annotate show-coords.xml @ 0:f8734af48332 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
author iuc
date Wed, 05 Dec 2018 02:38:25 -0500
parents
children b8e2c2f95d26
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
3 <macros>
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
4 <import>macros.xml</import>
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
5 </macros>
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
6 <expand macro="requirements" />
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
7 <command detect_errors="exit_code">
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
8 <![CDATA[
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
9 show-coords
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
10 $merge
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
11 -c
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
12 -H
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
13 -I '$identity'
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
14 -l
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
15 -L '$min_alignment_length'
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
16 $annotate
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
17 $sort
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
18 -T
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
19 '${delta}' > '${output}'
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
20 ]]>
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
21 </command>
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
22 <inputs>
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
31 <option value="-q">Sort output by query IDs and coordinates (-q)</option>
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
33 </param>
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
34 </inputs>
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
35 <outputs>
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
36 <data name="output" format="tabular" from_work_dir="show-coords.txt" >
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
37 <actions>
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
39 </actions>
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
40 </data>
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
41 </outputs>
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
42 <tests>
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
43 <test>
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
44 <param name="delta" ftype="tabular" value="nucmer.txt" />
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
45 <output name="output" ftype="tabular" compare="diff" value="show-coords.txt" />
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
46 </test>
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
47 </tests>
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
48 <help><![CDATA[
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
49 This program parses the delta alignment output of nucmer and displays the coordinates, and other useful information about the alignments.
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
50
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
51 Output is tabular. Below is a description of each column:
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
52 * **[S1]** Start of the alignment region in the reference sequence
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
53 * **[E1]** End of the alignment region in the reference sequence
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
54 * **[S2]** Start of the alignment region in the query sequence
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
55 * **[E2]** End of the alignment region in the query sequence
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
56 * **[LEN 1]** Length of the alignment region in the reference sequence, measured in nucleotides
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
57 * **[LEN 2]** Length of the alignment region in the query sequence, measured in nucleotides
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
58 * **[% IDY]** Percent identity of the alignment, calculated as (number of exact matches) / ([LEN 1] + insertions in the query)
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
59 * **[LEN R]** Length of the reference sequence
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
60 * **[LEN Q]** Length of the query sequence
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
61 * **[COV R]** Percent coverage of the alignment on the reference sequence, calculated as [LEN 1] / [LEN R]
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
62 * **[COV Q]** Percent coverage of the alignment on the query sequence, calculated as [LEN 2] / [LEN Q]
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
63 * **[REF TAG]** The reference FastA ID
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
64 * **[QUERY TAG]** The query FastA ID
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
65
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
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.
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
67
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
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
iuc
parents:
diff changeset
69
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
70 **Options:**::
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
71
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
72 -b Merges overlapping alignments regardless of match dir or frame and does not display any
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
73 identity information.
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
74
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
75 -I Set minimum percent identity to display
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
76
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
77 -L Set minimum alignment length to display
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
78
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
79 -o Annotate maximal alignments between two sequences, i.e. overlaps between reference and query
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
80 sequences
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
81
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
82 -q Sort output lines by query IDs and coordinates
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
83
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
84 -r Sort output lines by reference IDs and coordinates
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
85
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
86 ]]></help>
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
87 <expand macro="citation" />
f8734af48332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
88 </tool>