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annotate macros.xml @ 0:a18fb4f826fc draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
author iuc
date Wed, 05 Dec 2018 02:37:36 -0500
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children 5b0b49b5421c
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a18fb4f826fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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1 <macros>
a18fb4f826fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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2 <xml name="citation">
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3 <citations>
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4 <citation type="bibtex">
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5 @misc{githubmummer,
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6 author = {Art Delcher, Stefan Kurtz, Adam Phillippy, Steven Salzberg},
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7 year = {2012},
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8 title = {mummer4},
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9 publisher = {GitHub},
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10 journal = {GitHub repository},
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11 url = {https://github.com/mummer4/mummer},
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12 }</citation>
a18fb4f826fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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13 </citations>
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14 </xml>
a18fb4f826fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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15 <token name="@MUMMER_VERSION@">4.0.0beta2</token>
a18fb4f826fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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16 <xml name="requirements">
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17 <requirements>
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18 <requirement type="package" version="@MUMMER_VERSION@">mummer4</requirement>
a18fb4f826fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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19 <yield />
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20 </requirements>
a18fb4f826fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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21 </xml>
a18fb4f826fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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22 <xml name="mumplot_input" >
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23 <yield />
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24 <param name="breaklen" type="integer" argument="-b" value="20" label="Break Length"
a18fb4f826fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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25 help="Highlight alignments with breakpoints further than breaklen nucleotides from the nearest sequence end. (-b)" />
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26 <param name="color" type="select" label="Color" help="Color plot lines with a percent similarity gradient or turn off all plot color." >
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27 <option value="">Color</option>
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28 <option value="-color">No color (-color)</option>
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29 </param>
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30 <param name="coverage" type="select" label="Coverage Plot" help="Generate a reference coverage plot (default for .tiling) or the defualt dotplot." >
a18fb4f826fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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31 <option value="">Dotplot</option>
a18fb4f826fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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32 <option value="-c">Coverage Plot (-c)</option>
a18fb4f826fc 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="filter" type="boolean" argument="--filter" truevalue="--filter" falsevalue="" label="Filter"
a18fb4f826fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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35 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)" />
a18fb4f826fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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36 <param name="fat" type="boolean" argument="--fat" truevalue="--fat" falsevalue="" label="Layout sequences using fattest alignment only" help="(--fat)" />
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37 <conditional name="labels" >
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38 <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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39 <option value="no">NO</option>
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40 <option value="yes">YES</option>
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41 </param>
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42 <when value="yes" >
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43 <param name="ref_id" type="text" value="ref_id" label="Reference sequence ID" help="(-IdR)" />
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44 <param name="query_id" type="text" value="query_id" label="Query sequence ID" help="(-IdQ)" />
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45 </when>
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46 <when value="no" />
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47 </conditional>
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48 <param name="size" type="select" label="Plot Size" help="Set the output size to small, medium or large. (-s)" >
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49 <option value="small">Small</option>
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50 <option value="medium">Medium</option>
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51 <option value="large">Large</option>
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52 </param>
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53 <param name="snp" type="boolean" argument="--SNP" truevalue="--SNP" falsevalue="" label="SNPs" help="Highlight SNP locations in each alignment. (--SNP)" />
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54 <param name="title" type="text" argument="-title" value="Title" label="Plot Title" help="(-title)" />
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55 <conditional name="range" >
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56 <param name="custom" type="select" label="Choose custom X and Y axis ranges?" >
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57 <option value="no">NO</option>
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58 <option value="yes">YES</option>
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59 </param>
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60 <when value="yes" >
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61 <param name="min_x" type="integer" argument="-x" value="0" label="Minimum X-axis range" help="(-x)" />
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62 <param name="max_x" type="integer" argument="-x" value="100" label="Maximum X-axis range" help="(-x)" />
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63 <param name="min_y" type="integer" argument="-y" value="0" label="Minimum Y-axis range" help="(-y)" />
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64 <param name="max_y" type="integer" argument="-y" value="100" label="Maximum Y-axis range" help="(-y)" />
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65 </when>
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66 <when value="no" />
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67 </conditional>
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68 </xml>
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69 </macros>