Mercurial > repos > iuc > mummer_show_coords
comparison macros.xml @ 4:cf3c9489c088 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 026db7297e987c1b7ce7f5dd4f8746d1bd435538
author | iuc |
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date | Mon, 18 Mar 2024 12:41:14 +0000 |
parents | b4124df98b26 |
children |
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3:b4124df98b26 | 4:cf3c9489c088 |
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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> |