompt>
          <type>
            <datatype>
              <class>Boolean</class>
            </datatype>
          </type>
          <vdef>
            <value>0</value>
          </vdef>
          <format>
            <code proglang="python">("", " -only")[ bool(value) ]</code>
          </format>
          <argpos>5</argpos>
          <comment>
            <text lang="en">This is a way of shortening the command line if you only want a few things to be displayed. Instead of specifying: 
  '-nohead -noname -nousa -noacc -nodesc' 
  to get only the name output, you can specify 
  '-only -name'</text>
          </comment>
        </parameter>

        <parameter>
          <name>e_heading</name>
          <prompt lang="en">Display column headings</prompt>
          <type>
            <datatype>
              <class>Boolean</class>
            </datatype>
          </type>
          <precond>
            <code proglang="python">not e_only</code>
          </precond>
          <vdef>
            <value>0</value>
          </vdef>
          <format>
            <code proglang="python">("", " -heading")[ bool(value) ]</code>
          </format>
          <argpos>6</argpos>
        </parameter>

        <parameter>
          <name>e_usa</name>
          <prompt lang="en">Display the usa of the sequence</prompt>
          <type>
            <datatype>
              <class>Boolean</class>
            </datatype>
          </type>
          <precond>
            <code proglang="python">not e_only</code>
          </precond>
          <vdef>
            <value>0</value>
          </vdef>
          <format>
            <code proglang="python">("", " -usa")[ bool(value) ]</code>
          </format>
          <argpos>7</argpos>
        </parameter>

        <parameter>
          <name>e_accession</name>
          <prompt lang="en">Display 'accession' column</prompt>
          <type>
            <datatype>
              <class>Boolean</class>
            </datatype>
          </type>
          <precond>
            <code proglang="python">not e_only</code>
          </precond>
          <vdef>
            <value>0</value>
          </vdef>
          <format>
            <code proglang="python">("", " -accession")[ bool(value) ]</code>
          </format>
          <argpos>8</argpos>
        </parameter>

        <parameter>
          <name>e_name</name>
          <prompt lang="en">Display 'name' column</prompt>
          <type>
            <datatype>
              <class>Boolean</class>
            </datatype>
          </type>
          <precond>
            <code proglang="python">not e_only</code>
          </precond>
          <vdef>
            <value>0</value>
          </vdef>
          <format>
            <code proglang="python">("", " -name")[ bool(value) ]</code>
          </format>
          <argpos>9</argpos>
        </parameter>

        <parameter>
          <name>e_description</name>
          <prompt lang="en">Display 'description' column</prompt>
          <type>
            <datatype>
              <class>Boolean</class>
            </datatype>
          </type>
          <precond>
            <code proglang="python">not e_only</code>
          </precond>
          <vdef>
            <value>0</value>
          </vdef>
          <format>
            <code proglang="python">("", " -description")[ bool(value) ]</code>
          </format>
          <argpos>10</argpos>
        </parameter>

        <parameter>
          <name>e_outfile</name>
          <prompt lang="en">Name of the output file (e_outfile)</prompt>
          <type>
            <datatype>
              <class>Filename</class>
            </datatype>
          </type>
          <vdef>
            <value>textsearch.e_outfile</value>
          </vdef>
          <format>
            <code proglang="python">("" , " -outfile=" + str(value))[value is not None]</code>
          </format>
          <argpos>11</argpos>
        </parameter>

        <parameter isout="1">
          <name>e_outfile_out</name>
          <prompt lang="en">outfile_out option</prompt>
          <type>
            <datatype>
              <class>TextsearchReport</class>
              <superclass>Report</superclass>
            </datatype>
          </type>
          <filenames>
            <code proglang="python">e_outfile</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>12</argpos>
    </parameter>
  </parameters>
</program>

APT Browse - Built by Thomas Orozco.