/var/lib/mobyle/programs/showfeat.xml is in mobyle-programs 5.1.2-1.
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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>showfeat</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>showfeat</title>
<description>
<text lang="en">Display features of a sequence in pretty format</text>
</description>
<doclink>http://bioweb2.pasteur.fr/docs/EMBOSS/showfeat.html</doclink>
<doclink>http://emboss.sourceforge.net/docs/themes</doclink>
</doc>
<category>display:feature_table</category>
<command>showfeat</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_additional</name>
<prompt lang="en">Additional section</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>2</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>3</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_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>4</argpos>
<comment>
<text lang="en">Tags are the types of extra values that a feature may have. For example in the EMBL feature table, a 'CDS' type of feature may have the tags '/codon', '/codon_start', '/db_xref', '/EC_number', '/evidence', '/exception', '/function', '/gene', '/label', '/map', '/note', '/number', '/partial', '/product', '/protein_id', '/pseudo', '/standard_name', '/translation', '/transl_except', '/transl_table', or '/usedin'. Some of these tags also have values, for example '/gene' can have the value of the gene name.
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>5</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. For example in the EMBL feature table, a 'CDS' type of feature may have the tags '/codon', '/codon_start', '/db_xref', '/EC_number', '/evidence', '/exception', '/function', '/gene', '/label', '/map', '/note', '/number', '/partial', '/product', '/protein_id', '/pseudo', '/standard_name', '/translation', '/transl_except', '/transl_table', or '/usedin'. Only some of these tags can have values, for example '/gene' can have the value of the gene name. 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_sort</name>
<prompt lang="en">Sorting features</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>start</value>
</vdef>
<vlist>
<velem>
<value>source</value>
<label>Sort by source</label>
</velem>
<velem>
<value>start</value>
<label>Sort by start position</label>
</velem>
<velem>
<value>type</value>
<label>Sort by type</label>
</velem>
<velem>
<value>nosort</value>
<label>No sorting done</label>
</velem>
</vlist>
<format>
<code proglang="python">("", " -sort=" + str(value))[value is not None and value!=vdef]</code>
</format>
<argpos>6</argpos>
</parameter>
<parameter>
<name>e_joinfeatures</name>
<prompt lang="en">Join coding regions together</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -joinfeatures")[ bool(value) ]</code>
</format>
<argpos>7</argpos>
</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>8</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>
</parameters>
</paragraph>
<paragraph>
<name>e_advanced</name>
<prompt lang="en">Advanced section</prompt>
<parameters>
<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>9</argpos>
</parameter>
<parameter>
<name>e_id</name>
<prompt lang="en">Show sequence id</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -noid", "")[ bool(value) ]</code>
</format>
<argpos>10</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>11</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_scale</name>
<prompt lang="en">Show scale line</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -noscale", "")[ bool(value) ]</code>
</format>
<argpos>12</argpos>
<comment>
<text lang="en">Set this to be false if you do not wish to display the scale line.</text>
</comment>
</parameter>
<parameter>
<name>e_width</name>
<prompt lang="en">Width of graphics lines (value greater than or equal to 0)</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 0 is required</text>
</message>
<code proglang="python">value >= 0</code>
</ctrl>
<argpos>13</argpos>
<comment>
<text lang="en">You can expand (or contract) the width of the ASCII-character graphics display of the positions of the features using this value.
For example, a width of 80 characters would cover a standard page width and a width a 10 characters would be nearly unreadable.
If the width is set to less than 4, the graphics lines and the scale line will not be displayed.</text>
</comment>
</parameter>
<parameter>
<name>e_collapse</name>
<prompt lang="en">Display features with the same type on one line</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -collapse")[ bool(value) ]</code>
</format>
<argpos>14</argpos>
<comment>
<text lang="en">If this is set, then features from the same source and of the same type and sense are all printed on the same line. For instance if there are several features from the EMBL feature table (ie. the same source) which are all of type 'exon' in the same sense, then they will all be displayed on the same line. This makes it hard to distinguish overlapping features.
If this is set to false then each feature is displayed on a separate line making it easier to distinguish where features start and end.</text>
</comment>
</parameter>
<parameter>
<name>e_forward</name>
<prompt lang="en">Display forward sense features</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -noforward", "")[ bool(value) ]</code>
</format>
<argpos>15</argpos>
<comment>
<text lang="en">Set this to be false if you do not wish to display forward sense features.</text>
</comment>
</parameter>
<parameter>
<name>e_reverse</name>
<prompt lang="en">Display reverse sense features</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -noreverse", "")[ bool(value) ]</code>
</format>
<argpos>16</argpos>
<comment>
<text lang="en">Set this to be false if you do not wish to display reverse sense features.</text>
</comment>
</parameter>
<parameter>
<name>e_unknown</name>
<prompt lang="en">Display unknown sense features</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -nounknown", "")[ bool(value) ]</code>
</format>
<argpos>17</argpos>
<comment>
<text lang="en">Set this to be false if you do not wish to display unknown sense features. (ie. features with no directionality - all protein features are of this type and some nucleic features (for example, CG-rich regions)).</text>
</comment>
</parameter>
<parameter>
<name>e_strand</name>
<prompt lang="en">Display strand of features</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -strand")[ bool(value) ]</code>
</format>
<argpos>18</argpos>
<comment>
<text lang="en">Set this if you wish to display the strand of the features. Protein features are always directionless (indicated by '0'), forward is indicated by '+' and reverse is '-'.</text>
</comment>
</parameter>
<parameter>
<name>e_origin</name>
<prompt lang="en">Display source of features</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -origin")[ bool(value) ]</code>
</format>
<argpos>19</argpos>
<comment>
<text lang="en">Set this if you wish to display the origin of the features.
The source name is usually either the name of the program that detected the feature or it is the name of the feature table (eg: EMBL) that the feature came from.</text>
</comment>
</parameter>
<parameter>
<name>e_position</name>
<prompt lang="en">Display position of features</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -position")[ bool(value) ]</code>
</format>
<argpos>20</argpos>
<comment>
<text lang="en">Set this if you wish to display the start and end position of the features. If several features are being displayed on the same line, then the start and end positions will be joined by a comma, for example: '189-189,225-225'.</text>
</comment>
</parameter>
<parameter>
<name>e_type</name>
<prompt lang="en">Display type of features</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -notype", "")[ bool(value) ]</code>
</format>
<argpos>21</argpos>
<comment>
<text lang="en">Set this to be false if you do not wish to display the type of the features.</text>
</comment>
</parameter>
<parameter>
<name>e_tags</name>
<prompt lang="en">Display tags of features</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="python">("", " -tags")[ bool(value) ]</code>
</format>
<argpos>22</argpos>
<comment>
<text lang="en">Set this to be false if you do not wish to display the tags and values of the features.</text>
</comment>
</parameter>
<parameter>
<name>e_values</name>
<prompt lang="en">Display tag values of features</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="python">(" -novalues", "")[ bool(value) ]</code>
</format>
<argpos>23</argpos>
<comment>
<text lang="en">Set this to be false if you do not wish to display the tag values of the features. If this is set to be false, only the tag names will be displayed. If the tags are not displayed, then the values will not be displayed. The value of the 'translation' tag is never displayed as it is often extremely long.</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>24</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>
<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>outfile.showfeat</value>
</vdef>
<format>
<code proglang="python">("" , " -outfile=" + str(value))[value is not None]</code>
</format>
<argpos>25</argpos>
</parameter>
<parameter isout="1">
<name>e_outfile_out</name>
<prompt lang="en">outfile_out option</prompt>
<type>
<datatype>
<class>ShowfeatReport</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>26</argpos>
</parameter>
</parameters>
</program>
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