Mercurial > repos > iuc > hyphy_meme

annotate hyphy_meme.xml @ 4:8366d5b28b49 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/hyphy/ commit e31ca8967662206fc17d608efea398502569437a"
author iuc
date Mon, 17 Feb 2020 14:53:45 -0500
parents 33040ebb30c6
children 4d5768ad6316
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
1 <?xml version="1.0"?>
3
33040ebb30c6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6b2cd926797bb94fba9d0e319a2dbcff6ee37735"
iuc
parents: 2
diff changeset
2 <tool id="hyphy_meme" name="HyPhy-MEME" version="@VERSION@+galaxy0">
0
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
3 <description>Mixed Effects Model of Evolution</description>
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
4 <macros>
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
5 <import>macros.xml</import>
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
6 </macros>
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
7 <expand macro="requirements"/>
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
9 ln -s '$input_file' meme_input.fa &&
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
10 ln -s '$input_nhx' meme_input.nhx &&
2
b15d64d85c03 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"
iuc
parents: 1
diff changeset
11 @HYPHYMPI@ meme
0
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
12 --alignment ./meme_input.fa
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
13 --tree ./meme_input.nhx
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
14 --code '$gencodeid'
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
15 --branches '$branches'
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
16 --pvalue '$p_value'
2
b15d64d85c03 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"
iuc
parents: 1
diff changeset
17 --output '$meme_output'
0
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
18 > '$meme_log'
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
19 ]]></command>
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
20 <inputs>
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
21 <expand macro="inputs"/>
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
22 <expand macro="gencode"/>
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
23 <expand macro="branches"/>
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
24 <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value threshold"/>
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
25 </inputs>
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
26 <outputs>
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
27 <data name="meme_log" format="txt"/>
2
b15d64d85c03 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"
iuc
parents: 1
diff changeset
28 <data name="meme_output" format="hyphy_results.json" />
0
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
29 </outputs>
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
30 <tests>
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
31 <test>
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
32 <param name="input_file" ftype="fasta" value="meme-in1.fa"/>
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
33 <param name="input_nhx" ftype="nhx" value="meme-in1.nhx"/>
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
34 <param name="branches" value="All"/>
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
35 <param name="p_value" value="0.1"/>
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
36 <output name="meme_output" file="meme-out1.json" compare="sim_size"/>
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
37 </test>
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
38 </tests>
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
39 <help><![CDATA[
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
40 MEME employs a mixed-effects maximum likelihood approach to test the hypothesis that individual sites have been subject to episodic positive or diversifying selection. In other words, MEME aims to detect sites evolving under positive selection under a proportion of branches.
1
d02c8e6f7f2a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
iuc
parents: 0
diff changeset
41
d02c8e6f7f2a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
iuc
parents: 0
diff changeset
42 See the online documentation_ for more information.
d02c8e6f7f2a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
iuc
parents: 0
diff changeset
43
d02c8e6f7f2a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
iuc
parents: 0
diff changeset
44 .. _documentation: http://hyphy.org/methods/selection-methods/#meme
0
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
45 ]]></help>
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
46 <expand macro="citations">
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
47 <citation type="doi">10.1371/journal.pgen.1002764</citation>
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
48 </expand>
7b3f9c78cf6d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
diff changeset
49 </tool>