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