Mercurial > repos > devteam > emboss_5

annotate emboss_lindna.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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children 0e2484b6829b
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10
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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1 <tool id="EMBOSS: lindna48" name="lindna" version="5.0.0">
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2 <!-- tool produces memory error in ajmem.c -->
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3 <description>Draws linear maps of DNA constructs</description>
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4 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements>
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5 <command>lindna -infile $input1 -graphout png -goutfile $out_file1 -ruler $ruler -blocktype $blocktype -maxgroups $maxgroups -maxlabels $maxlabels -intersymbol $intersymbol -intercolour $intercolour
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6 -interticks $interticks -gapsize $gapsize -ticklines $ticklines -textheight $textheight -textlength $textlength -margin $margin -tickheight $tickheight -blockheight $blockheight -rangeheight
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7 $rangeheight -gapgroup $gapgroup -postext $postext -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="ruler" type="select">
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13 <label>Draw a ruler</label>
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14 <option value="yes">Yes</option>
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15 <option value="no">No</option>
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16 </param>
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17 <param name="blocktype" type="select">
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18 <label>Type of blocks</label>
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19 <option value="Filled">Filled blocks</option>
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20 <option value="Open">Open blocks</option>
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21 <option value="Outline">Black border</option>
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22 </param>
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23 <param name="maxgroups" type="text" value="20">
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24 <label>Maximum number of groups</label>
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25 </param>
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26 <param name="maxlabels" type="text" value="10000">
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27 <label>Maximum number of labels</label>
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28 </param>
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29 <param name="intersymbol" type="select">
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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30 <label>Type of blocks</label>
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31 <option value="Straight">Straight</option>
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32 </param>
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33 <param name="intercolour" type="select">
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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34 <label>Colour of junctions between blocks</label>
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35 <option value="1">Red</option>
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36 <option value="0">Black</option>
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37 <option value="2">Yellow</option>
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38 <option value="3">Green</option>
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39 <option value="4">Aquamarine</option>
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40 <option value="5">Pink</option>
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41 <option value="6">Wheat</option>
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42 <option value="7">Grey</option>
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43 <option value="8">Brown</option>
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44 <option value="9">Blue</option>
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45 <option value="10">Blue-violet</option>
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46 <option value="11">Cyan</option>
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47 <option value="12">Turquoise</option>
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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48 <option value="13">Magenta</option>
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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49 <option value="14">Salmon</option>
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50 <option value="15">White</option>
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51 </param>
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52 <param name="interticks" type="select">
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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53 <label>Horizontal junctions between ticks</label>
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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54 <option value="no">No</option>
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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55 <option value="yes">Yes</option>
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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56 </param>
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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57 <param name="gapsize" type="text" value="500">
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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58 <label>Interval between ticks in the ruler</label>
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59 </param>
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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60 <param name="ticklines" type="select">
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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61 <label>Vertical lines at the ruler's ticks</label>
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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62 <option value="no">No</option>
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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63 <option value="yes">Yes</option>
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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64 </param>
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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65 <param name="textheight" type="text" value="1.0">
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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66 <label>Height of text. Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively</label>
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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67 </param>
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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68 <param name="textlength" type="text" value="1.0">
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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69 <label>Length of text. Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively</label>
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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70 </param>
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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71 <param name="margin" type="text" value="1.0">
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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72 <label>Width of left margin. This is the region left to the groups where the names of the groups are displayed. Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size,
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73 respectively</label>
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74 </param>
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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75 <param name="tickheight" type="text" value="1.0">
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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76 <label>Height of ticks. Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively</label>
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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77 </param>
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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78 <param name="blockheight" type="text" value="1.0">
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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79 <label>Height of blocks. Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively</label>
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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80 </param>
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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81 <param name="rangeheight" type="text" value="1.0">
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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82 <label>Height of range ends. Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively</label>
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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83 </param>
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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84 <param name="gapgroup" type="text" value="1.0">
9b98d3d903c6 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/emboss_5 commit fc158bfe5f5927dc199321a2cf43310373cbc8ba
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85 <label>Space between groups. Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively</label>
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86 </param>
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87 <param name="postext" type="text" value="1.0">
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88 <label>Space between text and ticks, blocks, and ranges. Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively</label>
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89 </param>
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90 </inputs>
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91 <outputs>
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92 <data format="png" name="out_file1" />
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93 </outputs>
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94 <help>
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95 You can view the original documentation here_.
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96
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97 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/lindna.html
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98
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99 ------
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100
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101 **Citation**
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102
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103 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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104
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105 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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106 </help>
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107 </tool>