Mercurial > repos > iuc > mummer_mummer

annotate mummer.xml @ 1:48badcd29c5d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 236c87334340aacfaaf1d5b027a363e32b82583d
author iuc
date Wed, 12 Dec 2018 02:45:48 -0500
parents 26f2cc1cc1e9
children fc143c06a842
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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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1 <tool id="mummer_mummer" name="Mummer" version="@MUMMER_VERSION@">
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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2 <description>Align two or more sequences</description>
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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3 <macros>
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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4 <import>macros.xml</import>
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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5 </macros>
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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6 <expand macro="requirements">
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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7 <requirement type="package" version="5.2.3">gnuplot</requirement>
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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8 </expand>
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9 <command detect_errors="exit_code">
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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10 <![CDATA[
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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11 mummer
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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12 $anchoring
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13 -l '$min'
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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14 $direction
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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15 $force
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16 $chars
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17 $print_length
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18 $substring
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19 $position
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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20 #if $options.advanced == 'enable'
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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21 -k '$options.suffix'
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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22 -threads '$options.threads'
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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23 -qthreads '$options.qthreads'
1
48badcd29c5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 236c87334340aacfaaf1d5b027a363e32b82583d
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24 -suflink '$options.suflink'
0
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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25 -child '$options.child'
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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26 -skip '$options.skip'
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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27 -kmer '$options.kmer'
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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28 #end if
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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29 '$reference_sequence' '$query_sequence' > '$output'
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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30 #if $mumplot.plot == 'yes':
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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31 && mummerplot
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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32 -b '$mumplot.breaklen'
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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33 $mumplot.color
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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34 $mumplot.coverage
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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35 $mumplot.filter
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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36 $mumplot.fat
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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37 #if $mumplot.labels.IDs == 'yes':
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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38 -IdR '$mumplot.labels.ref_id'
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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39 -IdQ '$mumplot.labels.query_id'
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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40 #end if
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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41 -s '$mumplot.size'
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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42 -terminal png
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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43 -title '$mumplot.title'
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44 $mumplot.snp
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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45 #if $mumplot.range.custom == 'yes':
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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46 -x [$mumplot.range.min_x:$mumplot.range.max_x]
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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47 -y [$mumplot.range.min_y:$mumplot.range.max_y]
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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48 #end if
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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49 '$output'
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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50 #end if
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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51 ]]>
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52 </command>
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53 <inputs>
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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54 <param name="reference_sequence" type="data" format="fasta" label="Reference Sequence" help="FastA or multi-FastA" />
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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55 <param name="query_sequence" type="data" format="fasta" label="Query Sequence" help="FastA or multi-FastA" />
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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56 <param name="anchoring" type="select" label="Anchoring" help="Choose a match anchoring strategy">
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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57 <option value="">Maximal matches unique in only reference sequence (-mumreference) (Default)</option>
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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58 <option value="-mum">Maximal matches unique in both sequences (-mum)</option>
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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59 <option value="-maxmatch">All matches reguardless of uniqueness (-maxmatch)</option>
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60 </param>
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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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)" />
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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62 <param name="direction" type="select" label="Direction" help="Direction of complement sequence to use">
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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63 <option value="-b">Compute forward and reverse complement matches (-b)</option>
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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64 <option value="-r">Compute only reverse complement matches (-r)</option>
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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65 </param>
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66 <param name="force" type="boolean" argument="-F" truevalue="-F" falsevalue="" label="Force 4 column output"
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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67 help="force 4 column output format regardless of the number of reference sequence inputs. (-F)" />
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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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)" />
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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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)" />
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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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)" />
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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71 <param name="position" type="boolean" argument="-c" truevalue="-c" falsevalue="" label="Position"
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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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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73 <conditional name="options">
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74 <param name="advanced" type="select" label="Additional options">
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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75 <option value="defaults">Use defaults</option>
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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76 <option value="enable">Select additional options</option>
26f2cc1cc1e9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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77 </param>
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78 <when value="enable" >
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79 <param name="suffix" type="integer" argument="-k" value="1" label="Suffix" help="Sampled suffix positions. (-k)" />
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"
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)" />
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)" />
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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84 <option value="0">No</option>
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85 <option value="1">Yes</option>
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86 </param>
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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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88 <option value="0">No</option>
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89 <option value="1">Yes</option>
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90 </param>
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91 <param name="skip" type="integer" argument="-skip" value="10" label="Sparsify"
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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93 <param name="kmer" type="integer" argument="-kmer" value="1" label="kmer Table"
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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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95 </when>
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96 <when value="defaults" />
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97 </conditional>
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98 <conditional name="mumplot" >
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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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100 <option value="yes">YES</option>
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101 <option value="no">NO</option>
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102 </param>
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103 <when value="yes" >
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104 <expand macro="mumplot_input" />
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105 </when>
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106 <when value="no" />
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107 </conditional>
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108 </inputs>
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109 <outputs>
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110 <data name="output" format="tabular" from_work_dir="mummer.txt" label="${tool.name} on ${on_string}: alignment" />
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111 <data name="png_output" format="png" from_work_dir="out.png" label="${tool.name} on ${on_string}: plot" >
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112 <filter>mumplot['plot'] == 'yes'</filter>
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113 </data>
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114 </outputs>
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115 <tests>
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116 <test>
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117 <param name="reference_sequence" ftype="fasta" value="human_aqp3.fasta" />
26f2cc1cc1e9 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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120 <param name="plot" value="yes" />
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121 <output name="output" ftype="tabular" compare="diff" value="mummer.txt" />
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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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124 </tests>
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125 <help><![CDATA[
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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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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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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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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>