/var/lib/mobyle/programs/showpep.xml is in mobyle-programs 5.1.2-1.
This file is owned by root:root, with mode 0o644.
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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>showpep</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>showpep</title>
<description>
<text lang="en">Displays protein sequences with features in pretty format</text>
</description>
<doclink>http://bioweb2.pasteur.fr/docs/EMBOSS/showpep.html</doclink>
<doclink>http://emboss.sourceforge.net/docs/themes</doclink>
</doc>
<category>display</category>
<command>showpep</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>Protein</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>
</parameters>
</paragraph>
<paragraph>
<name>e_required</name>
<prompt lang="en">Required section</prompt>
<parameters>
<parameter issimple="1" ismandatory="1">
<name>e_format</name>
<prompt lang="en">Things to display</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>2</value>
</vdef>
<vlist>
<velem>
<value>0</value>
<label>Enter your own list of things to display</label>
</velem>
<velem>
<value>1</value>
<label>Sequence only</label>
</velem>
<velem>
<value>2</value>
<label>Default sequence with features</label>
</velem>
<velem>
<value>3</value>
<label>Pretty sequence 4</label>
</velem>
</vlist>
<format>
<code proglang="python">("", " -format=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>2</argpos>
</parameter>
<parameter>
<name>e_things</name>
<prompt lang="en">Specify your own things to display (value from 1 to 100)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<precond>
<code proglang="python">e_format=="0"</code>
</precond>
<vdef>
<value>B,N,T,S,A,F</value>
</vdef>
<format>
<code proglang="python">("", " -things=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>3</argpos>
<comment>
<text lang="en">Specify a list of one or more code characters in the order in which you wish things to be displayed one above the other down the page. For example if you wish to see things displayed in the order: sequence, ticks line, blank line; then you should enter 'S,T,B'.</text>
<text lang="en">S: Sequence</text>
<text lang="en">B: Blank line</text>
<text lang="en">T: Ticks line</text>
<text lang="en">N: Number ticks line</text>
<text lang="en">F: Features</text>
<text lang="en">A: Annotation</text>
<text lang="en">For example if you wish to see things displayed in the order: sequence, ticks line, blank line; then you should enter 'S,T,B'.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>e_additional</name>
<prompt lang="en">Additional section</prompt>
<parameters>
<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>4</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>5</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_annotation</name>
<prompt lang="en">Regions to mark (eg: 4-57 promoter region 78-94 first exon)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="python">("", " -annotation=" + str(value))[value is not None]</code>
</format>
<argpos>6</argpos>
<comment>
<text lang="en">Regions to annotate by marking.
If this is left blank, then no annotation is added.
A set of regions is specified by a set of pairs of positions followed by optional text.
The positions are integers.
They are followed by any text (but not digits when on the command-line).
Examples of region specifications are:
24-45 new domain 56-78 match to Mouse
1-100 First part 120-156 oligo
A file of ranges to annotate (one range per line) can be specified as '@filename'.</text>
</comment>
</parameter>
<paragraph>
<name>e_featuresection</name>
<prompt lang="en">Feature display options</prompt>
<parameters>
<parameter>
<name>e_sourcematch</name>
<prompt lang="en">Source of feature to display</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="python">("", " -sourcematch=" + str(value))[value is not None]</code>
</format>
<argpos>7</argpos>
<comment>
<text lang="en">By default any feature source in the feature table is shown. You can set this to match any feature source you wish to show.
The source name is usually either the name of the program that detected the feature or it is the feature table (eg: EMBL) that the feature came from.
The source may be wildcarded by using '*'.
If you wish to show more than one source, separate their names with the character '|', eg:
gene* | embl</text>
</comment>
</parameter>
<parameter>
<name>e_typematch</name>
<prompt lang="en">Type of feature to display</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="python">("", " -typematch=" + str(value))[value is not None]</code>
</format>
<argpos>8</argpos>
<comment>
<text lang="en">By default any feature type in the feature table is shown. You can set this to match any feature type you wish to show.
See http://www.ebi.ac.uk/embl/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www.expasy.org/sprot/userman.html for a list of the Swissprot feature types.
The type may be wildcarded by using '*'.
If you wish to show more than one type, separate their names with the character '|', eg:
*UTR | intron</text>
</comment>
</parameter>
<parameter>
<name>e_minscore</name>
<prompt lang="en">Minimum score of feature to display</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>0.0</value>
</vdef>
<format>
<code proglang="python">("", " -minscore=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>9</argpos>
<comment>
<text lang="en">Minimum score of feature to display (see also maxscore)</text>
</comment>
</parameter>
<parameter>
<name>e_maxscore</name>
<prompt lang="en">Maximum score of feature to display</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>0.0</value>
</vdef>
<format>
<code proglang="python">("", " -maxscore=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>10</argpos>
<comment>
<text lang="en">Maximum score of feature to display.
If both minscore and maxscore are zero (the default), then any score is ignored</text>
</comment>
</parameter>
<parameter>
<name>e_tagmatch</name>
<prompt lang="en">Tag of feature to display</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="python">("", " -tagmatch=" + str(value))[value is not None]</code>
</format>
<argpos>11</argpos>
<comment>
<text lang="en">Tags are the types of extra values that a feature may have. By default any feature tag in the feature table is shown. You can set this to match any feature tag you wish to show.
The tag may be wildcarded by using '*'.
If you wish to show more than one tag, separate their names with the character '|', eg:
gene | label</text>
</comment>
</parameter>
<parameter>
<name>e_valuematch</name>
<prompt lang="en">Value of feature tags to display</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="python">("", " -valuematch=" + str(value))[value is not None]</code>
</format>
<argpos>12</argpos>
<comment>
<text lang="en">Tag values are the values associated with a feature tag. Tags are the types of extra values that a feature may have. By default any feature tag value in the feature table is shown. You can set this to match any feature tag value you wish to show.
The tag value may be wildcarded by using '*'.
If you wish to show more than one tag value, separate their names with the character '|', eg:
pax* | 10</text>
</comment>
</parameter>
<parameter>
<name>e_stricttags</name>
<prompt lang="en">Only display the matching tags</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -stricttags")[ bool(value) ]</code>
</format>
<argpos>13</argpos>
<comment>
<text lang="en">By default if any tag/value pair in a feature matches the specified tag and value, then all the tags/value pairs of that feature will be displayed. If this is set to be true, then only those tag/value pairs in a feature that match the specified tag and value will be displayed.</text>
</comment>
</parameter>
</parameters>
</paragraph>
</parameters>
</paragraph>
<paragraph>
<name>e_advanced</name>
<prompt lang="en">Advanced section</prompt>
<parameters>
<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>14</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>15</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>16</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>17</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>18</argpos>
</parameter>
<parameter>
<name>e_name</name>
<prompt lang="en">Show 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>19</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">Show description</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -nodescription", "")[ bool(value) ]</code>
</format>
<argpos>20</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>21</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>22</argpos>
</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>showpep.e_outfile</value>
</vdef>
<format>
<code proglang="python">("" , " -outfile=" + str(value))[value is not None]</code>
</format>
<argpos>23</argpos>
</parameter>
<parameter isout="1">
<name>e_outfile_out</name>
<prompt lang="en">outfile_out option</prompt>
<type>
<datatype>
<class>ShowpepReport</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>24</argpos>
</parameter>
</parameters>
</program>
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