annotate emboss_lindna.xml @ 17:ce385837c160 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 4812c313fd8762b11f7fd002436e3a93b4c67f00"
author iuc
date Fri, 20 Nov 2020 16:51:11 +0000
parents 8992d258e42f
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8992d258e42f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 9844cae766e7471d9fa6b2e8356e5194e77f6753
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1 <tool id="EMBOSS: lindna48" name="lindna" version="@VERSION@.1">
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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 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command>lindna -infile '$input1' -graphout png -goutfile '$out_file1' -ruler $ruler -blocktype $blocktype -maxgroups $maxgroups -maxlabels $maxlabels -intersymbol $intersymbol -intercolour $intercolour
d49956b87f7e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
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9 -interticks $interticks -gapsize $gapsize -ticklines $ticklines -textheight $textheight -textlength $textlength -margin $margin -tickheight $tickheight -blockheight $blockheight -rangeheight
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10 $rangeheight -gapgroup $gapgroup -postext $postext -auto</command>
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11 <inputs>
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12 <param name="input1" type="data" format="data" label="Sequences" />
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13 <param name="ruler" type="select" label="Draw a ruler">
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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" label="Type of blocks">
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18 <option value="Filled">Filled blocks</option>
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19 <option value="Open">Open blocks</option>
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20 <option value="Outline">Black border</option>
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21 </param>
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22 <param name="maxgroups" type="integer" value="20" label="Maximum number of groups" />
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23 <param name="maxlabels" type="integer" value="10000" label="Maximum number of labels" />
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24 <param name="intersymbol" type="select" label="Type of blocks">
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25 <option value="Straight">Straight</option>
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26 </param>
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27 <param name="intercolour" type="select" label="Colour of junctions between blocks">
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28 <option value="1">Red</option>
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29 <option value="0">Black</option>
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30 <option value="2">Yellow</option>
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31 <option value="3">Green</option>
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32 <option value="4">Aquamarine</option>
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33 <option value="5">Pink</option>
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34 <option value="6">Wheat</option>
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35 <option value="7">Grey</option>
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36 <option value="8">Brown</option>
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37 <option value="9">Blue</option>
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38 <option value="10">Blue-violet</option>
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39 <option value="11">Cyan</option>
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40 <option value="12">Turquoise</option>
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41 <option value="13">Magenta</option>
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42 <option value="14">Salmon</option>
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43 <option value="15">White</option>
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44 </param>
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45 <param name="interticks" type="select" label="Horizontal junctions between ticks">
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46 <option value="no">No</option>
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47 <option value="yes">Yes</option>
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48 </param>
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49 <param name="gapsize" type="integer" value="500" label="Interval between ticks in the ruler" />
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50 <param name="ticklines" type="select" label="Vertical lines at the ruler's ticks">
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51 <option value="no">No</option>
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52 <option value="yes">Yes</option>
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53 </param>
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54 <param name="textheight" type="float" value="1.0" label="Height of text" help="Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively" />
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55 <param name="textlength" type="float" value="1.0" label="Length of text" help="Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively" />
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56 <param name="margin" type="float" value="1.0" label="Width of left margin" help="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, respectively" />
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57 <param name="tickheight" type="float" value="1.0" label="Height of ticks" help="Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively" />
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58 <param name="blockheight" type="float" value="1.0" label="Height of blocks" help="Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively" />
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59 <param name="rangeheight" type="float" value="1.0" label="Height of range ends" help="Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively" />
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60 <param name="gapgroup" type="float" value="1.0" label="Space between groups" help="Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively" />
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61 <param name="postext" type="float" value="1.0" label="Space between text and ticks, blocks, and ranges" help="Enter a number &lt;1.0 or &gt;1.0 to decrease or increase the size, respectively" />
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62 </inputs>
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63 <outputs>
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64 <data name="out_file1" format="png" />
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65 </outputs>
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66 <help>
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67 You can view the original documentation here_.
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68
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69 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/lindna.html
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70 </help>
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71 <expand macro="citations" />
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72 </tool>