Mercurial > repos > devteam > emboss_5
comparison emboss_showfeat.xml @ 11:0e2484b6829b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
| author | iuc |
|---|---|
| date | Mon, 30 Jan 2017 13:27:40 -0500 |
| parents | 9b98d3d903c6 |
| children | 27c43fb015f0 |
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| 10:9b98d3d903c6 | 11:0e2484b6829b |
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| 1 <tool id="EMBOSS: showfeat85" name="showfeat" version="5.0.0"> | 1 <tool id="EMBOSS: showfeat85" name="showfeat" version="5.0.0.1"> |
| 2 <!-- tool gives memory errors --> | 2 <!-- tool gives memory errors --> |
| 3 <description>Show features of a sequence</description> | 3 <description>Show features of a sequence</description> |
| 4 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> | 4 <macros> |
| 5 <command>showfeat -sequence $input1 -outfile $out_file1 -matchsource "$matchsource" -matchtype "$matchtype" -matchtag "$matchtag" -matchvalue "$matchvalue" -sort $sort -annotation "$annotation" -id | 5 <import>macros.xml</import> |
| 6 $id -description "$description" -scale "$scale" -width "$width" -collapse $collapse -forward $forward -reverse $reverse -unknown $unknown -strand $strand -source $source -position $position -type | 6 </macros> |
| 7 <expand macro="requirements" /> | |
| 8 <code file="emboss_format_corrector.py" /> | |
| 9 <command>showfeat -sequence '$input1' -outfile '$out_file1' -matchsource '$matchsource' -matchtype '$matchtype' -matchtag '$matchtag' -matchvalue '$matchvalue' -sort $sort -annotation '$annotation' -id | |
| 10 $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> | 11 $type -tags $tags -values $values -stricttags $stricttags -html $html_out1 -auto</command> |
| 8 <inputs> | 12 <inputs> |
| 9 <param format="data" name="input1" type="data"> | 13 <param name="input1" type="data" format="data" label="Sequences" /> |
| 10 <label>Sequences</label> | 14 <param name="html_out1" type="select" label="Format output as an HTML table"> |
| 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="no">No</option> |
| 15 <option value="yes">Yes</option> | 16 <option value="yes">Yes</option> |
| 16 </param> | 17 </param> |
| 17 <param name="matchsource" type="text" value="*"> | 18 <param name="matchsource" type="text" value="*" label="Feature source to match" /> |
| 18 <label>Feature source to match</label> | 19 <param name="matchtype" type="text" value="*" label="Feature type to match" /> |
| 19 </param> | 20 <param name="matchtag" type="text" value="*" label="Feature tags to match" /> |
| 20 <param name="matchtype" type="text" value="*"> | 21 <param name="matchvalue" type="text" value="*" label="Tag values to match" /> |
| 21 <label>Feature type to match</label> | 22 <param name="sort" type="select" label="Sort by"> |
| 22 </param> | |
| 23 <param name="matchtag" type="text" value="*"> | |
| 24 <label>Feature tags to match</label> | |
| 25 </param> | |
| 26 <param name="matchvalue" 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> | 23 <option value="start">Start position</option> |
| 32 <option value="source">Source</option> | 24 <option value="source">Source</option> |
| 33 <option value="type">Type</option> | 25 <option value="type">Type</option> |
| 34 <option value="nosort">No sorting done</option> | 26 <option value="nosort">No sorting done</option> |
| 35 <option value="join">Join coding regions together</option> | 27 <option value="join">Join coding regions together</option> |
| 36 </param> | 28 </param> |
| 37 <param name="annotation" type="text" value=""> | 29 <param name="annotation" type="text" value="" label="Regions to annotate by marking" /> |
| 38 <label>Regions to annotate by marking</label> | 30 <param name="id" type="select" label="Display the ID name of the sequence"> |
| 39 </param> | |
| 40 <param name="id" type="select"> | |
| 41 <label>Display the ID name of the sequence</label> | |
| 42 <option value="yes">Yes</option> | 31 <option value="yes">Yes</option> |
| 43 <option value="no">No</option> | 32 <option value="no">No</option> |
| 44 </param> | 33 </param> |
| 45 <param name="description" type="select"> | 34 <param name="description" type="select" label="Display the description of the sequence"> |
| 46 <label>Display the description of the sequence</label> | |
| 47 <option value="yes">Yes</option> | 35 <option value="yes">Yes</option> |
| 48 <option value="no">No</option> | 36 <option value="no">No</option> |
| 49 </param> | 37 </param> |
| 50 <param name="scale" type="select"> | 38 <param name="scale" type="select" label="Display the scale line"> |
| 51 <label>Display the scale line</label> | |
| 52 <option value="yes">Yes</option> | 39 <option value="yes">Yes</option> |
| 53 <option value="no">No</option> | 40 <option value="no">No</option> |
| 54 </param> | 41 </param> |
| 55 <param name="width" type="text" value="60"> | 42 <param name="width" type="integer" value="60" label="Screen width" /> |
| 56 <label>Screen width</label> | 43 <param name="collapse" type="select" label="Collapse features"> |
| 57 </param> | |
| 58 <param name="collapse" type="select"> | |
| 59 <label>Collapse features</label> | |
| 60 <option value="no">No</option> | 44 <option value="no">No</option> |
| 61 <option value="yes">Yes</option> | 45 <option value="yes">Yes</option> |
| 62 </param> | 46 </param> |
| 63 <param name="forward" type="select"> | 47 <param name="forward" type="select" label="Display forward sense features"> |
| 64 <label>Display forward sense features</label> | |
| 65 <option value="yes">Yes</option> | 48 <option value="yes">Yes</option> |
| 66 <option value="no">No</option> | 49 <option value="no">No</option> |
| 67 </param> | 50 </param> |
| 68 <param name="reverse" type="select"> | 51 <param name="reverse" type="select" label="Display reverse sense features"> |
| 69 <label>Display reverse sense features</label> | |
| 70 <option value="yes">Yes</option> | 52 <option value="yes">Yes</option> |
| 71 <option value="no">No</option> | 53 <option value="no">No</option> |
| 72 </param> | 54 </param> |
| 73 <param name="unknown" type="select"> | 55 <param name="unknown" type="select" label="Display unknown sense features"> |
| 74 <label>Display unknown sense features</label> | |
| 75 <option value="yes">Yes</option> | 56 <option value="yes">Yes</option> |
| 76 <option value="no">No</option> | 57 <option value="no">No</option> |
| 77 </param> | 58 </param> |
| 78 <param name="strand" type="select"> | 59 <param name="strand" type="select" label="Display the strand of the features"> |
| 79 <label>Display the strand of the features</label> | |
| 80 <option value="no">No</option> | 60 <option value="no">No</option> |
| 81 <option value="yes">Yes</option> | 61 <option value="yes">Yes</option> |
| 82 </param> | 62 </param> |
| 83 <param name="source" type="select"> | 63 <param name="source" type="select" label="Display the source of the features"> |
| 84 <label>Display the source of the features</label> | |
| 85 <option value="no">No</option> | 64 <option value="no">No</option> |
| 86 <option value="yes">Yes</option> | 65 <option value="yes">Yes</option> |
| 87 </param> | 66 </param> |
| 88 <param name="position" type="select"> | 67 <param name="position" type="select" label="Display the start and end position of the features"> |
| 89 <label>SDisplay the start and end position of the features</label> | |
| 90 <option value="no">No</option> | 68 <option value="no">No</option> |
| 91 <option value="yes">Yes</option> | 69 <option value="yes">Yes</option> |
| 92 </param> | 70 </param> |
| 93 <param name="type" type="select"> | 71 <param name="type" type="select" label="Display the type of the features"> |
| 94 <label>Display the type of the features</label> | |
| 95 <option value="yes">Yes</option> | 72 <option value="yes">Yes</option> |
| 96 <option value="no">No</option> | 73 <option value="no">No</option> |
| 97 </param> | 74 </param> |
| 98 <param name="tags" type="select"> | 75 <param name="tags" type="select" label="Display the tags and values of the features"> |
| 99 <label>Display the tags and values of the features</label> | |
| 100 <option value="no">No</option> | 76 <option value="no">No</option> |
| 101 <option value="yes">Yes</option> | 77 <option value="yes">Yes</option> |
| 102 </param> | 78 </param> |
| 103 <param name="values" type="select"> | 79 <param name="values" type="select" label="Display the tag values of the features"> |
| 104 <label>Display the tag values of the features</label> | |
| 105 <option value="yes">Yes</option> | 80 <option value="yes">Yes</option> |
| 106 <option value="no">No</option> | 81 <option value="no">No</option> |
| 107 </param> | 82 </param> |
| 108 <param name="stricttags" type="select"> | 83 <param name="stricttags" type="select" label="Display only those tag/value pairs in a feature that match the specified tag and value"> |
| 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> | 84 <option value="no">No</option> |
| 111 <option value="yes">Yes</option> | 85 <option value="yes">Yes</option> |
| 112 </param> | 86 </param> |
| 113 </inputs> | 87 </inputs> |
| 114 <outputs> | 88 <outputs> |
| 115 <data format="showfeat" name="out_file1" /> | 89 <data name="out_file1" format="showfeat" /> |
| 116 </outputs> | 90 </outputs> |
| 117 <code file="emboss_format_corrector.py" /> | |
| 118 <help> | 91 <help> |
| 119 You can view the original documentation here_. | 92 You can view the original documentation here_. |
| 120 | |
| 121 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/showfeat.html | |
| 122 | 93 |
| 123 ------ | 94 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/showfeat.html |
| 124 | |
| 125 **Citation** | |
| 126 | |
| 127 For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ | |
| 128 | |
| 129 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ | |
| 130 </help> | 95 </help> |
| 96 <expand macro="citations" /> | |
| 131 </tool> | 97 </tool> |