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<!-- 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>sixpack</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>sixpack</title>
<description>
<text lang="en">Display a DNA sequence with 6-frame translation and ORFs</text>
</description>
<doclink>http://bioweb2.pasteur.fr/docs/EMBOSS/sixpack.html</doclink>
<doclink>http://emboss.sourceforge.net/docs/themes</doclink>
</doc>
<category>display:nucleic:gene_finding</category>
<category>display:nucleic:translation</category>
<command>sixpack</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>
<biotype>DNA</biotype>
<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_additional</name>
<prompt lang="en">Additional section</prompt>
<parameters>
<parameter>
<name>e_table</name>
<prompt lang="en">Genetic codes</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<vlist>
<velem>
<value>0</value>
<label>Standard</label>
</velem>
<velem>
<value>1</value>
<label>Standard (with alternative initiation codons)</label>
</velem>
<velem>
<value>2</value>
<label>Vertebrate mitochondrial</label>
</velem>
<velem>
<value>3</value>
<label>Yeast mitochondrial</label>
</velem>
<velem>
<value>4</value>
<label>Mold, protozoan, coelenterate mitochondrial and mycoplasma/spiroplasma</label>
</velem>
<velem>
<value>5</value>
<label>Invertebrate mitochondrial</label>
</velem>
<velem>
<value>6</value>
<label>Ciliate macronuclear and dasycladacean</label>
</velem>
<velem>
<value>9</value>
<label>Echinoderm mitochondrial</label>
</velem>
<velem>
<value>10</value>
<label>Euplotid nuclear</label>
</velem>
<velem>
<value>11</value>
<label>Bacterial</label>
</velem>
<velem>
<value>12</value>
<label>Alternative yeast nuclear</label>
</velem>
<velem>
<value>13</value>
<label>Ascidian mitochondrial</label>
</velem>
<velem>
<value>14</value>
<label>Flatworm mitochondrial</label>
</velem>
<velem>
<value>15</value>
<label>Blepharisma macronuclear</label>
</velem>
<velem>
<value>16</value>
<label>Chlorophycean mitochondrial</label>
</velem>
<velem>
<value>21</value>
<label>Trematode mitochondrial</label>
</velem>
<velem>
<value>22</value>
<label>Scenedesmus obliquus</label>
</velem>
<velem>
<value>23</value>
<label>Thraustochytrium mitochondrial</label>
</velem>
</vlist>
<format>
<code proglang="python">("", " -table=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>2</argpos>
<comment>
<text lang="en">Genetics code used for the translation</text>
</comment>
</parameter>
<parameter>
<name>e_firstorf</name>
<prompt lang="en">Orf at the beginning of the sequence</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -nofirstorf", "")[ bool(value) ]</code>
</format>
<argpos>3</argpos>
<comment>
<text lang="en">Count the beginning of a sequence as a possible ORF, even if it's inferior to the minimal ORF size.</text>
</comment>
</parameter>
<parameter>
<name>e_lastorf</name>
<prompt lang="en">Orf at the end of the sequence</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -nolastorf", "")[ bool(value) ]</code>
</format>
<argpos>4</argpos>
<comment>
<text lang="en">Count the end of a sequence as a possible ORF, even if it's not finishing with a STOP, or inferior to the minimal ORF size.</text>
</comment>
</parameter>
<parameter>
<name>e_mstart</name>
<prompt lang="en">Orf start with an m</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -mstart")[ bool(value) ]</code>
</format>
<argpos>5</argpos>
<comment>
<text lang="en">Displays only ORFs starting with an M.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>e_output</name>
<prompt lang="en">Output section</prompt>
<parameters>
<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>sixpack.e_outfile</value>
</vdef>
<format>
<code proglang="python">("" , " -outfile=" + str(value))[value is not None]</code>
</format>
<argpos>6</argpos>
</parameter>
<parameter isout="1">
<name>e_outfile_out</name>
<prompt lang="en">outfile_out option</prompt>
<type>
<datatype>
<class>SixpackReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<filenames>
<code proglang="python">e_outfile</code>
</filenames>
</parameter>
<parameter>
<name>e_outseq</name>
<prompt lang="en">Name of the output sequence file (e_outseq)</prompt>
<type>
<biotype>Protein</biotype>
<datatype>
<class>Filename</class>
</datatype>
</type>
<vdef>
<value>sixpack.e_outseq</value>
</vdef>
<format>
<code proglang="python">("" , " -outseq=" + str(value))[value is not None]</code>
</format>
<argpos>7</argpos>
<comment>
<text lang="en">ORF sequence output</text>
</comment>
</parameter>
<parameter>
<name>e_osformat_outseq</name>
<prompt lang="en">Choose the sequence output format</prompt>
<type>
<biotype>Protein</biotype>
<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>8</argpos>
</parameter>
<parameter isout="1">
<name>e_outseq_out</name>
<prompt lang="en">outseq_out option</prompt>
<type>
<biotype>Protein</biotype>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>
<ref param="e_osformat_outseq">
</ref>
</dataFormat>
</type>
<filenames>
<code proglang="python">e_outseq</code>
</filenames>
</parameter>
<parameter>
<name>e_reverse</name>
<prompt lang="en">Display translation of reverse sense</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -noreverse", "")[ bool(value) ]</code>
</format>
<argpos>9</argpos>
<comment>
<text lang="en">Display also the translation of the DNA sequence in the 3 reverse frames</text>
</comment>
</parameter>
<parameter>
<name>e_orfminsize</name>
<prompt lang="en">Minimum size of orfs (value greater than or equal to 1)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">("", " -orfminsize=" + str(value))[value is not None and value!=vdef]</code>
</format>
<ctrl>
<message>
<text lang="en">Value greater than or equal to 1 is required</text>
</message>
<code proglang="python">value >= 1</code>
</ctrl>
<argpos>10</argpos>
<comment>
<text lang="en">Minimum size of Open Reading Frames (ORFs) to display in the translations.</text>
</comment>
</parameter>
<parameter>
<name>e_uppercase</name>
<prompt lang="en">Regions to put in uppercase (eg: 4-57,78-94)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="python">("", " -uppercase=" + str(value))[value is not None]</code>
</format>
<argpos>11</argpos>
<comment>
<text lang="en">Regions to put in uppercase.
If this is left blank, then the sequence case is left alone.
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>
<parameter>
<name>e_highlight</name>
<prompt lang="en">Regions to colour in html (eg: 4-57 red 78-94 green)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="python">("", " -highlight=" + str(value))[value is not None]</code>
</format>
<argpos>12</argpos>
<comment>
<text lang="en">Regions to colour if formatting for HTML.
If this is left blank, then the sequence is left alone.
A set of regions is specified by a set of pairs of positions.
The positions are integers.
They are followed by any valid HTML font colour.
Examples of region specifications are:
24-45 blue 56-78 orange
1-100 green 120-156 red
A file of ranges to colour (one range per line) can be specified as '@filename'.</text>
</comment>
</parameter>
<parameter>
<name>e_number</name>
<prompt lang="en">Number the sequences</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -nonumber", "")[ bool(value) ]</code>
</format>
<argpos>13</argpos>
<comment>
<text lang="en">Number the sequence at the beginning and the end of each line.</text>
</comment>
</parameter>
<parameter>
<name>e_width</name>
<prompt lang="en">Width of sequence to display (value greater than or equal to 1)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>60</value>
</vdef>
<format>
<code proglang="python">("", " -width=" + str(value))[value is not None and value!=vdef]</code>
</format>
<ctrl>
<message>
<text lang="en">Value greater than or equal to 1 is required</text>
</message>
<code proglang="python">value >= 1</code>
</ctrl>
<argpos>14</argpos>
<comment>
<text lang="en">Number of nucleotides displayed on each line</text>
</comment>
</parameter>
<parameter>
<name>e_length</name>
<prompt lang="en">Line length of page (0 for indefinite) (value greater than or equal to 0)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -length=" + str(value))[value is not None and value!=vdef]</code>
</format>
<ctrl>
<message>
<text lang="en">Value greater than or equal to 0 is required</text>
</message>
<code proglang="python">value >= 0</code>
</ctrl>
<argpos>15</argpos>
</parameter>
<parameter>
<name>e_margin</name>
<prompt lang="en">Margin around sequence for numbering. (value greater than or equal to 0)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>10</value>
</vdef>
<format>
<code proglang="python">("", " -margin=" + str(value))[value is not None and value!=vdef]</code>
</format>
<ctrl>
<message>
<text lang="en">Value greater than or equal to 0 is required</text>
</message>
<code proglang="python">value >= 0</code>
</ctrl>
<argpos>16</argpos>
</parameter>
<parameter>
<name>e_name</name>
<prompt lang="en">Display sequence id</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -noname", "")[ bool(value) ]</code>
</format>
<argpos>17</argpos>
<comment>
<text lang="en">Set this to be false if you do not wish to display the ID name of the sequence.</text>
</comment>
</parameter>
<parameter>
<name>e_description</name>
<prompt lang="en">Display description</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -nodescription", "")[ bool(value) ]</code>
</format>
<argpos>18</argpos>
<comment>
<text lang="en">Set this to be false if you do not wish to display the description of the sequence.</text>
</comment>
</parameter>
<parameter>
<name>e_offset</name>
<prompt lang="en">Offset to start numbering the sequence from</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">("", " -offset=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>19</argpos>
<comment>
<text lang="en">Number from which you want the DNA sequence to be numbered.</text>
</comment>
</parameter>
<parameter>
<name>e_html</name>
<prompt lang="en">Use html formatting</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -html")[ bool(value) ]</code>
</format>
<argpos>20</argpos>
</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>21</argpos>
</parameter>
</parameters>
</program>
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