/var/lib/mobyle/programs/remap.xml is in mobyle-programs 5.1.1-1.
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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>remap</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>remap</title>
<description>
<text lang="en">Display restriction enzyme binding sites in a nucleotide sequence</text>
</description>
<doclink>http://bioweb2.pasteur.fr/docs/EMBOSS/remap.html</doclink>
<doclink>http://emboss.sourceforge.net/docs/themes</doclink>
</doc>
<category>display:nucleic:restriction</category>
<category>display:nucleic:translation</category>
<command>remap</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,n</card>
</type>
<format>
<code proglang="python">("", " -sequence=" + str(value))[value is not None]</code>
</format>
<argpos>1</argpos>
</parameter>
<parameter>
<name>e_mfile</name>
<prompt lang="en">Restriction enzyme methylation data file</prompt>
<type>
<datatype>
<class>RestrictionEnzymeMethylationData</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<format>
<code proglang="python">("", " -mfile=" + str(value))[value is not None ]</code>
</format>
<argpos>2</argpos>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>e_required</name>
<prompt lang="en">Required section</prompt>
<parameters>
<parameter issimple="1" ismandatory="1">
<name>e_enzymes</name>
<prompt lang="en">Comma separated enzyme list</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<vdef>
<value>all</value>
</vdef>
<format>
<code proglang="python">("", " -enzymes=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>3</argpos>
<comment>
<text lang="en">The name 'all' reads in all enzyme names from the REBASE database. You can specify enzymes by giving their names with commas between then, such as: 'HincII,hinfI,ppiI,hindiii'.
The case of the names is not important. You can specify a file of enzyme names to read in by giving the name of the file holding the enzyme names with a '@' character in front of it, for example, '@enz.list'.
Blank lines and lines starting with a hash character or '!' are ignored and all other lines are concatenated together with a comma character ',' and then treated as the list of enzymes to search for.
An example of a file of enzyme names is:
! my enzymes
HincII, ppiII
! other enzymes
hindiii
HinfI
PpiI</text>
</comment>
</parameter>
<parameter issimple="1" ismandatory="1">
<name>e_sitelen</name>
<prompt lang="en">Minimum recognition site length (value from 2 to 20)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>4</value>
</vdef>
<format>
<code proglang="python">("", " -sitelen=" + str(value))[value is not None and value!=vdef]</code>
</format>
<ctrl>
<message>
<text lang="en">Value greater than or equal to 2 is required</text>
</message>
<code proglang="python">value >= 2</code>
</ctrl>
<ctrl>
<message>
<text lang="en">Value less than or equal to 20 is required</text>
</message>
<code proglang="python">value <= 20</code>
</ctrl>
<argpos>4</argpos>
<comment>
<text lang="en">This sets the minimum length of the restriction enzyme recognition site. Any enzymes with sites shorter than this will be ignored.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>e_additional</name>
<prompt lang="en">Additional section</prompt>
<parameters>
<parameter>
<name>e_mincuts</name>
<prompt lang="en">Minimum cuts per re (value from 1 to 1000)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">("", " -mincuts=" + 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>
<ctrl>
<message>
<text lang="en">Value less than or equal to 1000 is required</text>
</message>
<code proglang="python">value <= 1000</code>
</ctrl>
<argpos>5</argpos>
<comment>
<text lang="en">This sets the minimum number of cuts for any restriction enzyme that will be considered. Any enzymes that cut fewer times than this will be ignored.</text>
</comment>
</parameter>
<parameter>
<name>e_maxcuts</name>
<prompt lang="en">Maximum cuts per re</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>2000000000</value>
</vdef>
<format>
<code proglang="python">("", " -maxcuts=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>6</argpos>
<comment>
<text lang="en">This sets the maximum number of cuts for any restriction enzyme that will be considered. Any enzymes that cut more times than this will be ignored.</text>
</comment>
</parameter>
<parameter>
<name>e_single</name>
<prompt lang="en">Force single site only cuts</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -single")[ bool(value) ]</code>
</format>
<argpos>7</argpos>
<comment>
<text lang="en">If this is set then this forces the values of the mincuts and maxcuts qualifiers to both be 1. Any other value you may have set them to will be ignored.</text>
</comment>
</parameter>
<parameter>
<name>e_blunt</name>
<prompt lang="en">Allow blunt end cutters</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -noblunt", "")[ bool(value) ]</code>
</format>
<argpos>8</argpos>
<comment>
<text lang="en">This allows those enzymes which cut at the same position on the forward and reverse strands to be considered.</text>
</comment>
</parameter>
<parameter>
<name>e_sticky</name>
<prompt lang="en">Allow sticky end cutters</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -nosticky", "")[ bool(value) ]</code>
</format>
<argpos>9</argpos>
<comment>
<text lang="en">This allows those enzymes which cut at different positions on the forward and reverse strands, leaving an overhang, to be considered.</text>
</comment>
</parameter>
<parameter>
<name>e_ambiguity</name>
<prompt lang="en">Allow ambiguous matches</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -noambiguity", "")[ bool(value) ]</code>
</format>
<argpos>10</argpos>
<comment>
<text lang="en">This allows those enzymes which have one or more 'N' ambiguity codes in their pattern to be considered</text>
</comment>
</parameter>
<parameter>
<name>e_plasmid</name>
<prompt lang="en">Allow circular dna</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -plasmid")[ bool(value) ]</code>
</format>
<argpos>11</argpos>
<comment>
<text lang="en">If this is set then this allows searches for restriction enzyme recognition site and cut positions that span the end of the sequence to be considered.</text>
</comment>
</parameter>
<parameter>
<name>e_methylation</name>
<prompt lang="en">Use methylation data</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -methylation")[ bool(value) ]</code>
</format>
<argpos>12</argpos>
<comment>
<text lang="en">If this is set then RE recognition sites will not match methylated bases.</text>
</comment>
</parameter>
<parameter>
<name>e_commercial</name>
<prompt lang="en">Only enzymes with suppliers</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -nocommercial", "")[ bool(value) ]</code>
</format>
<argpos>13</argpos>
<comment>
<text lang="en">If this is set, then only those enzymes with a commercial supplier will be searched for. This qualifier is ignored if you have specified an explicit list of enzymes to search for, rather than searching through 'all' the enzymes in the REBASE database. It is assumed that, if you are asking for an explicit enzyme, then you probably know where to get it from and so all enzymes names that you have asked to be searched for, and which cut, will be reported whether or not they have a commercial supplier.</text>
</comment>
</parameter>
<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>14</argpos>
</parameter>
<parameter>
<name>e_frame</name>
<prompt lang="en">Translation frames (value from 1 to 6)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>6</value>
</vdef>
<vlist>
<velem>
<value>1</value>
<label>1</label>
</velem>
<velem>
<value>2</value>
<label>2</label>
</velem>
<velem>
<value>3</value>
<label>3</label>
</velem>
<velem>
<value>F</value>
<label>Forward three frames</label>
</velem>
<velem>
<value>-1</value>
<label>-1</label>
</velem>
<velem>
<value>-2</value>
<label>-2</label>
</velem>
<velem>
<value>-3</value>
<label>-3</label>
</velem>
<velem>
<value>R</value>
<label>Reverse three frames</label>
</velem>
<velem>
<value>6</value>
<label>All six frames</label>
</velem>
</vlist>
<format>
<code proglang="python">("", " -frame=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>15</argpos>
<comment>
<text lang="en">This allows you to specify the frames that are translated. If you are not displaying cut sites on the reverse sense, then the reverse sense translations will not be displayed even if you have requested frames 4, 5 or 6. By default, all six frames will be displayed.</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>remap.e_outfile</value>
</vdef>
<format>
<code proglang="python">("" , " -outfile=" + str(value))[value is not None]</code>
</format>
<argpos>16</argpos>
</parameter>
<parameter isout="1">
<name>e_outfile_out</name>
<prompt lang="en">outfile_out option</prompt>
<type>
<datatype>
<class>RemapReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<filenames>
<code proglang="python">e_outfile</code>
</filenames>
</parameter>
<parameter>
<name>e_cutlist</name>
<prompt lang="en">List the enzymes that cut</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -nocutlist", "")[ bool(value) ]</code>
</format>
<argpos>17</argpos>
<comment>
<text lang="en">This produces lists in the output of the enzymes that cut, those that cut but are excluded because that cut fewer times than mincut or more times than maxcut and those enzymes that do not cut.</text>
</comment>
</parameter>
<parameter>
<name>e_flatreformat</name>
<prompt lang="en">Display re sites in flat format</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -flatreformat")[ bool(value) ]</code>
</format>
<argpos>18</argpos>
<comment>
<text lang="en">This changes the output format to one where the recognition site is indicated by a row of '===' characters and the cut site is pointed to by a '>' character in the forward sense, or a '<' in the reverse sense strand.</text>
</comment>
</parameter>
<parameter>
<name>e_limit</name>
<prompt lang="en">Limits reports to one isoschizomer</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -nolimit", "")[ bool(value) ]</code>
</format>
<argpos>19</argpos>
<comment>
<text lang="en">This limits the reporting of enzymes to just one enzyme from each group of isoschizomers. The enzyme chosen to represent an isoschizomer group is the prototype indicated in the data file 'embossre.equ', which is created by the program 'rebaseextract'. If you prefer different prototypes to be used, make a copy of embossre.equ in your home directory and edit it. If this value is set to be false then all of the input enzymes will be reported. You might like to set this to false if you are supplying an explicit set of enzymes rather than searching 'all' of them.</text>
</comment>
</parameter>
<parameter>
<name>e_translation</name>
<prompt lang="en">Display translation</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -notranslation", "")[ bool(value) ]</code>
</format>
<argpos>20</argpos>
<comment>
<text lang="en">This displays the 6-frame translations of the sequence in the output.</text>
</comment>
</parameter>
<parameter>
<name>e_reverse</name>
<prompt lang="en">Display cut sites and 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>21</argpos>
<comment>
<text lang="en">This displays the cut sites and translation of the reverse sense.</text>
</comment>
</parameter>
<parameter>
<name>e_orfminsize</name>
<prompt lang="en">Minimum size of orfs (value greater than or equal to 0)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>0</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 0 is required</text>
</message>
<code proglang="python">value >= 0</code>
</ctrl>
<argpos>22</argpos>
<comment>
<text lang="en">This sets the minimum size of Open Reading Frames (ORFs) to display in the translations. All other translation regions are masked by changing the amino acids to '-' characters.</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>23</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>24</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_threeletter</name>
<prompt lang="en">Display protein sequences in three-letter code</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -threeletter")[ bool(value) ]</code>
</format>
<argpos>25</argpos>
</parameter>
<parameter>
<name>e_number</name>
<prompt lang="en">Number the sequences</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -number")[ bool(value) ]</code>
</format>
<argpos>26</argpos>
</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>27</argpos>
</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>28</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>29</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>30</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>31</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>32</argpos>
</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>33</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>34</argpos>
</parameter>
</parameters>
</program>
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