Mercurial > repos > xuebing > sharplabtool
comparison tools/emboss_5/emboss_showfeat.xml @ 0:9071e359b9a3
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| author | xuebing |
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| date | Fri, 09 Mar 2012 19:37:19 -0500 |
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| -1:000000000000 | 0:9071e359b9a3 |
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| 1 <tool id="EMBOSS: showfeat85" name="showfeat" version="5.0.0"> | |
| 2 <!-- tool gives memory errors --> | |
| 3 <description>Show features of a sequence</description> | |
| 4 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> | |
| 5 <command>showfeat -sequence $input1 -outfile $out_file1 -matchsource "$matchsource" -matchtype "$matchtype" -matchtag "$matchtag" -matchvalue "$matchvalue" -sort $sort -annotation "$annotation" -id | |
| 6 $id -description "$description" -scale "$scale" -width "$width" -collapse $collapse -forward $forward -reverse $reverse -unknown $unknown -strand $strand -source $source -position $position -type | |
| 7 $type -tags $tags -values $values -stricttags $stricttags -html $html_out1 -auto</command> | |
| 8 <inputs> | |
| 9 <param format="data" name="input1" type="data"> | |
| 10 <label>Sequences</label> | |
| 11 </param> | |
| 12 <param name="html_out1" type="select"> | |
| 13 <label>Format output as an HTML table</label> | |
| 14 <option value="no">No</option> | |
| 15 <option value="yes">Yes</option> | |
| 16 </param> | |
| 17 <param name="matchsource" size="50" type="text" value="*"> | |
| 18 <label>Feature source to match</label> | |
| 19 </param> | |
| 20 <param name="matchtype" size="50" type="text" value="*"> | |
| 21 <label>Feature type to match</label> | |
| 22 </param> | |
| 23 <param name="matchtag" size="50" type="text" value="*"> | |
| 24 <label>Feature tags to match</label> | |
| 25 </param> | |
| 26 <param name="matchvalue" size="50" type="text" value="*"> | |
| 27 <label>Tag values to match</label> | |
| 28 </param> | |
| 29 <param name="sort" type="select"> | |
| 30 <label>Sort by</label> | |
| 31 <option value="start">Start position</option> | |
| 32 <option value="source">Source</option> | |
| 33 <option value="type">Type</option> | |
| 34 <option value="nosort">No sorting done</option> | |
| 35 <option value="join">Join coding regions together</option> | |
| 36 </param> | |
| 37 <param name="annotation" size="50" type="text" value=""> | |
| 38 <label>Regions to annotate by marking</label> | |
| 39 </param> | |
| 40 <param name="id" type="select"> | |
| 41 <label>Display the ID name of the sequence</label> | |
| 42 <option value="yes">Yes</option> | |
| 43 <option value="no">No</option> | |
| 44 </param> | |
| 45 <param name="description" type="select"> | |
| 46 <label>Display the description of the sequence</label> | |
| 47 <option value="yes">Yes</option> | |
| 48 <option value="no">No</option> | |
| 49 </param> | |
| 50 <param name="scale" type="select"> | |
| 51 <label>Display the scale line</label> | |
| 52 <option value="yes">Yes</option> | |
| 53 <option value="no">No</option> | |
| 54 </param> | |
| 55 <param name="width" size="50" type="text" value="60"> | |
| 56 <label>Screen width</label> | |
| 57 </param> | |
| 58 <param name="collapse" type="select"> | |
| 59 <label>Collapse features</label> | |
| 60 <option value="no">No</option> | |
| 61 <option value="yes">Yes</option> | |
| 62 </param> | |
| 63 <param name="forward" type="select"> | |
| 64 <label>Display forward sense features</label> | |
| 65 <option value="yes">Yes</option> | |
| 66 <option value="no">No</option> | |
| 67 </param> | |
| 68 <param name="reverse" type="select"> | |
| 69 <label>Display reverse sense features</label> | |
| 70 <option value="yes">Yes</option> | |
| 71 <option value="no">No</option> | |
| 72 </param> | |
| 73 <param name="unknown" type="select"> | |
| 74 <label>Display unknown sense features</label> | |
| 75 <option value="yes">Yes</option> | |
| 76 <option value="no">No</option> | |
| 77 </param> | |
| 78 <param name="strand" type="select"> | |
| 79 <label>Display the strand of the features</label> | |
| 80 <option value="no">No</option> | |
| 81 <option value="yes">Yes</option> | |
| 82 </param> | |
| 83 <param name="source" type="select"> | |
| 84 <label>Display the source of the features</label> | |
| 85 <option value="no">No</option> | |
| 86 <option value="yes">Yes</option> | |
| 87 </param> | |
| 88 <param name="position" type="select"> | |
| 89 <label>SDisplay the start and end position of the features</label> | |
| 90 <option value="no">No</option> | |
| 91 <option value="yes">Yes</option> | |
| 92 </param> | |
| 93 <param name="type" type="select"> | |
| 94 <label>Display the type of the features</label> | |
| 95 <option value="yes">Yes</option> | |
| 96 <option value="no">No</option> | |
| 97 </param> | |
| 98 <param name="tags" type="select"> | |
| 99 <label>Display the tags and values of the features</label> | |
| 100 <option value="no">No</option> | |
| 101 <option value="yes">Yes</option> | |
| 102 </param> | |
| 103 <param name="values" type="select"> | |
| 104 <label>Display the tag values of the features</label> | |
| 105 <option value="yes">Yes</option> | |
| 106 <option value="no">No</option> | |
| 107 </param> | |
| 108 <param name="stricttags" type="select"> | |
| 109 <label>Display only those tag/value pairs in a feature that match the specified tag and value</label> | |
| 110 <option value="no">No</option> | |
| 111 <option value="yes">Yes</option> | |
| 112 </param> | |
| 113 </inputs> | |
| 114 <outputs> | |
| 115 <data format="showfeat" name="out_file1" /> | |
| 116 </outputs> | |
| 117 <code file="emboss_format_corrector.py" /> | |
| 118 <help> | |
| 119 You can view the original documentation here_. | |
| 120 | |
| 121 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/showfeat.html | |
| 122 </help> | |
| 123 </tool> |