[2] | 1 | <tool id="EMBOSS: showfeat85" name="showfeat" version="5.0.0">
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| 2 | <!-- tool gives memory errors --> |
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| 3 | <description>Show features of a sequence</description>
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| 4 | <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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| 5 | <command>showfeat -sequence $input1 -outfile $out_file1 -matchsource "$matchsource" -matchtype "$matchtype" -matchtag "$matchtag" -matchvalue "$matchvalue" -sort $sort -annotation "$annotation" -id
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| 6 | $id -description "$description" -scale "$scale" -width "$width" -collapse $collapse -forward $forward -reverse $reverse -unknown $unknown -strand $strand -source $source -position $position -type
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| 7 | $type -tags $tags -values $values -stricttags $stricttags -html $html_out1 -auto</command>
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| 8 | <inputs>
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| 9 | <param format="data" name="input1" type="data">
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| 10 | <label>Sequences</label>
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| 11 | </param>
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| 12 | <param name="html_out1" type="select">
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| 13 | <label>Format output as an HTML table</label>
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| 14 | <option value="no">No</option>
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| 15 | <option value="yes">Yes</option>
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| 16 | </param>
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| 17 | <param name="matchsource" size="50" type="text" value="*">
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| 18 | <label>Feature source to match</label>
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| 19 | </param>
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| 20 | <param name="matchtype" size="50" type="text" value="*">
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| 21 | <label>Feature type to match</label>
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| 22 | </param>
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| 23 | <param name="matchtag" size="50" type="text" value="*">
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| 24 | <label>Feature tags to match</label>
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| 25 | </param>
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| 26 | <param name="matchvalue" size="50" type="text" value="*">
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| 27 | <label>Tag values to match</label>
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| 28 | </param>
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| 29 | <param name="sort" type="select">
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| 30 | <label>Sort by</label>
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| 31 | <option value="start">Start position</option>
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| 32 | <option value="source">Source</option>
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| 33 | <option value="type">Type</option>
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| 34 | <option value="nosort">No sorting done</option>
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| 35 | <option value="join">Join coding regions together</option>
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| 36 | </param>
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| 37 | <param name="annotation" size="50" type="text" value="">
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| 38 | <label>Regions to annotate by marking</label>
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| 39 | </param>
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| 40 | <param name="id" type="select">
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| 41 | <label>Display the ID name of the sequence</label>
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| 42 | <option value="yes">Yes</option>
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| 43 | <option value="no">No</option>
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| 44 | </param>
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| 45 | <param name="description" type="select">
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| 46 | <label>Display the description of the sequence</label>
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| 47 | <option value="yes">Yes</option>
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| 48 | <option value="no">No</option>
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| 49 | </param>
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| 50 | <param name="scale" type="select">
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| 51 | <label>Display the scale line</label>
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| 52 | <option value="yes">Yes</option>
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| 53 | <option value="no">No</option>
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| 54 | </param>
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| 55 | <param name="width" size="50" type="text" value="60">
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| 56 | <label>Screen width</label>
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| 57 | </param>
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| 58 | <param name="collapse" type="select">
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| 59 | <label>Collapse features</label>
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| 60 | <option value="no">No</option>
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| 61 | <option value="yes">Yes</option>
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| 62 | </param>
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| 63 | <param name="forward" type="select">
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| 64 | <label>Display forward sense features</label>
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| 65 | <option value="yes">Yes</option>
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| 66 | <option value="no">No</option>
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| 67 | </param>
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| 68 | <param name="reverse" type="select">
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| 69 | <label>Display reverse sense features</label>
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| 70 | <option value="yes">Yes</option>
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| 71 | <option value="no">No</option>
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| 72 | </param>
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| 73 | <param name="unknown" type="select">
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| 74 | <label>Display unknown sense features</label>
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| 75 | <option value="yes">Yes</option>
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| 76 | <option value="no">No</option>
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| 77 | </param>
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| 78 | <param name="strand" type="select">
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| 79 | <label>Display the strand of the features</label>
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| 80 | <option value="no">No</option>
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| 81 | <option value="yes">Yes</option>
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| 82 | </param>
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| 83 | <param name="source" type="select">
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| 84 | <label>Display the source of the features</label>
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| 85 | <option value="no">No</option>
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| 86 | <option value="yes">Yes</option>
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| 87 | </param>
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| 88 | <param name="position" type="select">
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| 89 | <label>SDisplay the start and end position of the features</label>
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| 90 | <option value="no">No</option>
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| 91 | <option value="yes">Yes</option>
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| 92 | </param>
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| 93 | <param name="type" type="select">
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| 94 | <label>Display the type of the features</label>
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| 95 | <option value="yes">Yes</option>
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| 96 | <option value="no">No</option>
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| 97 | </param>
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| 98 | <param name="tags" type="select">
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| 99 | <label>Display the tags and values of the features</label>
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| 100 | <option value="no">No</option>
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| 101 | <option value="yes">Yes</option>
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| 102 | </param>
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| 103 | <param name="values" type="select">
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| 104 | <label>Display the tag values of the features</label>
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| 105 | <option value="yes">Yes</option>
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| 106 | <option value="no">No</option>
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| 107 | </param>
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| 108 | <param name="stricttags" type="select">
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| 109 | <label>Display only those tag/value pairs in a feature that match the specified tag and value</label>
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| 110 | <option value="no">No</option>
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| 111 | <option value="yes">Yes</option>
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| 112 | </param>
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| 113 | </inputs>
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| 114 | <outputs>
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| 115 | <data format="showfeat" name="out_file1" />
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| 116 | </outputs>
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| 117 | <code file="emboss_format_corrector.py" />
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| 118 | <help> |
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| 119 | You can view the original documentation here_. |
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| 120 | |
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| 121 | .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/showfeat.html |
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| 122 | </help> |
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| 123 | </tool> |
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