Mercurial > repos > iuc > mummer_show_coords

annotate show-coords.xml @ 0:f8734af48332 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
author iuc
date Wed, 05 Dec 2018 02:38:25 -0500
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0
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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1 <tool id="mummer_show_coords" name="Show-Coords" version="@MUMMER_VERSION@">
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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2 <description>Parse delta file and report coordinates and other information</description>
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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3 <macros>
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4 <import>macros.xml</import>
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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5 </macros>
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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6 <expand macro="requirements" />
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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7 <command detect_errors="exit_code">
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8 <![CDATA[
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9 show-coords
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10 $merge
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11 -c
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12 -H
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13 -I '$identity'
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14 -l
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15 -L '$min_alignment_length'
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16 $annotate
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17 $sort
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18 -T
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19 '${delta}' > '${output}'
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20 ]]>
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21 </command>
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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22 <inputs>
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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23 <param name="delta" type="data" format="tabular" label="Match file from Nucmer" />
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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24 <param name="merge" type="boolean" argument="-b" truevalue="-b" falsevalue="" label="Merge"
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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25 help="Merges overlapping alignments regardless of match dir or frame and does not display any idenitity information. (-b)" />
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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26 <param name="identity" type="float" argument="-I" value="75.0" label="Identity" help="Set minimum percent identity to display (-I)" />
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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27 <param name="min_alignment_length" type="integer" argument="-L" value="100" label="Minimum Alignment Length" help="Set minimum alignment length to display (-L)" />
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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28 <param name="annotate" type="boolean" argument="-o" truevalue="-o" falsevalue="" label="Annotate"
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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29 help="Annotate maximal alignments between two sequences, i.e. overlaps between reference and query sequences (-o)" />
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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30 <param name="sort" type="select" label="Sorting strategy for output" >
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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31 <option value="-q">Sort output by query IDs and coordinates (-q)</option>
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32 <option value="-r">Sort output by reference IDs and coordinates (-r)</option>
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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33 </param>
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34 </inputs>
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35 <outputs>
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36 <data name="output" format="tabular" from_work_dir="show-coords.txt" >
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37 <actions>
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38 <action name="column_names" type="metadata" default="[S1], [E1], [S2], [E2], [LEN 1], [LEN 2], [% IDY], [LEN R], [LEN Q], [COV R], [COV Q], [REF TAG], [QUERY TAG]" />
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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39 </actions>
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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40 </data>
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41 </outputs>
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42 <tests>
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43 <test>
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44 <param name="delta" ftype="tabular" value="nucmer.txt" />
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45 <output name="output" ftype="tabular" compare="diff" value="show-coords.txt" />
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46 </test>
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47 </tests>
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48 <help><![CDATA[
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49 This program parses the delta alignment output of nucmer and displays the coordinates, and other useful information about the alignments.
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50
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51 Output is tabular. Below is a description of each column:
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52 * **[S1]** Start of the alignment region in the reference sequence
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53 * **[E1]** End of the alignment region in the reference sequence
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54 * **[S2]** Start of the alignment region in the query sequence
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55 * **[E2]** End of the alignment region in the query sequence
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56 * **[LEN 1]** Length of the alignment region in the reference sequence, measured in nucleotides
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57 * **[LEN 2]** Length of the alignment region in the query sequence, measured in nucleotides
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58 * **[% IDY]** Percent identity of the alignment, calculated as (number of exact matches) / ([LEN 1] + insertions in the query)
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59 * **[LEN R]** Length of the reference sequence
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60 * **[LEN Q]** Length of the query sequence
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61 * **[COV R]** Percent coverage of the alignment on the reference sequence, calculated as [LEN 1] / [LEN R]
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62 * **[COV Q]** Percent coverage of the alignment on the query sequence, calculated as [LEN 2] / [LEN Q]
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63 * **[REF TAG]** The reference FastA ID
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64 * **[QUERY TAG]** The query FastA ID
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65
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66 There is also an optional final column (turned on with the "Annotate" parameter) that will contain some 'annotations'. The Annotate option will annotate alignments that represent overlaps between two sequences. Sometimes, nucmer will extend adjacent clusters past one another, thus causing a somewhat redundant output, this option will notify users of such rare occurrences.
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67
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68 The Percent Coverage and Sequence Length options are useful when comparing two sets of assembly contigs, in that these options help determine if an alignment spans an entire contig, or is just a partial hit to a different read. The Merge option is useful when the user wishes to identify sytenic regions between two genomes, but is not particularly interested in the actual alignment similarity or appearance. This option also disregards match orientation, so should not be used if this information is needed.
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
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69
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70 **Options:**::
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71
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72 -b Merges overlapping alignments regardless of match dir or frame and does not display any
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73 identity information.
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74
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75 -I Set minimum percent identity to display
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76
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77 -L Set minimum alignment length to display
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78
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79 -o Annotate maximal alignments between two sequences, i.e. overlaps between reference and query
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80 sequences
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81
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82 -q Sort output lines by query IDs and coordinates
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83
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84 -r Sort output lines by reference IDs and coordinates
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85
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86 ]]></help>
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87 <expand macro="citation" />
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88 </tool>