Mercurial > repos > iuc > mummer_mummerplot

annotate macros.xml @ 4:fb43e8887350 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 026db7297e987c1b7ce7f5dd4f8746d1bd435538
author iuc
date Mon, 18 Mar 2024 12:41:02 +0000
parents 4fc0cb2ac8ae
children
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e8c60daa41e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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1 <macros>
1
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2 <token name="@MUMMER_GNUPLOT_MANUAL@"><![CDATA[&& gnuplot < out.gp]]></token>
3
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3 <xml name="bio_tools">
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4 <xrefs>
4
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5 <xref type="bio.tools">mummer4</xref>
3
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6 </xrefs>
4fc0cb2ac8ae "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit bacb32814054404587451948b3a6682cf0d1a33a"
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7 </xml>
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8 <xml name="citation">
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9 <citations>
3
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10 <citation type="doi">10.1371/journal.pcbi.1005944</citation>
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11 </citations>
e8c60daa41e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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12 </xml>
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13 <token name="@TOOL_VERSION@">4.0.0rc1</token>
fb43e8887350 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 026db7297e987c1b7ce7f5dd4f8746d1bd435538
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14 <token name="@VERSION_SUFFIX@">3</token>
fb43e8887350 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 026db7297e987c1b7ce7f5dd4f8746d1bd435538
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15 <token name="@PROFILE@">20.05</token>
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16 <xml name="gnuplot_requirement">
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17 <requirement type="package" version="5.4.8">gnuplot</requirement>
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18 </xml>
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19 <xml name="requirements">
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20 <requirements>
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21 <requirement type="package" version="@TOOL_VERSION@">mummer4</requirement>
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fb43e8887350 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 026db7297e987c1b7ce7f5dd4f8746d1bd435538
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22 <requirement type="package" version="1.19.2">samtools</requirement>
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23 <yield />
e8c60daa41e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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24 </requirements>
e8c60daa41e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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25 </xml>
e8c60daa41e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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26 <xml name="mumplot_input" >
e8c60daa41e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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27 <yield />
e8c60daa41e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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28 <param name="breaklen" type="integer" argument="-b" value="20" label="Break Length"
e8c60daa41e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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29 help="Highlight alignments with breakpoints further than breaklen nucleotides from the nearest sequence end. (-b)" />
e8c60daa41e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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30 <param name="color" type="select" label="Color" help="Color plot lines with a percent similarity gradient or turn off all plot color." >
e8c60daa41e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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31 <option value="">Color</option>
e8c60daa41e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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32 <option value="-color">No color (-color)</option>
e8c60daa41e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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33 </param>
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34 <param name="coverage" type="select" label="Coverage Plot" help="Generate a reference coverage plot (default for .tiling) or the default dotplot." >
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35 <option value="">Dotplot</option>
e8c60daa41e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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36 <option value="-c">Coverage Plot (-c)</option>
e8c60daa41e0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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37 </param>
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38 <param type="boolean" argument="--filter" truevalue="--filter" falsevalue="" label="Filter"
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39 help="Only display .delta alignments which represent the 'best' hit to any particular spot on either sequence, i.e. a one-to-one mapping of reference and query subsequences. (--filter)" />
4
fb43e8887350 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 026db7297e987c1b7ce7f5dd4f8746d1bd435538
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40 <param type="boolean" argument="--fat" truevalue="--fat" falsevalue="" label="Layout sequences using fattest alignment only" help="(--fat)" />
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41 <conditional name="labels" >
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42 <param name="IDs" type="select" label="Plot a particular reference or query sequence?" help="For alignments that used more than one reference/query." >
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43 <option value="no">NO</option>
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44 <option value="yes">YES</option>
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45 </param>
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46 <when value="yes" >
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47 <param name="ref_id" type="text" value="ref_id" label="Reference sequence ID" help="(-IdR)" />
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48 <param name="query_id" type="text" value="query_id" label="Query sequence ID" help="(-IdQ)" />
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49 </when>
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50 <when value="no" />
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51 </conditional>
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52 <param name="size" type="select" label="Plot Size" help="Set the output size to small, medium or large. (-s)" >
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53 <option value="small">Small</option>
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54 <option value="medium">Medium</option>
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55 <option value="large">Large</option>
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56 </param>
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57 <param name="snp" type="boolean" argument="--SNP" truevalue="--SNP" falsevalue="" label="SNPs" help="Highlight SNP locations in each alignment. (--SNP)" />
4
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58 <param type="text" argument="-title" value="Title" label="Plot Title" help="(-title)" />
0
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59 <conditional name="range" >
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60 <param name="custom" type="select" label="Choose custom X and Y axis ranges?" >
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61 <option value="no">NO</option>
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62 <option value="yes">YES</option>
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63 </param>
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64 <when value="yes" >
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65 <param name="min_x" type="integer" argument="-x" value="0" label="Minimum X-axis range" help="(-x)" />
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66 <param name="max_x" type="integer" argument="-x" value="100" label="Maximum X-axis range" help="(-x)" />
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67 <param name="min_y" type="integer" argument="-y" value="0" label="Minimum Y-axis range" help="(-y)" />
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68 <param name="max_y" type="integer" argument="-y" value="100" label="Maximum Y-axis range" help="(-y)" />
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69 </when>
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70 <when value="no" />
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71 </conditional>
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72 </xml>
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73 </macros>