Mercurial > repos > galaxy-australia > smudgeplot

annotate smudgeplot.xml @ 2:e53b0473d575 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 72c2236cfd6e175ca3b0aed888e3de544d884e3f-dirty"
author galaxy-australia
date Sun, 08 May 2022 10:43:40 +0000
parents 28f5d7ea992a
children 24e471d13fe9
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
1 <tool id="smudgeplot" name="Smudgeplot" version="@TOOL_VERSION@+galaxy+@VERSION_SUFFIX@">
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
2 <description> - inference of ploidy and heterozygosity structure using whole genome sequencing</description>
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
3
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
4 <macros>
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
5 <token name="@TOOL_VERSION@">0.2.5</token>
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
6 <token name="@VERSION_SUFFIX@">1</token>
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
7 </macros>
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
8
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
9 <xrefs>
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
10 <xref type="bio.tools">smudgeplots</xref>
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
11 </xrefs>
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
12
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
13 <requirements>
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
14 <requirement type="package" version="@TOOL_VERSION@">smudgeplot</requirement>
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
15 <requirement type="package" version="2.3.0">kmer-jellyfish</requirement>
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
16 </requirements>
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
17
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
18 <command detect_errors="exit_code"><![CDATA[
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
19
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
20 #if $file.input.input_select == 'reads'
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
21
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
22 ## ~~~~~~~~~~~~~~~ Generate kmer-dump with presets ~~~~~~~~~~~~~~~~~~~~~
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
23
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
24 ## Jellyfish kmer count
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
25 ## ---------------------------------------------------------------------
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
26
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
27 #if $file.input.reads[0].is_of_type("fastq.gz") or $file.input.reads[0].is_of_type("fasta.gz")
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
28 gunzip -c
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
29 #for $f in $file.input.reads
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
30 #if $f
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
31 '$f'
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
32 #end if
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
33 | jellyfish count -m 21 -t 4 -s 1M -o 1_counts.jf -C /dev/stdin
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
34 #end for
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
35
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
36 #else
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
37 jellyfish count -m 21 -t 4 -s 1M -o 1_counts.jf -C
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
38 #for $f in $file.input.reads
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
39 #if $f
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
40 '$f'
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
41 #end if
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
42 #end for
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
43 #end if
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
44
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
45 && jellyfish histo 1_counts.jf > 1_kmer_k21.hist
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
46
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
47 ## Calculate lower and upper kmer count cutoffs
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
48 ## ---------------------------------------------------------------------
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
49
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
50 #if $file.input.lower_cutoff is not None:
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
51 && L=$file.input.lower_cutoff
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
52 #else
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
53 && L=\$(smudgeplot.py cutoff 1_kmer_k21.hist L)
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
54 #end if
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
55
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
56 #if $file.input.upper_cutoff is not None:
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
57 && U=$file.input.upper_cutoff
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
58 #else
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
59 && U=\$(smudgeplot.py cutoff 1_kmer_k21.hist U)
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
60 #end if
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
61
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
62 ## ---------------------------------------------------------------------
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
63 ## Dump and extract coverage
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
64
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
65 && echo "Dump with cutoffs L=\$L, U=\$U"
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
66 && jellyfish dump -c -L \$L -U \$U 1_counts.jf > 2_dump.jf
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
67 && smudgeplot.py hetkmers -o 2_kmer_pairs 2_dump.jf
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
68
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
69 #else
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
70
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
71 ## ~~~~~~~~~~~~~~~~~~~ Use provided kmer dump ~~~~~~~~~~~~~~~~~~~~~~~~~~
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
72
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
73 smudgeplot.py hetkmers -o 2_kmer_pairs '$file.input.dump'
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
74
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
75 #end if
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
76
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
77 ## ---------------------------------------------------------------------
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
78 ## Plot
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
79
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
80 && smudgeplot.py plot 2_kmer_pairs_coverages.tsv -o my_genome
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
81
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
82 ]]></command>
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
83
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
84 <inputs>
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
85 <section name="file" title="File inputs" expanded="true">
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
86 <conditional name="input">
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
87 <param
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
88 name="input_select" type="select" label="Select input type"
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
89 help="For more control, create your own Kmer dump using Jellyfish.
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
90 See Smudgeplot on GitHub for more details: https://github.com/KamilSJaron/smudgeplot"
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
91 >
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
92 <option value="reads" selected="true"> Sequencing reads </option>
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
93 <option value="dump"> Kmer dump file </option>
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
94 </param>
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
95
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
96 <when value="reads">
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
97 <param
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
98 name="reads" type="data" format="fastq,fasta"
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
99 label="Sequencing reads" multiple="true"
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
100 help="Sequencing reads corresponding to your genome.
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
101 Don't worry about read pairing as it is not used in Kmer-counting.
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
102 If selecting multiple datasets, please do not mix datatypes!"
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
103 />
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
104
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
105 <param
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
106 name="lower_cutoff"
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
107 label="Lower kmer cutoff"
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
108 type="integer"
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
109 optional="true"
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
110 help="Optionally set a manual lower limit for filtering kmers with
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
111 smudgeplot hetkmers. If no value is set, a cutoff will be
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
112 estimated with smudgeplot cutoff. Use the GenomeScope tool to
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
113 visualize your kmer histogram when choosing cutoff values."
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
114 />
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
115
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
116 <param
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
117 name="upper_cutoff"
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
118 label="Upper kmer cutoff"
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
119 type="integer"
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
120 optional="true"
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
121 help="Optionally set a manual upper limit for filtering kmers with
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
122 smudgeplot hetkmers. If no value is set, a cutoff will be
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
123 estimated with smudgeplot cutoff. Use the GenomeScope tool to
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
124 visualize your kmer histogram when choosing cutoff values."
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
125 />
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
126 </when>
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
127
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
128 <when value="dump">
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
129 <param
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
130 name="dump" type="data" format="txt"
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
131 label="Kmer dump"
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
132 help="Upload your own Kmer dump file created with the Jellyfish or KMC tool.
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
133 This enables control over kmer-counting parameters."
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
134 />
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
135 </when>
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
136 </conditional>
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
137 </section>
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
138
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
139 <param name="table_output" type="boolean" label="Output summary table"></param>
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
140 <param name="verbose_output" type="boolean" label="Output verbose summary"></param>
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
141 <param name="warnings_output" type="boolean" label="Output genome warnings"></param>
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
142 </inputs>
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
143
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
144 <outputs>
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
145 <data
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
146 name="smudgeplot" format="png"
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
147 from_work_dir="my_genome_smudgeplot.png"
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
148 label="${tool.name} on ${on_string}: Smudgeplot"
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
149 />
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
150 <data
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
151 name="smudgeplot_log" format="png"
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
152 from_work_dir="my_genome_smudgeplot_log10.png"
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
153 label="${tool.name} on ${on_string}: Smudgeplot (log10)"
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
154 />
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
155 <data
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
156 name="genome_summary" format="tabular"
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
157 from_work_dir="my_genome_summary_table.tsv"
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
158 label="${tool.name} on ${on_string}: Genome summary table"
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
159 >
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
160 <filter>table_output</filter>
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
161 </data>
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
162 <data
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
163 name="genome_summary_verbose" format="txt"
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
164 from_work_dir="my_genome_verbose_summary.txt"
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
165 label="${tool.name} on ${on_string}: Genome verbose summary"
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
166 >
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
167 <filter>verbose_output</filter>
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
168 </data>
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
169 <data
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
170 name="genome_warnings" format="txt"
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
171 from_work_dir="my_genome_warnings.txt"
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
172 label="${tool.name} on ${on_string}: Genome warnings"
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
173 >
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
174 <filter>warnings_output</filter>
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
175 </data>
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
176 </outputs>
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
177
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
178 <tests>
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
179 <test>
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
180 <param name="input_select" value="reads"/>
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
181 <param name="reads" value="test_reads.fasta" ftype="fasta"/>
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
182 <param name="lower_cutoff" value="2"/>
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
183 <param name="upper_cutoff" value="25"/>
1
28f5d7ea992a "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 77b725548ca96873177fd13be0175032558ffe68"
galaxy-australia
parents: 0
diff changeset
184 <output name="smudgeplot" ftype="png" file="my_genome_smudgeplot.png" compare="sim_size"/>
0
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
185 </test>
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
186 </tests>
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
187
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
188 <help><![CDATA[
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
189
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
190 .. class:: infomark
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
191
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
192 **What it does**
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
193
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
194 This tool extracts heterozygous kmer pairs from kmer count databases and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovB / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc.
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
195
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
196 Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example:
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
197
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
198 .. image:: https://raw.githubusercontent.com/usegalaxy-au/tools-au/master/tools/smudgeplot/static/img/smudge.png
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
199 :height: 520
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
200 :alt: Smudge plot image
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
201
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
202 Every haplotype structure has a unique smudge on the graph and the heat of the smudge indicates how frequently the haplotype structure is represented in the genome compared to the other structures. The image above is an ideal case, where the sequencing coverage is sufficient to beautifully separate all the smudges, providing very strong and clear evidence of triploidy.
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
203
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
204 Please see `Smudgeplot on GitHub <https://github.com/KamilSJaron/smudgeplot>`_
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
205 for further documentation and tutorials.
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
206
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
207 **Inputs**
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
208
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
209 You have two choices when running Smudgeplot in Galaxy:
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
210
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
211 1. Input reads file(s) for default kmer-counting with Jellyfish
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
212
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
213 This should be at least one file which providing coverage of your genome of interest.
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
214 The tool accepts compressed (.gz) inputs. If choosing this option, you can
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
215 (optionally) specify manual cutoff values for the kmer dump step. The Smudgeplot
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
216 docs suggest that you can use GenomeScope on a kmer histogram in order to choose
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
217 reasonable lower and upper cutoff values.
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
218
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
219 2. Input your own kmer dump file for more control of kmer counting parameters
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
220
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
221 This file would be created by running ``jellyfish count`` and then ``jellyfish dump`` - the process is well described
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
222 `on GitHub <https://github.com/KamilSJaron/smudgeplot>`_.
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
223
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
224 **Outputs**
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
225
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
226 - ``smudgeplot.png`` smudgeplot image
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
227 - ``smudgeplot_log10.png`` smudgeplot with log scale
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
228 - ``my_genome_summary.tsv`` summarized genome statistics
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
229 - ``my_genome_verbose.txt`` detailed genome statistics
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
230 - ``my_genome_warnings.txt`` warnings emitted from the Smudgeplot tool
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
231
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
232 **Default operation**
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
233
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
234 If choosing reads as the input, a default kmer counting procedure will be used
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
235 to create a kmer dump. This default process is summarized as follows:
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
236
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
237 - ``jellyfish count -m 21 > counts.jf``
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
238 - ``jellyfish histo counts.jf > counts.hist``
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
239 - ``smudgeplot.py cutoff counts.hist`` to get kmer cutoff values (U & L)
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
240 - ``jellyfish dump -c -L <L> -U <U> counts.jf > dump.jf``
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
241
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
242 The kmer dump file is then used to create a smudgeplot:
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
243
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
244 - ``smudgeplot.py hetkmers -o kmer_pairs dump.jf``
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
245 - ``smudgeplot.py plot kmer_pairs_coverages.tsv -o my_genome``
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
246
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
247 ]]></help>
2
e53b0473d575 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 72c2236cfd6e175ca3b0aed888e3de544d884e3f-dirty"
galaxy-australia
parents: 1
diff changeset
248 <citations>
e53b0473d575 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 72c2236cfd6e175ca3b0aed888e3de544d884e3f-dirty"
galaxy-australia
parents: 1
diff changeset
249 <citation type="doi">https://doi.org/10.1038/s41467-020-14998-3</citation>
e53b0473d575 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 72c2236cfd6e175ca3b0aed888e3de544d884e3f-dirty"
galaxy-australia
parents: 1
diff changeset
250 </citations>
0
19462781bfe4 "planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7a48d3cb54e682fb7dad612417391f327288dd0a-dirty"
galaxy-australia
parents:
diff changeset
251 </tool>