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comparison 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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1 <tool id="mummer_show_coords" name="Show-Coords" version="@MUMMER_VERSION@">
2 <description>Parse delta file and report coordinates and other information</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code">
8 <![CDATA[
9 show-coords
10 $merge
11 -c
12 -H
13 -I '$identity'
14 -l
15 -L '$min_alignment_length'
16 $annotate
17 $sort
18 -T
19 '${delta}' > '${output}'
20 ]]>
21 </command>
22 <inputs>
23 <param name="delta" type="data" format="tabular" label="Match file from Nucmer" />
24 <param name="merge" type="boolean" argument="-b" truevalue="-b" falsevalue="" label="Merge"
25 help="Merges overlapping alignments regardless of match dir or frame and does not display any idenitity information. (-b)" />
26 <param name="identity" type="float" argument="-I" value="75.0" label="Identity" help="Set minimum percent identity to display (-I)" />
27 <param name="min_alignment_length" type="integer" argument="-L" value="100" label="Minimum Alignment Length" help="Set minimum alignment length to display (-L)" />
28 <param name="annotate" type="boolean" argument="-o" truevalue="-o" falsevalue="" label="Annotate"
29 help="Annotate maximal alignments between two sequences, i.e. overlaps between reference and query sequences (-o)" />
30 <param name="sort" type="select" label="Sorting strategy for output" >
31 <option value="-q">Sort output by query IDs and coordinates (-q)</option>
32 <option value="-r">Sort output by reference IDs and coordinates (-r)</option>
33 </param>
34 </inputs>
35 <outputs>
36 <data name="output" format="tabular" from_work_dir="show-coords.txt" >
37 <actions>
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]" />
39 </actions>
40 </data>
41 </outputs>
42 <tests>
43 <test>
44 <param name="delta" ftype="tabular" value="nucmer.txt" />
45 <output name="output" ftype="tabular" compare="diff" value="show-coords.txt" />
46 </test>
47 </tests>
48 <help><![CDATA[
49 This program parses the delta alignment output of nucmer and displays the coordinates, and other useful information about the alignments.
50
51 Output is tabular. Below is a description of each column:
52 * **[S1]** Start of the alignment region in the reference sequence
53 * **[E1]** End of the alignment region in the reference sequence
54 * **[S2]** Start of the alignment region in the query sequence
55 * **[E2]** End of the alignment region in the query sequence
56 * **[LEN 1]** Length of the alignment region in the reference sequence, measured in nucleotides
57 * **[LEN 2]** Length of the alignment region in the query sequence, measured in nucleotides
58 * **[% IDY]** Percent identity of the alignment, calculated as (number of exact matches) / ([LEN 1] + insertions in the query)
59 * **[LEN R]** Length of the reference sequence
60 * **[LEN Q]** Length of the query sequence
61 * **[COV R]** Percent coverage of the alignment on the reference sequence, calculated as [LEN 1] / [LEN R]
62 * **[COV Q]** Percent coverage of the alignment on the query sequence, calculated as [LEN 2] / [LEN Q]
63 * **[REF TAG]** The reference FastA ID
64 * **[QUERY TAG]** The query FastA ID
65
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.
67
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.
69
70 **Options:**::
71
72 -b Merges overlapping alignments regardless of match dir or frame and does not display any
73 identity information.
74
75 -I Set minimum percent identity to display
76
77 -L Set minimum alignment length to display
78
79 -o Annotate maximal alignments between two sequences, i.e. overlaps between reference and query
80 sequences
81
82 -q Sort output lines by query IDs and coordinates
83
84 -r Sort output lines by reference IDs and coordinates
85
86 ]]></help>
87 <expand macro="citation" />
88 </tool>