Mercurial > repos > iuc > mummer_nucmer
annotate macros.xml @ 2:636b049e6141 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 7ea9a5c6d9e7212c38be96baa6615af1ea9d5a8e"
author | iuc |
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date | Tue, 13 Oct 2020 21:40:12 +0000 |
parents | 5b0b49b5421c |
children | e18267f90096 |
rev | line source |
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a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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1 <macros> |
1
5b0b49b5421c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 96608e94742d17cb73d57201099ff5f5abbef276"
iuc
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2 <token name="@MUMMER_GNUPLOT_MANUAL@"><![CDATA[&& gnuplot < out.gp]]></token> |
0
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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3 <xml name="citation"> |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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4 <citations> |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff
changeset
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5 <citation type="bibtex"> |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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6 @misc{githubmummer, |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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7 author = {Art Delcher, Stefan Kurtz, Adam Phillippy, Steven Salzberg}, |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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8 year = {2012}, |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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9 title = {mummer4}, |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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10 publisher = {GitHub}, |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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11 journal = {GitHub repository}, |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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12 url = {https://github.com/mummer4/mummer}, |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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13 }</citation> |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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changeset
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14 </citations> |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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15 </xml> |
1
5b0b49b5421c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 96608e94742d17cb73d57201099ff5f5abbef276"
iuc
parents:
0
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16 <xml name="gnuplot_requirement"> |
5b0b49b5421c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 96608e94742d17cb73d57201099ff5f5abbef276"
iuc
parents:
0
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17 <requirement type="package" version="5.2.7">gnuplot</requirement> |
5b0b49b5421c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 96608e94742d17cb73d57201099ff5f5abbef276"
iuc
parents:
0
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18 </xml> |
0
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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19 <token name="@MUMMER_VERSION@">4.0.0beta2</token> |
2
636b049e6141
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 7ea9a5c6d9e7212c38be96baa6615af1ea9d5a8e"
iuc
parents:
1
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20 <token name="@WRAPPER_VERSION@">+galaxy1</token> |
0
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff
changeset
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21 <xml name="requirements"> |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff
changeset
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22 <requirements> |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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changeset
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23 <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
iuc
parents:
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24 <yield /> |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff
changeset
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25 </requirements> |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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changeset
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26 </xml> |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff
changeset
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27 <xml name="mumplot_input" > |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff
changeset
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28 <yield /> |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff
changeset
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29 <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
iuc
parents:
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30 help="Highlight alignments with breakpoints further than breaklen nucleotides from the nearest sequence end. (-b)" /> |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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changeset
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31 <param name="color" type="select" label="Color" help="Color plot lines with a percent similarity gradient or turn off all plot color." > |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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32 <option value="">Color</option> |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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33 <option value="-color">No color (-color)</option> |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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34 </param> |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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35 <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
iuc
parents:
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36 <option value="">Dotplot</option> |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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37 <option value="-c">Coverage Plot (-c)</option> |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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38 </param> |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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39 <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
iuc
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40 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
iuc
parents:
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41 <param name="fat" type="boolean" argument="--fat" truevalue="--fat" falsevalue="" label="Layout sequences using fattest alignment only" help="(--fat)" /> |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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42 <conditional name="labels" > |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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43 <param name="IDs" type="select" label="Plot a particular reference or query sequence?" help="For alignments that used more than one reference/query." > |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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44 <option value="no">NO</option> |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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45 <option value="yes">YES</option> |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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46 </param> |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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47 <when value="yes" > |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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48 <param name="ref_id" type="text" value="ref_id" label="Reference sequence ID" help="(-IdR)" /> |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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49 <param name="query_id" type="text" value="query_id" label="Query sequence ID" help="(-IdQ)" /> |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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50 </when> |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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51 <when value="no" /> |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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52 </conditional> |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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53 <param name="size" type="select" label="Plot Size" help="Set the output size to small, medium or large. (-s)" > |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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54 <option value="small">Small</option> |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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55 <option value="medium">Medium</option> |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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56 <option value="large">Large</option> |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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57 </param> |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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58 <param name="snp" type="boolean" argument="--SNP" truevalue="--SNP" falsevalue="" label="SNPs" help="Highlight SNP locations in each alignment. (--SNP)" /> |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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59 <param name="title" type="text" argument="-title" value="Title" label="Plot Title" help="(-title)" /> |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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60 <conditional name="range" > |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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61 <param name="custom" type="select" label="Choose custom X and Y axis ranges?" > |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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62 <option value="no">NO</option> |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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63 <option value="yes">YES</option> |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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64 </param> |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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65 <when value="yes" > |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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66 <param name="min_x" type="integer" argument="-x" value="0" label="Minimum X-axis range" help="(-x)" /> |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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67 <param name="max_x" type="integer" argument="-x" value="100" label="Maximum X-axis range" help="(-x)" /> |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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68 <param name="min_y" type="integer" argument="-y" value="0" label="Minimum Y-axis range" help="(-y)" /> |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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69 <param name="max_y" type="integer" argument="-y" value="100" label="Maximum Y-axis range" help="(-y)" /> |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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70 </when> |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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71 <when value="no" /> |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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72 </conditional> |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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73 </xml> |
a18fb4f826fc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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74 </macros> |