Mercurial > repos > iuc > mummer_mummer
annotate mummer.xml @ 0:26f2cc1cc1e9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
| author | iuc |
|---|---|
| date | Wed, 05 Dec 2018 02:38:48 -0500 |
| parents | |
| children | 48badcd29c5d |
| rev | line source |
|---|---|
|
0
26f2cc1cc1e9
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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1 <tool id="mummer_mummer" name="Mummer" version="@MUMMER_VERSION@"> |
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26f2cc1cc1e9
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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2 <description>Align two or more sequences</description> |
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26f2cc1cc1e9
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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3 <macros> |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff
changeset
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4 <import>macros.xml</import> |
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26f2cc1cc1e9
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 </macros> |
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26f2cc1cc1e9
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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6 <expand macro="requirements"> |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff
changeset
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7 <requirement type="package" version="5.2.3">gnuplot</requirement> |
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26f2cc1cc1e9
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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8 </expand> |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff
changeset
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9 <command detect_errors="exit_code"> |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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10 <![CDATA[ |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff
changeset
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11 mummer |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff
changeset
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12 $anchoring |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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changeset
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13 -l '$min' |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff
changeset
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14 $direction |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff
changeset
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15 $force |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff
changeset
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16 $chars |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff
changeset
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17 $print_length |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff
changeset
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18 $substring |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff
changeset
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19 $position |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff
changeset
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20 #if $options.advanced == 'enable' |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff
changeset
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21 -k '$options.suffix' |
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26f2cc1cc1e9
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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22 -threads '$options.threads' |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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changeset
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23 -qthreads '$options.qthreads' |
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26f2cc1cc1e9
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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24 -suflink '$'options.suflink' |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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changeset
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25 -child '$options.child' |
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26f2cc1cc1e9
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 -skip '$options.skip' |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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changeset
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27 -kmer '$options.kmer' |
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26f2cc1cc1e9
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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28 #end if |
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26f2cc1cc1e9
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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29 '$reference_sequence' '$query_sequence' > '$output' |
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26f2cc1cc1e9
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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30 #if $mumplot.plot == 'yes': |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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changeset
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31 && mummerplot |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff
changeset
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32 -b '$mumplot.breaklen' |
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26f2cc1cc1e9
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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33 $mumplot.color |
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26f2cc1cc1e9
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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34 $mumplot.coverage |
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26f2cc1cc1e9
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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35 $mumplot.filter |
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26f2cc1cc1e9
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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36 $mumplot.fat |
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26f2cc1cc1e9
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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37 #if $mumplot.labels.IDs == 'yes': |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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changeset
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38 -IdR '$mumplot.labels.ref_id' |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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39 -IdQ '$mumplot.labels.query_id' |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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changeset
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40 #end if |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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changeset
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41 -s '$mumplot.size' |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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42 -terminal png |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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43 -title '$mumplot.title' |
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26f2cc1cc1e9
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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44 $mumplot.snp |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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45 #if $mumplot.range.custom == 'yes': |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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46 -x [$mumplot.range.min_x:$mumplot.range.max_x] |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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47 -y [$mumplot.range.min_y:$mumplot.range.max_y] |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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48 #end if |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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49 '$output' |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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50 #end if |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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51 ]]> |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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52 </command> |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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53 <inputs> |
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26f2cc1cc1e9
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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54 <param name="reference_sequence" type="data" format="fasta" label="Reference Sequence" help="FastA or multi-FastA" /> |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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55 <param name="query_sequence" type="data" format="fasta" label="Query Sequence" help="FastA or multi-FastA" /> |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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56 <param name="anchoring" type="select" label="Anchoring" help="Choose a match anchoring strategy"> |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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57 <option value="">Maximal matches unique in only reference sequence (-mumreference) (Default)</option> |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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58 <option value="-mum">Maximal matches unique in both sequences (-mum)</option> |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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59 <option value="-maxmatch">All matches reguardless of uniqueness (-maxmatch)</option> |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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60 </param> |
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26f2cc1cc1e9
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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61 <param name="min" type="integer" argument="-l" value="20" label="Minimum Match Length" help="Minimum length of a match. (-l)" /> |
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26f2cc1cc1e9
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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62 <param name="direction" type="select" label="Direction" help="Direction of complement sequence to use"> |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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63 <option value="-b">Compute forward and reverse complement matches (-b)</option> |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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64 <option value="-r">Compute only reverse complement matches (-r)</option> |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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65 </param> |
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26f2cc1cc1e9
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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66 <param name="force" type="boolean" argument="-F" truevalue="-F" falsevalue="" label="Force 4 column output" |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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67 help="force 4 column output format regardless of the number of reference sequence inputs. (-F)" /> |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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68 <param name="chars" type="boolean" argument="-n" truevalue="-n" falsevalue="" label="Match only the characters a, c, g, or t" help="(-n)" /> |
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26f2cc1cc1e9
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="print_length" type="boolean" argument="-L" truevalue="-L" falsevalue="" label="Print length of query sequence in header of matches" help="(-L)" /> |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
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70 <param name="substring" type="boolean" argument="-s" truevalue="-s" falsevalue="" label= "Print first 53 characters of the matching substring" help="(-s)" /> |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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71 <param name="position" type="boolean" argument="-c" truevalue="-c" falsevalue="" label="Position" |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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72 help="Report the query position of a reverse complement match relative to the forward strand of the query sequence. (-c)" /> |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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73 <conditional name="options"> |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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74 <param name="advanced" type="select" label="Additional options"> |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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75 <option value="defaults">Use defaults</option> |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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76 <option value="enable">Select additional options</option> |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
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77 </param> |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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78 <when value="enable" > |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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79 <param name="suffix" type="integer" argument="-k" value="1" label="Suffix" help="Sampled suffix positions. (-k)" /> |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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80 <param name="threads" type="integer" argument="-threads" value="3" label="Threads" |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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81 help="Number of threads to use for -maxmatch; only valid if above parameter is greater than one. (-threads)" /> |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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82 <param name="qthreads" type="integer" argument="-qthreads" value="3" label="Qthreads" help="Number of threads to use for queries. (-qthreads)" /> |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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83 <param name="suflink" type="select" label="Suflink" help="Use suffix links in the index and during search? (-suflink)" > |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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84 <option value="0">No</option> |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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85 <option value="1">Yes</option> |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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86 </param> |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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87 <param name="child" type="select" label="Child" help="Use child table in the index and during search? (-child)" > |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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88 <option value="0">No</option> |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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89 <option value="1">Yes</option> |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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90 </param> |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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91 <param name="skip" type="integer" argument="-skip" value="10" label="Sparsify" |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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92 help="Sparsify the MEM-finding algorithm even more, performing jumps of skip*k [auto (l-10)/k]. (-skip)" /> |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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93 <param name="kmer" type="integer" argument="-kmer" value="1" label="kmer Table" |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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94 help="Use kmer table containing sa-intervals (speeds up searching first k characters) in the index and during search. (-kmer)" /> |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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95 </when> |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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96 <when value="defaults" /> |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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97 </conditional> |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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98 <conditional name="mumplot" > |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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99 <param name="plot" type="select" label="Do you want to output a 2-D dotplot of the input sequences?" > |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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100 <option value="yes">YES</option> |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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101 <option value="no">NO</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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102 </param> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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103 <when value="yes" > |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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104 <expand macro="mumplot_input" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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105 </when> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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106 <when value="no" /> |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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107 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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108 </inputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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109 <outputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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110 <data name="output" format="tabular" from_work_dir="mummer.txt" label="${tool.name} on ${on_string}: alignment" /> |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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111 <data name="png_output" format="png" from_work_dir="out.png" label="${tool.name} on ${on_string}: plot" > |
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26f2cc1cc1e9
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112 <filter>mumplot['plot'] == 'yes'</filter> |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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113 </data> |
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114 </outputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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115 <tests> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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116 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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117 <param name="reference_sequence" ftype="fasta" value="human_aqp3.fasta" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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118 <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta" /> |
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119 <param name="options" value="defaults" /> |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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120 <param name="plot" value="yes" /> |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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121 <output name="output" ftype="tabular" compare="diff" value="mummer.txt" /> |
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26f2cc1cc1e9
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122 <output name="png_output" ftype="png" compare="sim_size" value="plot.png" /> |
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123 </test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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124 </tests> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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125 <help><![CDATA[ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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126 This is the core program of the MUMmer package. It is the suffix-tree based match finding routine, and the main part of every MUMmer script. By default, mummer now finds maximal matches regardless of their uniqueness. Limiting the output to only unique matches can be specified by choosing alternative Anchoring strategies. |
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26f2cc1cc1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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127 |
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128 **Options:**:: |
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129 |
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130 mummer |
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131 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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132 -mumreference Compute maximal matches that are unique in the reference- sequence but not |
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133 necessarily in the query-sequence (default) |
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134 |
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135 -maxmatch Compute all maximal matches regardless of their uniqueness |
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136 |
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137 -l Set the minimum length of a match |
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138 |
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139 -b Compute forward and reverse complement matches |
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140 |
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141 -r Compute only reverse complement matches |
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142 |
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143 -mum Compute maximal matches that are unique in both sequences |
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144 |
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145 -F Force 4 column output format regardless of the number of reference sequence inputs |
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146 |
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147 -n Match only the characters a, c, g, or t |
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148 |
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149 -L Print length of query sequence in header of matches |
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150 |
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151 -s Print first 53 characters of the matching substring |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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152 |
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153 -c Report the query position of a reverse complement match |
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154 relative to the forward strand of the query sequence |
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155 |
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156 mummerplot |
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157 |
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158 -b Highlight alignments with breakpoints further than breaklen nucleotides from the nearest |
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159 sequence end |
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160 |
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161 -color Color plot lines with a percent similarity gradient or turn off all plot color (default |
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162 color by match dir) If the plot is very sparse, edit the .gp script to plot with |
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163 'linespoints' instead of 'lines' |
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164 |
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165 -c Generate a reference coverage plot (default for .tiling) |
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166 |
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167 --filter Only display .delta alignments which represent the "best" hit to any particular spot on |
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168 either sequence, i.e. a one-to-one mapping of reference and query subsequences |
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169 |
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170 --fat Layout sequences using fattest alignment only |
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171 |
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172 -IdR Plot a particular reference sequence ID on the X-axis |
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173 |
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174 -IdQ Plot a particular query sequence ID on the Y-axis |
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175 |
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176 -s Set the output size to small, medium or large (--small) (--medium) (--large) (default 'small') |
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177 |
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178 --SNP Highlight SNP locations in each alignment |
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179 |
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180 -title Specify the gnuplot plot title (default none) |
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181 |
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182 -x Set the xrange for the plot '[min:max]' |
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183 |
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184 -y Set the yrange for the plot '[min:max]' |
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185 |
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186 -R Plot an ordered set of reference sequences from Rfile |
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187 |
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188 -Q Plot an ordered set of query sequences from Qfile |
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189 |
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190 --layout Layout a .delta multiplot in an intelligible fashion, this option requires the -R -Q options |
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191 |
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192 ]]></help> |
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193 <expand macro="citation" /> |
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194 </tool> |