[2] | 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" size="4" 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" size="6" 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">
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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">
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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>
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| 48 | <option value="13">Magenta</option>
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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">
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| 53 | <label>Horizontal junctions between ticks</label>
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| 54 | <option value="no">No</option>
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| 55 | <option value="yes">Yes</option>
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| 56 | </param>
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| 57 | <param name="gapsize" size="6" type="text" value="500">
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| 58 | <label>Interval between ticks in the ruler</label>
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| 59 | </param>
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| 60 | <param name="ticklines" type="select">
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| 61 | <label>Vertical lines at the ruler's ticks</label>
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| 62 | <option value="no">No</option>
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| 63 | <option value="yes">Yes</option>
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| 64 | </param>
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| 65 | <param name="textheight" size="4" type="text" value="1.0">
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| 66 | <label>Height of text. Enter a number <1.0 or >1.0 to decrease or increase the size, respectively</label>
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| 67 | </param>
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| 68 | <param name="textlength" size="4" type="text" value="1.0">
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| 69 | <label>Length of text. Enter a number <1.0 or >1.0 to decrease or increase the size, respectively</label>
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| 70 | </param>
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| 71 | <param name="margin" size="4" type="text" value="1.0">
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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 <1.0 or >1.0 to decrease or increase the size,
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| 73 | respectively</label>
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| 74 | </param>
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| 75 | <param name="tickheight" size="4" type="text" value="1.0">
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| 76 | <label>Height of ticks. Enter a number <1.0 or >1.0 to decrease or increase the size, respectively</label>
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| 77 | </param>
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| 78 | <param name="blockheight" size="4" type="text" value="1.0">
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| 79 | <label>Height of blocks. Enter a number <1.0 or >1.0 to decrease or increase the size, respectively</label>
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| 80 | </param>
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| 81 | <param name="rangeheight" size="4" type="text" value="1.0">
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| 82 | <label>Height of range ends. Enter a number <1.0 or >1.0 to decrease or increase the size, respectively</label>
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| 83 | </param>
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| 84 | <param name="gapgroup" size="4" type="text" value="1.0">
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| 85 | <label>Space between groups. Enter a number <1.0 or >1.0 to decrease or increase the size, respectively</label>
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| 86 | </param>
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| 87 | <param name="postext" size="4" type="text" value="1.0">
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| 88 | <label>Space between text and ticks, blocks, and ranges. Enter a number <1.0 or >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 | </help> |
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| 99 | </tool> |
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