Mercurial > repos > iuc > mummer_mummerplot

comparison mummerplot.xml @ 4:fb43e8887350 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 026db7297e987c1b7ce7f5dd4f8746d1bd435538
author iuc
date Mon, 18 Mar 2024 12:41:02 +0000
parents 4fc0cb2ac8ae
children
comparison
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3:4fc0cb2ac8ae 4:fb43e8887350
47 <param name="seq_input" type="select" label="Plot an ordered set of reference/query sequences?" > 47 <param name="seq_input" type="select" label="Plot an ordered set of reference/query sequences?" >
48 <option value="no">NO</option> 48 <option value="no">NO</option>
49 <option value="yes">YES</option> 49 <option value="yes">YES</option>
50 </param> 50 </param>
51 <when value="yes"> 51 <when value="yes">
52 <param name="layout" type="boolean" argument="--layout" truevalue="--layout" falsevalue="" label="Layout" help="Layout a .delta multiplot in an intelligible fashion. (--layout)" /> 52 <param type="boolean" argument="--layout" truevalue="--layout" falsevalue="" label="Layout" help="Layout a .delta multiplot in an intelligible fashion. (--layout)" />
53 </when> 53 </when>
54 <when value="no" /> 54 <when value="no" />
55 </conditional> 55 </conditional>
56 </expand> 56 </expand>
57 <param name="extra_outs" type="select" label="Output files used to create the plot or just the plot?" > 57 <param name="extra_outs" type="select" label="Output files used to create the plot or just the plot?" >
73 <filter> extra_outs == 'all' </filter> 73 <filter> extra_outs == 'all' </filter>
74 </data> 74 </data>
75 <data name="output_png" format="png" from_work_dir="out.png" label="${tool.name} on ${on_string}: plot" /> 75 <data name="output_png" format="png" from_work_dir="out.png" label="${tool.name} on ${on_string}: plot" />
76 </outputs> 76 </outputs>
77 <tests> 77 <tests>
78 <test> 78 <test expect_num_outputs="5">
79 <param name="delta" value="nucmer.txt" ftype="tabular" /> 79 <param name="delta" value="nucmer.txt" ftype="tabular" />
80 <param name="reference_sequence" ftype="fasta" value="human_aqp3.fasta" /> 80 <param name="reference_sequence" ftype="fasta" value="human_aqp3.fasta" />
81 <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta" /> 81 <param name="query_sequence" ftype="fasta" value="mouse_aqp3.fasta" />
82 <param name="seq_input" value="no" /> 82 <param name="seq_input" value="no" />
83 <param name="extra_outs" value="all" /> 83 <param name="extra_outs" value="all" />
97 * plot: The plotted image file 97 * plot: The plotted image file
98 98
99 **Options:**:: 99 **Options:**::
100 100
101 101
102 -b Highlight alignments with breakpoints further than breaklen nucleotides from the nearest 102 -b Highlight alignments with breakpoints further than breaklen nucleotides from the nearest
103 sequence end 103 sequence end
104 104
105 -color Color plot lines with a percent similarity gradient or turn off all plot color (default 105 -color Color plot lines with a percent similarity gradient or turn off all plot color (default
106 color by match dir) If the plot is very sparse, edit the .gp script to plot with 106 color by match dir) If the plot is very sparse, edit the .gp script to plot with
107 'linespoints' instead of 'lines' 107 'linespoints' instead of 'lines'
108 108
109 -c Generate a reference coverage plot (default for .tiling) 109 -c Generate a reference coverage plot (default for .tiling)
110 110
111 --filter Only display .delta alignments which represent the "best" hit to any particular spot on 111 --filter Only display .delta alignments which represent the "best" hit to any particular spot on
112 either sequence, i.e. a one-to-one mapping of reference and query subsequences 112 either sequence, i.e. a one-to-one mapping of reference and query subsequences
113 113
114 --fat Layout sequences using fattest alignment only 114 --fat Layout sequences using fattest alignment only
115 115
116 -IdR Plot a particular reference sequence ID on the X-axis 116 -IdR Plot a particular reference sequence ID on the X-axis