mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-24 02:04:04 +08:00
123 lines
5.0 KiB
XML
123 lines
5.0 KiB
XML
<tool id="EMBOSS: showfeat85" name="showfeat" version="5.0.0">
|
|
<!-- tool gives memory errors -->
|
|
<description>Show features of a sequence</description>
|
|
<requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
|
|
<command>showfeat -sequence $input1 -outfile $out_file1 -matchsource "$matchsource" -matchtype "$matchtype" -matchtag "$matchtag" -matchvalue "$matchvalue" -sort $sort -annotation "$annotation" -id
|
|
$id -description "$description" -scale "$scale" -width "$width" -collapse $collapse -forward $forward -reverse $reverse -unknown $unknown -strand $strand -source $source -position $position -type
|
|
$type -tags $tags -values $values -stricttags $stricttags -html $html_out1 -auto</command>
|
|
<inputs>
|
|
<param format="data" name="input1" type="data">
|
|
<label>Sequences</label>
|
|
</param>
|
|
<param name="html_out1" type="select">
|
|
<label>Format output as an HTML table</label>
|
|
<option value="no">No</option>
|
|
<option value="yes">Yes</option>
|
|
</param>
|
|
<param name="matchsource" size="50" type="text" value="*">
|
|
<label>Feature source to match</label>
|
|
</param>
|
|
<param name="matchtype" size="50" type="text" value="*">
|
|
<label>Feature type to match</label>
|
|
</param>
|
|
<param name="matchtag" size="50" type="text" value="*">
|
|
<label>Feature tags to match</label>
|
|
</param>
|
|
<param name="matchvalue" size="50" type="text" value="*">
|
|
<label>Tag values to match</label>
|
|
</param>
|
|
<param name="sort" type="select">
|
|
<label>Sort by</label>
|
|
<option value="start">Start position</option>
|
|
<option value="source">Source</option>
|
|
<option value="type">Type</option>
|
|
<option value="nosort">No sorting done</option>
|
|
<option value="join">Join coding regions together</option>
|
|
</param>
|
|
<param name="annotation" size="50" type="text" value="">
|
|
<label>Regions to annotate by marking</label>
|
|
</param>
|
|
<param name="id" type="select">
|
|
<label>Display the ID name of the sequence</label>
|
|
<option value="yes">Yes</option>
|
|
<option value="no">No</option>
|
|
</param>
|
|
<param name="description" type="select">
|
|
<label>Display the description of the sequence</label>
|
|
<option value="yes">Yes</option>
|
|
<option value="no">No</option>
|
|
</param>
|
|
<param name="scale" type="select">
|
|
<label>Display the scale line</label>
|
|
<option value="yes">Yes</option>
|
|
<option value="no">No</option>
|
|
</param>
|
|
<param name="width" size="50" type="text" value="60">
|
|
<label>Screen width</label>
|
|
</param>
|
|
<param name="collapse" type="select">
|
|
<label>Collapse features</label>
|
|
<option value="no">No</option>
|
|
<option value="yes">Yes</option>
|
|
</param>
|
|
<param name="forward" type="select">
|
|
<label>Display forward sense features</label>
|
|
<option value="yes">Yes</option>
|
|
<option value="no">No</option>
|
|
</param>
|
|
<param name="reverse" type="select">
|
|
<label>Display reverse sense features</label>
|
|
<option value="yes">Yes</option>
|
|
<option value="no">No</option>
|
|
</param>
|
|
<param name="unknown" type="select">
|
|
<label>Display unknown sense features</label>
|
|
<option value="yes">Yes</option>
|
|
<option value="no">No</option>
|
|
</param>
|
|
<param name="strand" type="select">
|
|
<label>Display the strand of the features</label>
|
|
<option value="no">No</option>
|
|
<option value="yes">Yes</option>
|
|
</param>
|
|
<param name="source" type="select">
|
|
<label>Display the source of the features</label>
|
|
<option value="no">No</option>
|
|
<option value="yes">Yes</option>
|
|
</param>
|
|
<param name="position" type="select">
|
|
<label>SDisplay the start and end position of the features</label>
|
|
<option value="no">No</option>
|
|
<option value="yes">Yes</option>
|
|
</param>
|
|
<param name="type" type="select">
|
|
<label>Display the type of the features</label>
|
|
<option value="yes">Yes</option>
|
|
<option value="no">No</option>
|
|
</param>
|
|
<param name="tags" type="select">
|
|
<label>Display the tags and values of the features</label>
|
|
<option value="no">No</option>
|
|
<option value="yes">Yes</option>
|
|
</param>
|
|
<param name="values" type="select">
|
|
<label>Display the tag values of the features</label>
|
|
<option value="yes">Yes</option>
|
|
<option value="no">No</option>
|
|
</param>
|
|
<param name="stricttags" type="select">
|
|
<label>Display only those tag/value pairs in a feature that match the specified tag and value</label>
|
|
<option value="no">No</option>
|
|
<option value="yes">Yes</option>
|
|
</param>
|
|
</inputs>
|
|
<outputs>
|
|
<data format="showfeat" name="out_file1" />
|
|
</outputs>
|
|
<code file="emboss_format_corrector.py" />
|
|
<help>
|
|
You can view the original documentation here_.
|
|
|
|
.. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/showfeat.html
|
|
</help>
|
|
</tool> |