Mercurial > repos > iuc > mummer_mummerplot

comparison macros.xml @ 5:fe7926c563f8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit d3549bc73d5fdfdded1c3e63485f5eb98c479d52
author iuc
date Sat, 19 Oct 2024 20:56:11 +0000
parents d42f78f9ab9b
children 466eb9d51f16
comparison
equal deleted inserted replaced
4:d42f78f9ab9b 5:fe7926c563f8
1 <macros> 1 <macros>
2 <token name="@MUMMER_GNUPLOT_MANUAL@"><![CDATA[&& gnuplot < out.gp]]></token> 2 <token name="@MUMMER_GNUPLOT_MANUAL@"><![CDATA[&& gnuplot < out.gp]]></token>
3 <xml name="bio_tools"> 3 <xml name="bio_tools">
4 <xrefs> 4 <xrefs>
5 <xref type="bio.tools">mumer4</xref> 5 <xref type="bio.tools">mummer4</xref>
6 </xrefs> 6 </xrefs>
7 </xml> 7 </xml>
8 <xml name="citation"> 8 <xml name="citation">
9 <citations> 9 <citations>
10 <citation type="doi">10.1371/journal.pcbi.1005944</citation> 10 <citation type="doi">10.1371/journal.pcbi.1005944</citation>
11 </citations> 11 </citations>
12 </xml> 12 </xml>
13 <token name="@TOOL_VERSION@">4.0.0rc1</token>
14 <token name="@VERSION_SUFFIX@">3</token>
15 <token name="@PROFILE@">20.05</token>
13 <xml name="gnuplot_requirement"> 16 <xml name="gnuplot_requirement">
14 <requirement type="package" version="5.4.1">gnuplot</requirement> 17 <requirement type="package" version="5.4.8">gnuplot</requirement>
15 </xml> 18 </xml>
16 <token name="@TOOL_VERSION@">4.0.0rc1</token>
17 <token name="@VERSION_SUFFIX@">2</token>
18 <token name="@PROFILE@">20.05</token>
19 <xml name="requirements"> 19 <xml name="requirements">
20 <requirements> 20 <requirements>
21 <requirement type="package" version="@TOOL_VERSION@">mummer4</requirement> 21 <requirement type="package" version="@TOOL_VERSION@">mummer4</requirement>
22 <requirement type="package" version="1.19.2">samtools</requirement>
22 <yield /> 23 <yield />
23 </requirements> 24 </requirements>
24 </xml> 25 </xml>
25 <xml name="mumplot_input" > 26 <xml name="mumplot_input" >
26 <yield /> 27 <yield />
28 help="Highlight alignments with breakpoints further than breaklen nucleotides from the nearest sequence end. (-b)" /> 29 help="Highlight alignments with breakpoints further than breaklen nucleotides from the nearest sequence end. (-b)" />
29 <param name="color" type="select" label="Color" help="Color plot lines with a percent similarity gradient or turn off all plot color." > 30 <param name="color" type="select" label="Color" help="Color plot lines with a percent similarity gradient or turn off all plot color." >
30 <option value="">Color</option> 31 <option value="">Color</option>
31 <option value="-color">No color (-color)</option> 32 <option value="-color">No color (-color)</option>
32 </param> 33 </param>
33 <param name="coverage" type="select" label="Coverage Plot" help="Generate a reference coverage plot (default for .tiling) or the defualt dotplot." > 34 <param name="coverage" type="select" label="Coverage Plot" help="Generate a reference coverage plot (default for .tiling) or the default dotplot." >
34 <option value="">Dotplot</option> 35 <option value="">Dotplot</option>
35 <option value="-c">Coverage Plot (-c)</option> 36 <option value="-c">Coverage Plot (-c)</option>
36 </param> 37 </param>
37 <param name="filter" type="boolean" argument="--filter" truevalue="--filter" falsevalue="" label="Filter" 38 <param type="boolean" argument="--filter" truevalue="--filter" falsevalue="" label="Filter"
38 help="Only display .delta alignments which represent the 'best' hit to any particular spot on either sequence, i.e. a one-to-one mapping of reference and query subsequences. (--filter)" /> 39 help="Only display .delta alignments which represent the 'best' hit to any particular spot on either sequence, i.e. a one-to-one mapping of reference and query subsequences. (--filter)" />
39 <param name="fat" type="boolean" argument="--fat" truevalue="--fat" falsevalue="" label="Layout sequences using fattest alignment only" help="(--fat)" /> 40 <param type="boolean" argument="--fat" truevalue="--fat" falsevalue="" label="Layout sequences using fattest alignment only" help="(--fat)" />
40 <conditional name="labels" > 41 <conditional name="labels" >
41 <param name="IDs" type="select" label="Plot a particular reference or query sequence?" help="For alignments that used more than one reference/query." > 42 <param name="IDs" type="select" label="Plot a particular reference or query sequence?" help="For alignments that used more than one reference/query." >
42 <option value="no">NO</option> 43 <option value="no">NO</option>
43 <option value="yes">YES</option> 44 <option value="yes">YES</option>
44 </param> 45 </param>
52 <option value="small">Small</option> 53 <option value="small">Small</option>
53 <option value="medium">Medium</option> 54 <option value="medium">Medium</option>
54 <option value="large">Large</option> 55 <option value="large">Large</option>
55 </param> 56 </param>
56 <param name="snp" type="boolean" argument="--SNP" truevalue="--SNP" falsevalue="" label="SNPs" help="Highlight SNP locations in each alignment. (--SNP)" /> 57 <param name="snp" type="boolean" argument="--SNP" truevalue="--SNP" falsevalue="" label="SNPs" help="Highlight SNP locations in each alignment. (--SNP)" />
57 <param name="title" type="text" argument="-title" value="Title" label="Plot Title" help="(-title)" /> 58 <param type="text" argument="-title" value="Title" label="Plot Title" help="(-title)" />
58 <conditional name="range" > 59 <conditional name="range" >
59 <param name="custom" type="select" label="Choose custom X and Y axis ranges?" > 60 <param name="custom" type="select" label="Choose custom X and Y axis ranges?" >
60 <option value="no">NO</option> 61 <option value="no">NO</option>
61 <option value="yes">YES</option> 62 <option value="yes">YES</option>
62 </param> 63 </param>