Mercurial > repos > iuc > mummer_mummerplot

annotate macros.xml @ 3:e89cbb3671a2 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Wed, 01 Sep 2021 07:44:10 +0000
parents 04c2610b97fe
children d42f78f9ab9b
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
1 <macros>
1
447a66c9f6e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 96608e94742d17cb73d57201099ff5f5abbef276"
iuc
parents: 0
diff changeset
2 <token name="@MUMMER_GNUPLOT_MANUAL@"><![CDATA[&& gnuplot < out.gp]]></token>
3
e89cbb3671a2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 2
diff changeset
3 <xml name="bio_tools">
e89cbb3671a2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 2
diff changeset
4 <xrefs>
e89cbb3671a2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 2
diff changeset
5 <xref type="bio.tools">mumer4</xref>
e89cbb3671a2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 2
diff changeset
6 </xrefs>
e89cbb3671a2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents: 2
diff changeset
7 </xml>
0
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
8 <xml name="citation">
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
9 <citations>
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
10 <citation type="bibtex">
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
11 @misc{githubmummer,
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
12 author = {Art Delcher, Stefan Kurtz, Adam Phillippy, Steven Salzberg},
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
13 year = {2012},
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
14 title = {mummer4},
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
15 publisher = {GitHub},
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
16 journal = {GitHub repository},
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
17 url = {https://github.com/mummer4/mummer},
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
18 }</citation>
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
19 </citations>
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
20 </xml>
1
447a66c9f6e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 96608e94742d17cb73d57201099ff5f5abbef276"
iuc
parents: 0
diff changeset
21 <xml name="gnuplot_requirement">
447a66c9f6e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 96608e94742d17cb73d57201099ff5f5abbef276"
iuc
parents: 0
diff changeset
22 <requirement type="package" version="5.2.7">gnuplot</requirement>
447a66c9f6e1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 96608e94742d17cb73d57201099ff5f5abbef276"
iuc
parents: 0
diff changeset
23 </xml>
0
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
24 <token name="@MUMMER_VERSION@">4.0.0beta2</token>
2
04c2610b97fe "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 7ea9a5c6d9e7212c38be96baa6615af1ea9d5a8e"
iuc
parents: 1
diff changeset
25 <token name="@WRAPPER_VERSION@">+galaxy1</token>
0
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
26 <xml name="requirements">
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
27 <requirements>
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
28 <requirement type="package" version="@MUMMER_VERSION@">mummer4</requirement>
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
29 <yield />
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
30 </requirements>
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
31 </xml>
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
32 <xml name="mumplot_input" >
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
33 <yield />
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
34 <param name="breaklen" type="integer" argument="-b" value="20" label="Break Length"
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
35 help="Highlight alignments with breakpoints further than breaklen nucleotides from the nearest sequence end. (-b)" />
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
36 <param name="color" type="select" label="Color" help="Color plot lines with a percent similarity gradient or turn off all plot color." >
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
37 <option value="">Color</option>
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
38 <option value="-color">No color (-color)</option>
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
39 </param>
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
40 <param name="coverage" type="select" label="Coverage Plot" help="Generate a reference coverage plot (default for .tiling) or the defualt dotplot." >
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
41 <option value="">Dotplot</option>
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
42 <option value="-c">Coverage Plot (-c)</option>
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
43 </param>
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
44 <param name="filter" type="boolean" argument="--filter" truevalue="--filter" falsevalue="" label="Filter"
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
45 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)" />
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
46 <param name="fat" type="boolean" argument="--fat" truevalue="--fat" falsevalue="" label="Layout sequences using fattest alignment only" help="(--fat)" />
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
47 <conditional name="labels" >
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
48 <param name="IDs" type="select" label="Plot a particular reference or query sequence?" help="For alignments that used more than one reference/query." >
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
49 <option value="no">NO</option>
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
50 <option value="yes">YES</option>
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
51 </param>
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
52 <when value="yes" >
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
53 <param name="ref_id" type="text" value="ref_id" label="Reference sequence ID" help="(-IdR)" />
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
54 <param name="query_id" type="text" value="query_id" label="Query sequence ID" help="(-IdQ)" />
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
55 </when>
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
56 <when value="no" />
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
57 </conditional>
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
58 <param name="size" type="select" label="Plot Size" help="Set the output size to small, medium or large. (-s)" >
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
59 <option value="small">Small</option>
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
60 <option value="medium">Medium</option>
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
61 <option value="large">Large</option>
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
62 </param>
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
63 <param name="snp" type="boolean" argument="--SNP" truevalue="--SNP" falsevalue="" label="SNPs" help="Highlight SNP locations in each alignment. (--SNP)" />
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
64 <param name="title" type="text" argument="-title" value="Title" label="Plot Title" help="(-title)" />
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
65 <conditional name="range" >
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
66 <param name="custom" type="select" label="Choose custom X and Y axis ranges?" >
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
67 <option value="no">NO</option>
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
68 <option value="yes">YES</option>
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
69 </param>
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
70 <when value="yes" >
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
71 <param name="min_x" type="integer" argument="-x" value="0" label="Minimum X-axis range" help="(-x)" />
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
72 <param name="max_x" type="integer" argument="-x" value="100" label="Maximum X-axis range" help="(-x)" />
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
73 <param name="min_y" type="integer" argument="-y" value="0" label="Minimum Y-axis range" help="(-y)" />
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
74 <param name="max_y" type="integer" argument="-y" value="100" label="Maximum Y-axis range" help="(-y)" />
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
75 </when>
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
76 <when value="no" />
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
77 </conditional>
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
78 </xml>
f52a30265797 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mummer4 commit 8133565adbfc012fa54b96449c2a18d044049107
iuc
parents:
diff changeset
79 </macros>