Mercurial > repos > devteam > emboss_5

annotate emboss_showfeat.xml @ 10:9b98d3d903c6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
author devteam
date Fri, 12 Aug 2016 19:17:10 -0400
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10
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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" 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" 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" 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" 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" 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">
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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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" 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">
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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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">
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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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
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123 ------
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124
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125 **Citation**
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126
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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. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
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128
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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. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
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130 </help>
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131 </tool>