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comparison mummerplot.xml @ 0:f52a30265797 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 02:39:59 -0500
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children 447a66c9f6e1
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-1:000000000000 0:f52a30265797
1 <tool id="mummer_mummerplot" name="Mummerplot" version="@MUMMER_VERSION@">
2 <description>Generate 2-D dotplot of aligned sequences</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements">
7 <requirement type="package" version="5.2.3">gnuplot</requirement>
8 </expand>
9 <command detect_errors="exit_code">
10 <![CDATA[
11 ln -s $reference_sequence reference.fa &&
12 ln -s $query_sequence query.fa &&
13 mummerplot
14 -b '$breaklen'
15 $color
16 $coverage
17 $filter
18 $fat
19 #if str($labels.IDs) == 'yes':
20 -IdR '$labels.ref_id'
21 -IdQ '$labels.query_id'
22 #end if
23 #if str($sequences.seq_input) == 'yes':
24 -R '$reference_sequence'
25 -Q '$query_sequence'
26 $sequences.layout
27 #end if
28 -s '$size'
29 -terminal png
30 -title '$title'
31 $snp
32 #if $range.custom == 'yes':
33 -x [$range.min_x:$range.max_x]
34 -y [$range.min_y:$range.max_y]
35 #end if
36 '$delta'
37 ]]>
38 </command>
39 <inputs>
40 <param name="delta" type="data" format="tabular" label="Match File" />
41 <param name="reference_sequence" type="data" format="fasta" label="Reference Sequence" />
42 <param name="query_sequence" type="data" format="fasta" label="Query Sequence(s)" />
43 <expand macro="mumplot_input" >
44 <conditional name="sequences" >
45 <param name="seq_input" type="select" label="Plot an ordered set of reference/query sequences?" >
46 <option value="no">NO</option>
47 <option value="yes">YES</option>
48 </param>
49 <when value="yes">
50 <param name="layout" type="boolean" argument="--layout" truevalue="--layout" falsevalue="" label="Layout" help="Layout a .delta multiplot in an intelligible fashion. (--layout)" />
51 </when>
52 <when value="no" />
53 </conditional>
54 </expand>
55 <param name="extra_outs" type="select" label="Output files used to create the plot or just the plot?" >
56 <option value="plot">Just the plot</option>
57 <option value="all">All outputs</option>
58 </param>
59 </inputs>
60 <outputs>
61 <data name="gnuplot" format="txt" from_work_dir="out.gp" label="${tool.name} on ${on_string}: gnuplot" >
62 <filter> extra_outs == 'all' </filter>
63 </data>
64 <data name="fplot" format="txt" from_work_dir="out.fplot" label="${tool.name} on ${on_string}: fplot" >
65 <filter> extra_outs == 'all' </filter>
66 </data>
67 <data name="rplot" format="txt" from_work_dir="out.rplot" label="${tool.name} on ${on_string}: rplot" >
68 <filter> extra_outs == 'all' </filter>
69 </data>
70 <data name="hplot" format="txt" from_work_dir="out.hplot" label="${tool.name} on ${on_string}: hplot" >
71 <filter> extra_outs == 'all' </filter>
72 </data>
73 <data name="output_png" format="png" from_work_dir="out.png" label="${tool.name} on ${on_string}: plot" />
74 </outputs>
75 <tests>
76 <test>
77 <param name="delta" ftype="txt" value="nucmer.txt" />
78 <param name="reference_sequence" ftype="fasta" value="human_aqp3.fasta" />
79 <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta" />
80 <param name="seq_input" value="no" />
81 <param name="extra_outs" value="all" />
82 <output name="gnuplot" ftype="txt" compare="diff" value="gnuplot.txt" />
83 <output name="fplot" ftype="txt" compare="diff" value="fplot.txt" />
84 <output name="rplot" ftype="txt" compare="diff" value="rplot.txt" />
85 <output name="hplot" ftype="txt" compare="diff" value="hplot.txt" />
86 <output name="output_png" ftype="png" compare="sim_size" value="plot.png" />
87 </test>
88 </tests>
89 <help><![CDATA[
90 Mummerplot is a perl script that generates gnuplot scripts and data collections for plotting with the gnuplot utility. It can generate 2-d dotplots and 1-d coverage plots for the output of mummer or nucmer. It can also color dotplots with an identity color gradient.
91
92 **Outputs:**
93 * gnuplot: The gnuplot script
94 * fplot, rplot, hplot: The forward, reverse, and highlighted match information for plotting with gnuplot.
95 * plot: The plotted image file
96
97 **Options:**::
98
99
100 -b Highlight alignments with breakpoints further than breaklen nucleotides from the nearest
101 sequence end
102
103 -color Color plot lines with a percent similarity gradient or turn off all plot color (default
104 color by match dir) If the plot is very sparse, edit the .gp script to plot with
105 'linespoints' instead of 'lines'
106
107 -c Generate a reference coverage plot (default for .tiling)
108
109 --filter Only display .delta alignments which represent the "best" hit to any particular spot on
110 either sequence, i.e. a one-to-one mapping of reference and query subsequences
111
112 --fat Layout sequences using fattest alignment only
113
114 -IdR Plot a particular reference sequence ID on the X-axis
115
116 -IdQ Plot a particular query sequence ID on the Y-axis
117
118 -s Set the output size to small, medium or large (--small) (--medium) (--large) (default 'small')
119
120 --SNP Highlight SNP locations in each alignment
121
122 -title Specify the gnuplot plot title (default none)
123
124 -x Set the xrange for the plot '[min:max]'
125
126 -y Set the yrange for the plot '[min:max]'
127
128 -R Plot an ordered set of reference sequences from Rfile
129
130 -Q Plot an ordered set of query sequences from Qfile
131
132 --layout Layout a .delta multiplot in an intelligible fashion, this option requires the -R -Q options
133
134 ]]></help>
135 <expand macro="citation" />
136 </tool>
137
138
139