Mercurial > repos > iuc > iqtree

annotate iqtree.xml @ 18:09961138fcaf draft default tip

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/iqtree/ commit ed98c907217fd95aa455f4f74de74e9b3893c1d3
author iuc
date Mon, 05 May 2025 16:50:48 +0000
parents 4e7fd03b0a13
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
12
df8bf04acdb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3b1c44e42b042ccbbe2d9e01c77d18f109d4984f"
iuc
parents: 11
diff changeset
1 <tool id="iqtree" name="IQ-TREE" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" >
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
2 <description>Phylogenomic / evolutionary tree construction from multiple sequences</description>
2
b2fbfb61f019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 686710a7d313b828f1daed20c4055479727f2d91
iuc
parents: 1
diff changeset
3 <macros>
b2fbfb61f019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 686710a7d313b828f1daed20c4055479727f2d91
iuc
parents: 1
diff changeset
4 <import>iqtree_macros.xml</import>
b2fbfb61f019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 686710a7d313b828f1daed20c4055479727f2d91
iuc
parents: 1
diff changeset
5 </macros>
13
9454e1c4f022 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 01204be0cb805c82785dcef994237b96a39ee40c
iuc
parents: 12
diff changeset
6 <expand macro="xrefs"/>
2
b2fbfb61f019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 686710a7d313b828f1daed20c4055479727f2d91
iuc
parents: 1
diff changeset
7 <expand macro="requirements" />
4
388a6d4a892b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
9 iqtree
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
10 --prefix PREF
4
388a6d4a892b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
11 #if $general_options.short_alignments:
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
12 -T 1
4
388a6d4a892b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
13 #else:
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
14 -T \${GALAXY_SLOTS:-10}
4
388a6d4a892b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
15 #end if
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
16 --redo
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
17
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
18 ## file
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
19 #if $general_options.s
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
20 -s '$general_options.s'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
21 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
22
7
cef78e63f746 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af"
iuc
parents: 6
diff changeset
23 #if $general_options.o
cef78e63f746 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af"
iuc
parents: 6
diff changeset
24 -o '$general_options.o'
cef78e63f746 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af"
iuc
parents: 6
diff changeset
25 #end if
12
df8bf04acdb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3b1c44e42b042ccbbe2d9e01c77d18f109d4984f"
iuc
parents: 11
diff changeset
26 --seqtype $general_options.seqtype
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
27 ## file
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
28 #if $general_options.t
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
29 -t '$general_options.t'
11
d460875c806a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f"
iuc
parents: 10
diff changeset
30 $tree_parameters.constructing_consensus.contree
d460875c806a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f"
iuc
parents: 10
diff changeset
31 $tree_parameters.constructing_consensus.connet
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
32 #if str($tree_parameters.constructing_consensus.burnin) != ''
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
33 --burnin '$tree_parameters.constructing_consensus.burnin'
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
34 #end if
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
35
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
36 ## file
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
37 #if $tree_parameters.constructing_consensus.support
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
38 --support '$tree_parameters.constructing_consensus.support'
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
39 #end if
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
40
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
41 #if str($tree_parameters.constructing_consensus.suptag) != ''
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
42 --suptag '$tree_parameters.constructing_consensus.suptag'
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
43 #end if
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
44
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
45 ## file
11
d460875c806a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f"
iuc
parents: 10
diff changeset
46 #if $tree_parameters.computing_robinson_foulds.tree_dist_all
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
47 $tree_parameters.computing_robinson_foulds.tree_dist_all
11
d460875c806a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f"
iuc
parents: 10
diff changeset
48 --tree-dist $tree_parameters.computing_robinson_foulds.tree_dist
d460875c806a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f"
iuc
parents: 10
diff changeset
49 --tree-dist2 $tree_parameters.computing_robinson_foulds.tree_dist2
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
50 #end if
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
51 $tree_parameters.ancestral_state.ancestral
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
52 #if $tree_parameters.ancestral_state.asr_min:
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
53 --asr-min $tree_parameters.ancestral_state.asr_min
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
54 #end if
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
55 #if $tree_parameters.concordance_factor.gcf:
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
56 --gcf '$tree_parameters.concordance_factor.gcf'
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
57 #end if
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
58 #if $tree_parameters.concordance_factor.scf:
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
59 --scf '$tree_parameters.concordance_factor.scf'
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
60 #end if
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
61 $tree_parameters.concordance_factor.df_tree
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
62 $tree_parameters.concordance_factor.cf_verbose
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
63 $tree_parameters.concordance_factor.cf_quartet
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
64 $tree_parameters.symmetry_test.symtest
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
65 $tree_parameters.symmetry_test.symtest_remove_bad
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
66 $tree_parameters.symmetry_test.symtest_remove_good
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
67 $tree_parameters.symmetry_test.symtest_keep_zero
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
68 #if $tree_parameters.symmetry_test.symtest_pval:
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
69 --symtest-pval $tree_parameters.symmetry_test.symtest_pval
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
70 #end if
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
71 #if $tree_parameters.symmetry_test.symtest_type:
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
72 --symtest-type $tree_parameters.symmetry_test.symtest_type
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
73 #end if
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
74 #end if
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
75
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
76 ## date options
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
77 #if str($time_tree.date_source.select_source) == 'dataset':
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
78 #if $time_tree.date_source.date:
8
2e0636f07c37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit a58c8d3c985688e49908dfeceab5be4352d71563"
iuc
parents: 7
diff changeset
79 --date '$time_tree.date_source.date'
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
80 #end if
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
81 #elif str($time_tree.date_source.select_source) == 'input':
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
82 --date TAXNAME
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
83 #if str($time_tree.date_source.date_tip) != '':
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
84 --date-tip '$time_tree.date_source.date_tip'
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
85 #end if
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
86 #if str($time_tree.date_source.date_root) != '':
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
87 --date-root '$time_tree.date_source.date_root'
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
88 #end if
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
89 #if str($time_tree.date_source.date_ci) != '':
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
90 --date-ci '$time_tree.date_source.date_ci'
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
91 #end if
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
92 #if str($time_tree.date_source.clock_sd) != '':
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
93 --clock-sd '$time_tree.date_source.clock_sd'
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
94 #end if
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
95 #if str($time_tree.date_source.date_outlier) != '':
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
96 --date-outlier '$time_tree.date_source.date_outlier'
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
97 #end if
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
98 #if str($time_tree.date_source.date_options) != '':
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
99 --date-options '$time_tree.date_source.date_options'
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
100 #end if
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
101 --dating LSD
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
102 $time_tree.date_source.date_no_outgroup
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
103 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
104
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
105 ## file
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
106 #if str($general_options.epsilon) != ''
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
107 --epsilon '$general_options.epsilon'
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
108 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
109
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
110 #if str($general_options.seed) != ''
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
111 --seed '$general_options.seed'
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
112 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
113
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
114 $general_options.keep_ident
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
115 $general_options.safe
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
116
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
117 #if str($likelihood_mapping.lmap) != ''
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
118 --lmap '$likelihood_mapping.lmap'
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
119 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
120
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
121 ## file
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
122 #if $likelihood_mapping.lmclust
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
123 --lmclust '$likelihood_mapping.lmclust'
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
124 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
125
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
126 $likelihood_mapping.quartetlh
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
127
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
128 #if $modelling_parameters.automatic_model.cond_model.opt_custommodel:
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
129 -m '$modelling_parameters.automatic_model.cond_model.m'
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
130 #else:
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
131 #if str($modelling_parameters.automatic_model.cond_model.m) != ''
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
132 #if $modelling_parameters.automatic_model.cond_model.additional_models:
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
133 -m '$modelling_parameters.automatic_model.cond_model.m${$modelling_parameters.automatic_model.cond_model.additional_models}'
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
134 #else:
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
135 -m '$modelling_parameters.automatic_model.cond_model.m'
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
136 #end if
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
137 #end if
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
138 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
139
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
140 #if str($modelling_parameters.automatic_model.merge_strategy.merge) != 'none':
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
141 --merge $modelling_parameters.automatic_model.merge_strategy.merge
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
142 #if str($modelling_parameters.automatic_model.merge_strategy.merge) == 'rcluster':
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
143 --rcluster $modelling_parameters.automatic_model.merge_strategy.rcluster
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
144 #end if
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
145 #if str($modelling_parameters.automatic_model.merge_strategy.merge) == 'rclusterf':
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
146 --rclusterf $modelling_parameters.automatic_model.merge_strategy.rclusterf
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
147 #end if
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
148 #if str($modelling_parameters.automatic_model.merge_strategy.merge) in ['rcluster', 'rclusterf']:
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
149 --rcluster-max $modelling_parameters.automatic_model.merge_strategy.rcluster_max
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
150 #end if
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
151 #end if
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
152
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
153 #if str($modelling_parameters.automatic_model.mset) != ''
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
154 --mset '$modelling_parameters.automatic_model.mset'
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
155 #end if
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
156
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
157 #if str($modelling_parameters.automatic_model.msub) != ''
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
158 --msub '$modelling_parameters.automatic_model.msub'
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
159 #end if
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
160
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
161 #if str($modelling_parameters.automatic_model.mfreq) != ''
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
162 --mfreq '$modelling_parameters.automatic_model.mfreq'
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
163 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
164
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
165 #if str($modelling_parameters.automatic_model.mrate) != ''
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
166 --mrate '$modelling_parameters.automatic_model.mrate'
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
167 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
168
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
169 #if str($modelling_parameters.automatic_model.cmin) != ''
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
170 --cmin '$modelling_parameters.automatic_model.cmin'
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
171 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
172
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
173 #if str($modelling_parameters.automatic_model.cmax) != ''
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
174 --cmax '$modelling_parameters.automatic_model.cmax'
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
175 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
176
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
177 #if str($modelling_parameters.automatic_model.merit) != ''
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
178 --merit '$modelling_parameters.automatic_model.merit'
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
179 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
180
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
181 $modelling_parameters.automatic_model.mtree
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
182
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
183 #if str($modelling_parameters.automatic_model.madd) != ''
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
184 --madd '$modelling_parameters.automatic_model.madd'
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
185 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
186
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
187 ## file
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
188 #if $modelling_parameters.automatic_model.mdef
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
189 --mdef '$modelling_parameters.automatic_model.mdef'
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
190 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
191
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
192 $modelling_parameters.automatic_model.modelomatic
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
193 $modelling_parameters.specifying_substitution.mix_opt
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
194
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
195 #if str($modelling_parameters.rate_heterogeneity.alpha_min) != ''
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
196 --alpha-min '$modelling_parameters.rate_heterogeneity.alpha_min'
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
197 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
198
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
199 $modelling_parameters.rate_heterogeneity.gamma_median
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
200
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
201 #if str($modelling_parameters.rate_heterogeneity.i) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
202 -i '$modelling_parameters.rate_heterogeneity.i'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
203 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
204
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
205 $modelling_parameters.rate_heterogeneity.opt_gamma_inv
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
206 $modelling_parameters.rate_heterogeneity.rate
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
207
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
208 #if str($modelling_parameters.partition_model.model_selection.model) != 'none':
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
209 -$modelling_parameters.partition_model.model_selection.model '$modelling_parameters.partition_model.model_selection.model_file'
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
210 #if str($modelling_parameters.partition_model.model_selection.subsample) != '':
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
211 --subsample $modelling_parameters.partition_model.model_selection.subsample
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
212 #end if
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
213 #if str($modelling_parameters.partition_model.model_selection.subsample_seed) != '':
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
214 --subsample-seed $modelling_parameters.partition_model.model_selection.subsample_seed
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
215 #end if
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
216 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
217
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
218 ## file
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
219 #if $modelling_parameters.site_specific_frequency.tree_freq
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
220 --tree-freq '$modelling_parameters.site_specific_frequency.tree_freq'
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
221 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
222
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
223 #if str($modelling_parameters.site_specific_frequency.site_freq) != ''
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
224 --site-freq '$modelling_parameters.site_specific_frequency.site_freq'
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
225 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
226
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
227 $modelling_parameters.site_specific_frequency.freq_max
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
228
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
229 #if str($tree_parameters.tree_search.ninit) != ''
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
230 --ninit '$tree_parameters.tree_search.ninit'
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
231 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
232
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
233 #if str($tree_parameters.tree_search.ntop) != ''
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
234 --ntop '$tree_parameters.tree_search.ntop'
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
235 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
236
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
237 #if str($tree_parameters.tree_search.nbest) != ''
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
238 --nbest '$tree_parameters.tree_search.nbest'
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
239 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
240
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
241 #if str($tree_parameters.tree_search.nstop) != ''
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
242 --nstop '$tree_parameters.tree_search.nstop'
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
243 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
244
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
245 #if str($tree_parameters.tree_search.n) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
246 -n '$tree_parameters.tree_search.n'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
247 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
248
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
249 #if str($tree_parameters.tree_search.radius) != ''
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
250 --radius '$tree_parameters.tree_search.radius'
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
251 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
252
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
253 #if str($tree_parameters.tree_search.perturb) != ''
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
254 --perturb '$tree_parameters.tree_search.perturb'
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
255 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
256
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
257 $tree_parameters.tree_search.allnni
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
258 $tree_parameters.tree_search.tree_fix
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
259 $tree_parameters.tree_search.fast
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
260 $tree_parameters.tree_search.polytomy
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
261 $tree_parameters.tree_search.treels
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
262 $tree_parameters.tree_search.show_lh
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
263 $tree_parameters.tree_search.terrace
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
264
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
265 ## file
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
266 #if $tree_parameters.tree_search.g
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
267 -g '$tree_parameters.tree_search.g'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
268 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
269
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
270 #if str($tree_parameters.single_branch.alrt) != ''
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
271 --alrt '$tree_parameters.single_branch.alrt'
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
272 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
273
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
274 $tree_parameters.single_branch.abayes
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
275
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
276 #if str($tree_parameters.single_branch.lbp) != ''
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
277 --lbp '$tree_parameters.single_branch.lbp'
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
278 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
279
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
280 ## file
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
281 #if $tree_parameters.tree_topology.trees
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
282 --trees '$tree_parameters.tree_topology.trees'
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
283 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
284
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
285 #if str($tree_parameters.tree_topology.test) != ''
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
286 --test '$tree_parameters.tree_topology.test'
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
287 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
288
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
289 $tree_parameters.tree_topology.test_weight
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
290 $tree_parameters.tree_topology.test_au
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
291
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
292 #if str($tree_parameters.constructing_consensus.sup_min) != ''
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
293 --sup-min '$tree_parameters.constructing_consensus.sup_min'
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
294 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
295
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
296
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
297 #if str($tree_parameters.generating_random.r) != ''
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
298 -r '$tree_parameters.generating_random.r'
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
299 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
300
6
5cd49ec56116 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01"
iuc
parents: 5
diff changeset
301 #if $tree_parameters.generating_random.rand
5cd49ec56116 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01"
iuc
parents: 5
diff changeset
302 $tree_parameters.generating_random.rand
5cd49ec56116 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01"
iuc
parents: 5
diff changeset
303 #end if
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
304
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
305 #if str($tree_parameters.generating_random.branch_min) != '' and str($tree_parameters.generating_random.branch_mean) != '' and str($tree_parameters.generating_random.branch_max) != ''
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
306 --rlen $tree_parameters.generating_random.branch_min $tree_parameters.generating_random.branch_mean $tree_parameters.generating_random.branch_max
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
307 #end if
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
308
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
309 #if str($bootstrap_parameters.ultrafast_bootstrap.ufboot) != ''
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
310 --ufboot '$bootstrap_parameters.ultrafast_bootstrap.ufboot'
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
311 #end if
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
312
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
313 #if str($bootstrap_parameters.ultrafast_bootstrap.ufjack) != ''
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
314 --ufjack '$bootstrap_parameters.ultrafast_bootstrap.ufjack'
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
315 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
316
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
317 #if str($bootstrap_parameters.ultrafast_bootstrap.jack_prop) != ''
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
318 --jack-prop '$bootstrap_parameters.ultrafast_bootstrap.jack_prop'
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
319 #end if
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
320
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
321 #if str($bootstrap_parameters.ultrafast_bootstrap.sampling) != ''
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
322 --sampling '$bootstrap_parameters.ultrafast_bootstrap.sampling'
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
323 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
324
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
325 $bootstrap_parameters.ultrafast_bootstrap.boot_trees
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
326 $bootstrap_parameters.ultrafast_bootstrap.wbtl
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
327
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
328 #if str($bootstrap_parameters.ultrafast_bootstrap.nmax) != ''
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
329 --nmax '$bootstrap_parameters.ultrafast_bootstrap.nmax'
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
330 #end if
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
331
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
332 #if str($bootstrap_parameters.ultrafast_bootstrap.nstep) != ''
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
333 --nstep '$bootstrap_parameters.ultrafast_bootstrap.nstep'
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
334 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
335
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
336 #if str($bootstrap_parameters.ultrafast_bootstrap.bcor) != ''
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
337 --bcor '$bootstrap_parameters.ultrafast_bootstrap.bcor'
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
338 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
339
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
340 #if str($bootstrap_parameters.ultrafast_bootstrap.beps) != ''
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
341 --beps '$bootstrap_parameters.ultrafast_bootstrap.beps'
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
342 #end if
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
343
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
344 $bootstrap_parameters.ultrafast_bootstrap.bnni
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
345
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
346 #if str($bootstrap_parameters.nonparametric_bootstrap.boot) != ''
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
347 --boot '$bootstrap_parameters.nonparametric_bootstrap.boot'
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
348 #end if
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
349
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
350 #if str($bootstrap_parameters.nonparametric_bootstrap.jack) != ''
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
351 --jack '$bootstrap_parameters.nonparametric_bootstrap.jack'
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
352 #end if
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
353
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
354 #if str($bootstrap_parameters.nonparametric_bootstrap.jack_prop) != ''
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
355 --jack-prop '$bootstrap_parameters.nonparametric_bootstrap.jack_prop'
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
356 #end if
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
357
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
358 $bootstrap_parameters.nonparametric_bootstrap.bcon
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
359 $bootstrap_parameters.nonparametric_bootstrap.bonly
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
360 $bootstrap_parameters.nonparametric_bootstrap.tbe
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
361
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
362 #if str($miscellaneous_options.fconst) != ''
15
f4adc3371cac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit fce566406340cd87aeae2cfaac40e53dfd0db5ff
iuc
parents: 13
diff changeset
363 -fconst '$miscellaneous_options.fconst'
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
364 #end if
16
8a15b044f890 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit fb879119df5cdf56921e5c0559069a36eb052490
iuc
parents: 15
diff changeset
365
8a15b044f890 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit fb879119df5cdf56921e5c0559069a36eb052490
iuc
parents: 15
diff changeset
366 #if str($miscellaneous_options.blmin) != ''
8a15b044f890 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit fb879119df5cdf56921e5c0559069a36eb052490
iuc
parents: 15
diff changeset
367 -blmin $miscellaneous_options.blmin
8a15b044f890 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit fb879119df5cdf56921e5c0559069a36eb052490
iuc
parents: 15
diff changeset
368 #end if
8a15b044f890 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit fb879119df5cdf56921e5c0559069a36eb052490
iuc
parents: 15
diff changeset
369
8a15b044f890 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit fb879119df5cdf56921e5c0559069a36eb052490
iuc
parents: 15
diff changeset
370 #if str($miscellaneous_options.blmax) != ''
8a15b044f890 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit fb879119df5cdf56921e5c0559069a36eb052490
iuc
parents: 15
diff changeset
371 -blmax $miscellaneous_options.blmax
8a15b044f890 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit fb879119df5cdf56921e5c0559069a36eb052490
iuc
parents: 15
diff changeset
372 #end if
8a15b044f890 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit fb879119df5cdf56921e5c0559069a36eb052490
iuc
parents: 15
diff changeset
373
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
374 ]]>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
375 </command>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
376 <inputs>
4
388a6d4a892b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
377 <section name="general_options" expanded="true" title="General options">
8
2e0636f07c37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit a58c8d3c985688e49908dfeceab5be4352d71563"
iuc
parents: 7
diff changeset
378 <param argument="-s" type="data" format="txt,fasta,phylip,nex,clustal,msf" optional="true" label="Specify input alignment file in PHYLIP, FASTA, NEXUS, CLUSTAL or MSF format."/>
15
f4adc3371cac planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit fce566406340cd87aeae2cfaac40e53dfd0db5ff
iuc
parents: 13
diff changeset
379 <param argument="-o" type="text" optional="true" label="Specify an outgroup taxon name to root the tree" help="If an outgroup taxon name is not specified, the first taxon in the alignment will be used to root the tree">
7
cef78e63f746 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af"
iuc
parents: 6
diff changeset
380 <expand macro="sanitize_query" />
cef78e63f746 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af"
iuc
parents: 6
diff changeset
381 </param>
cef78e63f746 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af"
iuc
parents: 6
diff changeset
382
cef78e63f746 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af"
iuc
parents: 6
diff changeset
383 <param type="boolean" name="short_alignments" label="Short alignments" help="IQ-TREE will fail if given too many threads on input data that consists of short alignments, this option will force the use of a single thread." />
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
384 <param argument="--seqtype" type="select" label="Specify sequence type as either of DNA, AA, BIN, MORPH, CODON or NT2AA for DNA, amino-acid, binary, morphological, codon or DNA-to-AA-translated sequences">
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
385 <help><![CDATA[
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
386 Note that --seqtype CODON is always necessary when using codon models and you also need to specify a genetic code like this if differed from the standard genetic code.
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
387 <br/><i>-st</i> NT2AA tells IQ-TREE to translate protein-coding DNA into AA sequences and then subsequent analysis will work on the AA sequences. You can also use a genetic code like --seqtype NT2AA5 for the Invertebrate Mitochondrial Code (see genetic code table).]]>
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
388 </help>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
389 <option value="DNA">DNA</option>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
390 <option value="AA">AA</option>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
391 <option value="BIN">BIN</option>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
392 <option value="MORPH">MORPH</option>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
393 <option value="CODON">CODON</option>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
394 <option value="NT2AA">NT2AA</option>
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
395 </param>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
396 <param argument="-t" type="data" format="nhx" optional="true" label="Specify a file containing starting tree for tree search"/>
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
397 <param argument="--seed" type="integer" optional="true" label="Specify a random number seed to reproduce a previous run (leave blank to randomize)"/>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
398 <param argument="--keep-ident" type="boolean" truevalue="--keep-ident" falsevalue="" checked="false" label="Keep identical sequences in the alignment" help="By default: IQ-TREE will remove them during the analysis and add them in the end."/>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
399 <param argument="--epsilon" type="float" optional="true" min="0" max="1" label="Likelihood epsilon for parameter estimate" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
400 <param argument="--safe" type="boolean" truevalue="--safe" falsevalue="" checked="false" label="Turn on safe numerical mode to avoid numerical underflow for large data sets with many sequences (typically in the order of thousands)" help="This mode is automatically turned on when having more than 2000 sequences."/>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
401 </section>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
402 <section name="time_tree" expanded="false" title="Time Tree Reconstruction">
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
403 <conditional name="date_source">
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
404 <param name="select_source" type="select" label="Source of date information">
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
405 <option value="none">Skip time tree reconstruction</option>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
406 <option value="dataset">Text file</option>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
407 <option value="input">Derive from input</option>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
408 </param>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
409 <when value="none" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
410 <when value="input" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
411 <when value="dataset">
8
2e0636f07c37 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit a58c8d3c985688e49908dfeceab5be4352d71563"
iuc
parents: 7
diff changeset
412 <param argument="--date" type="data" format="txt,tabular" optional="true" label="File containing dates of tips or ancestral nodes" />
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
413 </when>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
414 </conditional>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
415 <param argument="--date-tip" type="text" optional="true" label="Tip dates as a real number or YYYY-MM-DD">
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
416 <expand macro="sanitize_query" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
417 </param>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
418 <param argument="--date-root" type="text" optional="true" label="Root date as a real number or YYYY-MM-DD">
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
419 <expand macro="sanitize_query" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
420 </param>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
421 <param argument="--date-ci" type="integer" optional="true" label="Number of replicates to compute confidence interval" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
422 <param argument="--clock-sd" type="float" optional="true" label="Standard-deviation for lognormal relaxed clock" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
423 <param argument="--date-no-outgroup" type="boolean" truevalue="--date-no-outgroup" falsevalue="" label="Exclude outgroup from time tree" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
424 <param argument="--date-outlier" type="integer" optional="true" label="Z-score cutoff to remove outlier tips/nodes" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
425 <param argument="--date-options" type="text" optional="true" label="Extra options passing directly to LSD2">
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
426 <expand macro="sanitize_query" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
427 </param>
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
428 </section>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
429 <section name="likelihood_mapping" expanded="False" title="Likelihood mapping analysis">
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
430 <param argument="--lmap" type="integer" optional="true" label="Specify the number of quartets to be randomly drawn" help="If you specify -lmap ALL, all unique quartets will be drawn, instead."/>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
431 <param argument="--lmclust" type="data" format="txt" optional="true" label="Specify a NEXUS file containing taxon clusters (see below for example) for quartet mapping analysis."/>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
432 <param argument="--quartetlh" type="boolean" truevalue="--quartetlh" falsevalue="" checked="false" label="Write quartet log-likelihoods into .lmap.quartetlh file (typically not needed)."/>
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
433 </section>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
434 <section name="modelling_parameters" title="Modelling Parameters">
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
435 <section name="automatic_model" expanded="False" title="Automatic model selection">
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
436 <conditional name="cond_model" >
13
9454e1c4f022 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 01204be0cb805c82785dcef994237b96a39ee40c
iuc
parents: 12
diff changeset
437 <param name="opt_custommodel" type="select" label="Do you want to use a custom model" help="See http://www.iqtree.org/doc/Substitution-Models">
9454e1c4f022 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 01204be0cb805c82785dcef994237b96a39ee40c
iuc
parents: 12
diff changeset
438 <option value="true" selected="True">Yes, I want to use a custom model</option>
9454e1c4f022 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 01204be0cb805c82785dcef994237b96a39ee40c
iuc
parents: 12
diff changeset
439 <option value="false">No, a custom model is not needed</option>
9454e1c4f022 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 01204be0cb805c82785dcef994237b96a39ee40c
iuc
parents: 12
diff changeset
440 </param>
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
441 <when value="true">
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
442 <param argument="-m" type="text" label="Model">
3
edc5004afbaf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 73ef23e40772952e5fde0576d66fa81de4916058"
iuc
parents: 2
diff changeset
443 <expand macro="sanitize_query"
edc5004afbaf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 73ef23e40772952e5fde0576d66fa81de4916058"
iuc
parents: 2
diff changeset
444 validinitial="string.ascii_uppercase,string.digits,string.punctuation" />
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
445 </param>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
446 </when>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
447 <when value="false">
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
448 <param argument="-m" type="select" label="Perform standard model selection like jModelTest (for DNA) and ProtTest (for protein)" >
6
5cd49ec56116 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01"
iuc
parents: 5
diff changeset
449 <help><![CDATA[
5cd49ec56116 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01"
iuc
parents: 5
diff changeset
450 <b>Note:</b> Only <code>TEST</code> and custom models that do not rely on <code>MF</code> can be used in conjunction with bootstrap parameters (-b)<br/><br/>
13
9454e1c4f022 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 01204be0cb805c82785dcef994237b96a39ee40c
iuc
parents: 12
diff changeset
451 IQ-TREE also works for codon, binary and morphological data.
6
5cd49ec56116 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01"
iuc
parents: 5
diff changeset
452 <table>
5cd49ec56116 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01"
iuc
parents: 5
diff changeset
453 <tr>
5cd49ec56116 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01"
iuc
parents: 5
diff changeset
454 <td><i>TESTONLY</i></td>
5cd49ec56116 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01"
iuc
parents: 5
diff changeset
455 <td>Perform standard model selection like jModelTest (for DNA) and ProtTest (for protein). Moreover, IQ-TREE also works for codon, binary and morphogical data.</td>
5cd49ec56116 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01"
iuc
parents: 5
diff changeset
456 </tr>
5cd49ec56116 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01"
iuc
parents: 5
diff changeset
457 <tr>
5cd49ec56116 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01"
iuc
parents: 5
diff changeset
458 <td><i>TEST</i></td>
5cd49ec56116 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01"
iuc
parents: 5
diff changeset
459 <td>Like -m TESTONLY but immediately followed by tree reconstruction using the best-fit model found. So this performs both model selection and tree inference within a single run.</td>
5cd49ec56116 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01"
iuc
parents: 5
diff changeset
460 </tr>
5cd49ec56116 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01"
iuc
parents: 5
diff changeset
461 <tr>
5cd49ec56116 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01"
iuc
parents: 5
diff changeset
462 <td><i>MF</i></td>
5cd49ec56116 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01"
iuc
parents: 5
diff changeset
463 <td>Best-fit model selection without tree reconstruction.</td>
5cd49ec56116 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01"
iuc
parents: 5
diff changeset
464 </tr>
5cd49ec56116 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01"
iuc
parents: 5
diff changeset
465 <tr>
5cd49ec56116 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01"
iuc
parents: 5
diff changeset
466 <td><i>MFP</i></td>
5cd49ec56116 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01"
iuc
parents: 5
diff changeset
467 <td>Extended model selection with FreeRate heterogeneity immediately followed by tree inference.</td>
5cd49ec56116 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01"
iuc
parents: 5
diff changeset
468 </tr>
5cd49ec56116 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01"
iuc
parents: 5
diff changeset
469 </table>
5cd49ec56116 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01"
iuc
parents: 5
diff changeset
470 ]]>
5cd49ec56116 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01"
iuc
parents: 5
diff changeset
471 </help>
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
472 <option value="" selected="true">(None)</option>
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
473 <option value="TESTONLY">Standard model selection</option>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
474 <option value="TEST">Standard model selection followed by tree inference</option>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
475 <option value="MF">Extended model selection with FreeRate heterogeneity</option>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
476 <option value="MFP">Extended model selection followed by tree inference</option>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
477 </param>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
478 <param name="additional_models" type="text" optional="true" label="Additional model specifications" help="See http://www.iqtree.org/doc/Substitution-Models">
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
479 <expand macro="sanitize_query" />
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
480 </param>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
481 </when>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
482 </conditional>
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
483 <conditional name="merge_strategy">
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
484 <param argument="--merge" type="select" label="Merge partitions">
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
485 <option value="none">Do not merge</option>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
486 <option value="rclusterf">Merge using rcluster relaxed algorithm</option>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
487 <option value="rcluster">Merge using rcluster algorithm</option>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
488 <option value="greedy">Merge using greedy algorithm</option>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
489 </param>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
490 <when value="none" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
491 <when value="greedy" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
492 <when value="rcluster">
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
493 <param argument="--rcluster" type="integer" optional="true" label="Specify the percentage for the relaxed clustering algorithm (Lanfear et al., 2014)" help="This is similar to --rcluster-percent option of PartitionFinder. For example, giving the value 10 only the top 10% partition schemes are considered to save computations." />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
494 <param argument="--rcluster-max" type="integer" optional="true" label="Max number of partition pairs" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
495 </when>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
496 <when value="rclusterf">
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
497 <param argument="--rclusterf" type="integer" optional="true" label="Specify the percentage for the relaxed clustering algorithm (Lanfear et al., 2014)" help="This is similar to --rcluster-percent option of PartitionFinder. For example, giving the value 10 only the top 10% partition schemes are considered to save computations." />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
498 <param argument="--rcluster-max" type="integer" optional="true" label="Max number of partition pairs" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
499 </when>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
500 </conditional>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
501 <param argument="--mset" type="text" optional="true" label="Specify the name of a program (raxml, phyml or mrbayes) to restrict to only those models supported by the specified program" help="Alternatively, one can specify a comma-separated list of base models. For example, -mset WAG,LG,JTT will restrict model selection to WAG, LG, and JTT instead of all 18 AA models to save computations.">
2
b2fbfb61f019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 686710a7d313b828f1daed20c4055479727f2d91
iuc
parents: 1
diff changeset
502 <expand macro="sanitize_query"
10
93294f1f3cf5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1bda7ff567a523740d76eea8d7df6db97c905693"
iuc
parents: 9
diff changeset
503 validinitial="string.ascii_letters,string.punctuation" />
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
504 </param>
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
505 <param argument="--msub" type="select" label="Specify either nuclear, mitochondrial, chloroplast or viral to restrict to those AA models designed for specified source." help="">
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
506 <option value="nuclear">nuclear</option>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
507 <option value="mitochondrial">mitochondrial</option>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
508 <option value="chloroplast">chloroplast</option>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
509 <option value="viral">viral</option>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
510 </param>
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
511 <param argument="--mfreq" type="text" optional="true" label="Specify a comma-separated list of frequency types for model selection" >
2
b2fbfb61f019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 686710a7d313b828f1daed20c4055479727f2d91
iuc
parents: 1
diff changeset
512 <expand macro="sanitize_query"
b2fbfb61f019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 686710a7d313b828f1daed20c4055479727f2d91
iuc
parents: 1
diff changeset
513 validinitial="string.ascii_uppercase,string.digits,x,string.punctuation" />
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
514 </param>
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
515 <param argument="--mrate" type="text" optional="true" label="Specify a comma-separated list of rate heterogeneity types for model selection">
2
b2fbfb61f019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 686710a7d313b828f1daed20c4055479727f2d91
iuc
parents: 1
diff changeset
516 <expand macro="sanitize_query"
b2fbfb61f019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 686710a7d313b828f1daed20c4055479727f2d91
iuc
parents: 1
diff changeset
517 validinitial="string.ascii_uppercase,string.punctuation" />
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
518 </param>
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
519 <param argument="--cmin" type="integer" value="2" optional="true" label="Specify minimum number of categories for FreeRate model"/>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
520 <param argument="--cmax" type="integer" value="10" optional="true" label="Specify maximum number of categories for FreeRate model"/>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
521 <param argument="--merit" type="select" label="Specify either AIC, AICc or BIC for the optimality criterion to apply for new procedure" help="">
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
522 <option value="AIC">AIC</option>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
523 <option value="AICc">AICc</option>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
524 <option value="BIC">BIC</option>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
525 </param>
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
526 <param argument="--mtree" type="boolean" truevalue="-mtree" falsevalue="" checked="false" label="Turn on full tree search for each model considered, to obtain more accurate result"/>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
527 <param argument="--madd" type="text" optional="true" label="Specify a comma-separated list of mixture models to additionally consider for model selection" help="For example, -madd LG4M,LG4X to additionally include these two protein mixture models.">
2
b2fbfb61f019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 686710a7d313b828f1daed20c4055479727f2d91
iuc
parents: 1
diff changeset
528 <expand macro="sanitize_query"
b2fbfb61f019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 686710a7d313b828f1daed20c4055479727f2d91
iuc
parents: 1
diff changeset
529 validinitial="string.ascii_uppercase,string.digits,string.punctuation" />
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
530 </param>
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
531 <param argument="--mdef" type="data" format="txt" optional="true" label="Specify a NEXUS model file to define new models."/>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
532 <param argument="--modelomatic" type="boolean" truevalue="--modelomatic" falsevalue="" label="Find best codon/protein/DNA models" />
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
533 </section>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
534 <section name="specifying_substitution" expanded="False" title="Specifying substitution models">
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
535 <param argument="--mix-opt" type="boolean" truevalue="--mix-opt" falsevalue="" checked="false" label="Turn on optimizing weights of mixture models" help="Note that for models like LG+C20+F+G this mode is automatically turned on, but not for LG+C20+G."/>
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
536 </section>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
537 <section name="rate_heterogeneity" expanded="False" title="Rate heterogeneity">
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
538 <param argument="--alpha-min" type="text" optional="true" label="Specify the minimum Gamma shape parameter (default: estimate)">
2
b2fbfb61f019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 686710a7d313b828f1daed20c4055479727f2d91
iuc
parents: 1
diff changeset
539 <expand macro="sanitize_query" />
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
540 </param>
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
541 <param argument="--gamma-median" type="boolean" truevalue="--gamma-median" falsevalue="" checked="false" label="Perform the median approximation for Gamma rate heterogeneity instead of the default mean approximation (Yang, 1994)"/>
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
542 <param argument="-i" type="text" optional="true" label="Specify the proportion of invariable sites (default: estimate)">
2
b2fbfb61f019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 686710a7d313b828f1daed20c4055479727f2d91
iuc
parents: 1
diff changeset
543 <expand macro="sanitize_query" />
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
544 </param>
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
545 <param argument="--opt-gamma-inv" type="boolean" truevalue="--opt-gamma-inv" falsevalue="" checked="false" label="Perform more thorough estimation for +I+G model parameters"/>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
546 <param argument="--rate" type="boolean" truevalue="--rate" falsevalue="" checked="false" label="Write empirical Bayesian site rates to .rate file"/>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
547 <param argument="--mlrate" type="boolean" truevalue="--mlrate" falsevalue="" checked="false" label="Write maximum likelihood site rates to .mlrate file"/>
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
548 </section>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
549 <section name="partition_model" expanded="False" title="Partition model options">
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
550 <conditional name="model_selection">
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
551 <param name="model" type="select" label="Partition model">
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
552 <option value="none">No partition model</option>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
553 <option value="p">Edge-linked proportional partition model</option>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
554 <option value="q">Edge-linked equal partition model</option>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
555 <option value="Q">Edge-unlinked proportional partition model</option>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
556 <option value="S">Separate tree inference</option>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
557 </param>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
558 <when value="none" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
559 <when value="p">
12
df8bf04acdb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3b1c44e42b042ccbbe2d9e01c77d18f109d4984f"
iuc
parents: 11
diff changeset
560 <param argument="-p" name="model_file" type="data" format="nex" optional="true" label="Partition file" />
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
561 <param argument="--subsample" type="integer" optional="true" label="Subsample partitions" help="Use a negative value for complement" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
562 <param argument="--subsample-seed" type="integer" optional="true" label="Subsampling random seed" help="Use a negative value for complement" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
563 </when>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
564 <when value="q">
12
df8bf04acdb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3b1c44e42b042ccbbe2d9e01c77d18f109d4984f"
iuc
parents: 11
diff changeset
565 <param argument="-q" name="model_file" type="data" format="nex" optional="true" label="Partition file" />
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
566 <param argument="--subsample" type="integer" optional="true" label="Subsample partitions" help="Use a negative value for complement" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
567 <param argument="--subsample-seed" type="integer" optional="true" label="Subsampling random seed" help="Use a negative value for complement" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
568 </when>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
569 <when value="Q">
12
df8bf04acdb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3b1c44e42b042ccbbe2d9e01c77d18f109d4984f"
iuc
parents: 11
diff changeset
570 <param argument="-Q" name="model_file" type="data" format="nex" optional="true" label="Partition file" />
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
571 <param argument="--subsample" type="integer" optional="true" label="Subsample partitions" help="Use a negative value for complement" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
572 <param argument="--subsample-seed" type="integer" optional="true" label="Subsampling random seed" help="Use a negative value for complement" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
573 </when>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
574 <when value="S">
12
df8bf04acdb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3b1c44e42b042ccbbe2d9e01c77d18f109d4984f"
iuc
parents: 11
diff changeset
575 <param argument="-S" name="model_file" type="data" format="nex" optional="true" label="Partition file" />
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
576 <param argument="--subsample" type="integer" optional="true" label="Subsample partitions" help="Use a negative value for complement" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
577 <param argument="--subsample-seed" type="integer" optional="true" label="Subsampling random seed" help="Use a negative value for complement" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
578 </when>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
579 </conditional>
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
580 </section>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
581 <section name="site_specific_frequency" expanded="False" title="Site-specific frequency model options">
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
582 <param argument="--tree-freq" type="data" format="nhx" optional="true" label="Specify a guide tree to infer site frequency profiles."/>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
583 <param argument="--site-freq" type="float" optional="true" label="Specify a site frequency file, e.g" help="the .sitefreq file obtained from -ft run. This will save memory used for the first phase of the analysis."/>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
584 <param argument="--freq-max" type="boolean" truevalue="--freq-max" falsevalue="" checked="false" label="Switch to posterior maximum mode for obtaining site-specific profiles" help="Default: posterior mean."/>
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
585 </section>
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
586 </section>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
587 <section name="tree_parameters" title="Tree Parameters">
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
588 <section name="tree_search" expanded="False" title="Tree search parameters">
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
589 <param argument="-n" type="integer" optional="true" label="Skip subsequent tree search (n = 0), useful when you only want to assess the phylogenetic information of the alignment. Otherwise specify number of iterations to stop (this option overrides --nstop criterion)." />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
590 <param argument="--ninit" type="integer" value="100" optional="true" label="Specify number of initial parsimony trees"/>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
591 <param argument="--ntop" type="integer" value="20" optional="true" label="Specify number of top initial parsimony trees to optimize with ML nearest neighbor interchange (NNI) search to initialize the candidate set"/>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
592 <param argument="--nbest" type="integer" value="5" optional="true" label="Specify number of trees in the candidate set to maintain during ML tree search"/>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
593 <param argument="--nstop" type="integer" value="100" optional="true" label="Specify number of unsuccessful iterations to stop"/>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
594 <param argument="--radius" type="integer" value="6" optional="true" label="Specify SPR radius for the initial parsimony tree search"/>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
595 <param argument="--perturb" type="float" value="0.5" optional="true" label="Specify perturbation strength (between 0 and 1) for randomized NNI"/>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
596 <param argument="--allnni" type="boolean" truevalue="-allnni" falsevalue="" checked="false" label="Turn on more thorough and slower NNI search"/>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
597 <param argument="--tree-fix" type="boolean" truevalue="--tree-fix" falsevalue="" checked="false" label="Avoid computing ML pairwise distances and BIONJ tree."/>
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
598 <param argument="-g" type="data" format="txt" optional="true" label="Specify a topological constraint tree file in NEWICK format" help="The constraint tree can be a multifurcating tree and need not to include all taxa."/>
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
599 <param argument="--fast" type="boolean" truevalue="--fast" falsevalue="" label="Fast search to resemble FastTree" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
600 <param argument="--polytomy" type="boolean" truevalue="--polytomy" falsevalue="" label="Collapse near-zero branches into polytomy" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
601 <param argument="--treels" type="boolean" truevalue="--treels" falsevalue="" label="Write locally optimal trees into .treels file" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
602 <param argument="--show-lh" type="boolean" truevalue="--show-lh" falsevalue="" label="Compute tree likelihood without optimisation" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
603 <param argument="--terrace" type="boolean" truevalue="--terrace" falsevalue="" label="Check if the tree lies on a phylogenetic terrace" />
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
604 </section>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
605 <section name="single_branch" expanded="False" title="Single branch tests">
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
606 <param argument="--alrt" type="integer" optional="true" label="Specify number of replicates (&gt;=1000) to perform SH-like approximate likelihood ratio test (SH-aLRT) (Guindon et al., 2010)" help="If number of replicates is set to 0 (-alrt 0), then the parametric aLRT test (Anisimova and Gascuel 2006) is performed, instead of SH-aLRT."/>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
607 <param argument="--abayes" type="boolean" truevalue="-abayes" falsevalue="" checked="false" label="Perform approximate Bayes test (Anisimova et al., 2011)."/>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
608 <param argument="--lbp" type="integer" optional="true" label="Specify number of replicates (&gt;=1000) to perform fast local bootstrap probability method (Adachi and Hasegawa, 1996)."/>
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
609 </section>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
610 <section name="tree_topology" expanded="False" title="Tree topology tests">
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
611 <param argument="--trees" type="data" format="txt" optional="true" label="Specify a file containing a set of trees" help="IQ-TREE will compute the log-likelihoods of all trees."/>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
612 <param argument="--test" type="integer" optional="true" label="Specify the number of RELL (Kishino et al., 1990) replicates (&gt;=1000) to perform several tree topology tests for all trees passed via -z" help="The tests include bootstrap proportion (BP), KH test (Kishino and Hasegawa, 1989), SH test (Shimodaira and Hasegawa, 1999) and expected likelihood weights (ELW) (Strimmer and Rambaut, 2002)."/>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
613 <param argument="--test-weight" type="boolean" truevalue="--test-weight" falsevalue="" checked="false" label="Used together with --test to additionally perform the weighted-KH and weighted-SH tests."/>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
614 <param argument="--test-au" type="boolean" truevalue="--test-au" falsevalue="" checked="false" label="Used together with --test to additionally perform the approximately unbiased (AU) test (Shimodaira, 2002)" help="Note that you have to specify the number of replicates for the AU test via -test."/>
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
615 </section>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
616 <section name="constructing_consensus" expanded="False" title="Constructing consensus tree">
11
d460875c806a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f"
iuc
parents: 10
diff changeset
617 <param argument="--contree" type="boolean" truevalue="--contree" falsevalue="" checked="false" label="Compute consensus tree of the trees passed via -t" help="Resulting consensus tree is written to .contree file."/>
d460875c806a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f"
iuc
parents: 10
diff changeset
618 <param argument="--connet" type="boolean" truevalue="--connet" falsevalue="" checked="false" label="Compute consensus network of the trees passed via -t" help="Resulting consensus network is written to .nex file."/>
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
619 <param argument="--sup-min" type="float" value="0.0" optional="true" label="Specify a minimum threshold (between 0 and 1) to keep branches in the consensus tree"/>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
620 <param argument="--burnin" type="integer" optional="true" label="Specify a burn-in, which is the number of beginning trees passed via -t to discard before consensus construction" help="This is useful e.g. when summarizing trees from MrBayes analysis."/>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
621 <param argument="--support" type="data" format="nhx" optional="true" label="Specify an input “target” tree file" help="That means, support values are first extracted from the trees passed via -t, and then mapped onto the target tree. Resulting tree with assigned support values is written to .suptree file. This option is useful to map and compare support values from different approaches onto a single tree."/>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
622 <param argument="--suptag" type="text" optional="true" label="Specify name of a node in -sup target tree" help="The corresponding node of .suptree will then be assigned with IDs of trees where this node appears. Special option --suptag ALL will assign such IDs for all nodes of the target tree."/>
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
623 </section>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
624 <section name="computing_robinson_foulds" expanded="False" title="Computing Robinson-Foulds distance">
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
625 <param argument="--tree-dist-all" type="boolean" truevalue="--tree-dist-all" falsevalue="" checked="false" label="Compute all-to-all RF distances between all trees passed via -t"/>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
626 <param argument="--tree-dist" type="data" format="nhx" optional="true" label="Compute RF distances between -t trees and this set" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
627 <param argument="--tree-dist2" type="data" format="nhx" optional="true" label="Like -rf but trees can have unequal taxon sets" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
628
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
629 </section>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
630 <section name="generating_random" expanded="False" title="Generating random trees">
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
631 <param argument="-r" type="integer" optional="true" label="Specify number of taxa" help="IQ-TREE will create a random tree under Yule-Harding model with specified number of taxa"/>
6
5cd49ec56116 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01"
iuc
parents: 5
diff changeset
632 <param argument="--rand" type="select" optional="true" label="Random tree creation">
5cd49ec56116 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01"
iuc
parents: 5
diff changeset
633 <option value="--rand UNI">Uniform model</option>
5cd49ec56116 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01"
iuc
parents: 5
diff changeset
634 <option value="--rand CAT">Random caterpillar tree</option>
5cd49ec56116 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01"
iuc
parents: 5
diff changeset
635 <option value="--rand BAL">Random balanced tree</option>
5cd49ec56116 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 1c68667188a67a6b4c78af2a39b65beccae36e01"
iuc
parents: 5
diff changeset
636 </param>
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
637 <param name="branch_min" type="integer" optional="true" label="Minimum branch lengths of the random tree" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
638 <param name="branch_mean" type="integer" optional="true" label="Median branch lengths of the random tree" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
639 <param name="branch_max" type="integer" optional="true" label="Maximum branch lengths of the random tree" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
640 </section>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
641 <section name="ancestral_state" title="Ancestral State Reconstruction">
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
642 <param argument="--ancestral" type="boolean" truevalue="--ancestral" falsevalue="" label="Perform ancestral state reconstruction by empirical Bayes" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
643 <param argument="--asr-min" type="float" optional="true" min="0" max="1" label="Minimum probability of ancestral state" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
644 </section>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
645 <section name="symmetry_test" title="Symmetry Tests">
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
646 <param argument="--symtest" type="boolean" truevalue="--symtest" falsevalue="" label="Perform three tests of symmetry" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
647 <param argument="--symtest-remove-bad" type="boolean" truevalue="--symtest-remove-bad" falsevalue="" label="Do --symtest and remove bad partitions" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
648 <param argument="--symtest-remove-good" type="boolean" truevalue="--symtest-remove-good" falsevalue="" label="Do --symtest and remove good partitions" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
649 <param argument="--symtest-type" type="select" optional="true" label="Type of test to use">
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
650 <option value="MAR">Marginal</option>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
651 <option value="INT">Internal</option>
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
652 </param>
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
653 <param argument="--symtest-pval" type="float" optional="true" label="P-value cutoff" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
654 <param argument="--symtest-keep-zero" type="boolean" truevalue="--symtest-keep-zero" falsevalue="" label="Keep NAs in the tests" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
655 </section>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
656 <section name="concordance_factor" title="Concordance Factor Analysis">
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
657 <param argument="--gcf" type="data" format="nex" optional="true" label="Set of source trees for gene concordance factor" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
658 <param argument="--df-tree" type="boolean" truevalue="--df-tree" falsevalue="" label="Write discordant trees associated with gDF1" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
659 <param argument="--scf" type="integer" optional="true" label="Number of quartets for site concordance factor" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
660 <param argument="--cf-verbose" type="boolean" truevalue="--cf-verbose" falsevalue="" label="Write CF per tree/locus" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
661 <param argument="--cf-quartet" type="boolean" truevalue="--cf-quartet" falsevalue="" label="Write sCF for all resampled quartets to .cf.quartet" />
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
662 </section>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
663 </section>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
664 <section name="bootstrap_parameters" title="Bootstrap Parameters">
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
665 <section name="ultrafast_bootstrap" expanded="False" title="Ultrafast bootstrap parameters">
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
666 <param argument="--ufboot" type="integer" optional="true" label="Specify number of bootstrap replicates (&gt;=1000)."/>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
667 <param argument="--ufjack" type="integer" optional="true" label="Specify number of replicates for ultrafast jackknife (&gt;=1000)."/>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
668 <param argument="--jack-prop" type="float" optional="true" min="0" max="1" label="Subsampling proportion for jackknife." help="Default: 0.5"/>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
669 <param argument="--boot-trees" type="boolean" truevalue="--boot-trees" falsevalue="" checked="false" label="Turn on writing bootstrap trees to .ufboot file"/>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
670 <param argument="--wbtl" type="boolean" truevalue="--wbtl" falsevalue="" checked="false" label="Like -boot-trees but bootstrap trees written with branch lengths"/>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
671 <param argument="--nmax" type="integer" value="1000" optional="true" label="Specify maximum number of iterations to stop"/>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
672 <param argument="--bcor" type="float" value="0.99" optional="true" label="Specify minimum correlation coefficient for UFBoot convergence criterion"/>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
673 <param argument="--nstep" type="integer" value="100" optional="true" label="Specify iteration interval checking for UFBoot convergence"/>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
674 <param argument="--beps" type="float" value="0.5" optional="true" label="Specify a small epsilon to break tie in RELL evaluation for bootstrap trees"/>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
675 <param argument="--sampling" type="text" optional="true" label="Specify the resampling strategies for partitioned analysis" help="By default, IQ-TREE resamples alignment sites within partitions. With --sampling GENE IQ-TREE will resample partitions. With --sampling GENESITE IQ-TREE will resample partitions and then resample sites within resampled partitions (Gadagkar et al., 2005).">
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
676 <sanitizer>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
677 <valid initial="string.ascii_uppercase" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
678 </sanitizer>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
679 </param>
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
680 <param argument="--bnni" type="boolean" truevalue="--bnni" falsevalue="" checked="false" label="Perform an additional step to further optimize UFBoot trees by nearest neighbor interchange (NNI) based directly on bootstrap alignments" help="This option is recommended in the presence of severe model violations. It increases computing time by 2-fold but reduces the risk of overestimating branch supports due to severe model violations. Introduced in IQ-TREE 1.6."/>
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
681 </section>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
682 <section name="nonparametric_bootstrap" expanded="False" title="Nonparametric bootstrap">
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
683 <param argument="--boot" type="integer" optional="true" label="Replicates for bootstrap + ML tree + consensus tree" help="This will perform both bootstrap and analysis on original alignment and provide a consensus tree."/>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
684 <param argument="--jack" type="integer" optional="true" label="Replicates for jackknife + ML tree + consensus tree" help="This will perform both bootstrap and analysis on original alignment and provide a consensus tree."/>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
685 <param argument="--jack-prop" type="float" optional="true" min="0" max="1" label="Subsampling proportion for jackknife." help="Default: 0.5"/>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
686 <param argument="--bcon" type="integer" optional="true" label="Replicates for bootstrap + consensus tree"/>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
687 <param argument="--bonly" type="integer" optional="true" label="Replicates for bootstrap only"/>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
688 <param argument="--tbe" type="boolean" truevalue="--tbe" falsevalue="" checked="false" label="Transfer bootstrap expectation"/>
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
689 </section>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
690 </section>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
691 <section name="miscellaneous_options" expanded="False" title="Miscellaneous options">
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
692 <param argument="-fconst" type="text" optional="true" label="Specify a list of comma-separated integer numbers" help="The number of entries should be equal to the number of states in the model (e.g. 4 for DNA and 20 for protein). IQ-TREE will then add a number of constant sites accordingly. For example, -fconst 10,20,15,40 will add 10 constant sites of all A, 20 constant sites of all C, 15 constant sites of all G and 40 constant sites of all T into the alignment.">
2
b2fbfb61f019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 686710a7d313b828f1daed20c4055479727f2d91
iuc
parents: 1
diff changeset
693 <expand macro="sanitize_query"
b2fbfb61f019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 686710a7d313b828f1daed20c4055479727f2d91
iuc
parents: 1
diff changeset
694 validinitial="string.digits,string.punctuation" />
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
695 </param>
16
8a15b044f890 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit fb879119df5cdf56921e5c0559069a36eb052490
iuc
parents: 15
diff changeset
696 <param argument="-blmin" type="float" min="0" max="1" value="" optional="true" label="Specify minimum branch length" help="Default: the smaller of 0.000001 and 0.1/alignment_length." />
8a15b044f890 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit fb879119df5cdf56921e5c0559069a36eb052490
iuc
parents: 15
diff changeset
697 <param argument="-blmax" type="float" min="0" max="1" value="" optional="true" label="Specify the maximum branch length" help="Default: 10" />
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
698 </section>
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
699 </inputs>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
700 <outputs>
4
388a6d4a892b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
701 <data name="bionj" format="nhx" from_work_dir="*.bionj" label="${tool.name} on ${on_string}: BIONJ Tree" />
388a6d4a892b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
702 <data name="treefile" format="nhx" from_work_dir="*.treefile" label="${tool.name} on ${on_string}: MaxLikelihood Tree" />
11
d460875c806a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f"
iuc
parents: 10
diff changeset
703 <data name="consensus_tree" format="nhx" from_work_dir="*.contree" label="${tool.name} on ${on_string}: Consensus Tree">
d460875c806a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f"
iuc
parents: 10
diff changeset
704 <filter>tree_parameters['constructing_consensus']['contree']</filter>
d460875c806a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f"
iuc
parents: 10
diff changeset
705 </data>
4
388a6d4a892b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
706 <data name="mldist" format="mldist" from_work_dir="*.mldist" label="${tool.name} on ${on_string}: MaxLikelihood Distance Matrix"/>
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
707 <data name="splits" format="nex" from_work_dir="*.splits.nex" label="${tool.name} on ${on_string}: Occurence Frequencies in Bootstrap Trees" />
4
388a6d4a892b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
708 <data name="iqtree" format="iqtree" from_work_dir="*.iqtree" label="${tool.name} on ${on_string}: Report and Final Tree" />
7
cef78e63f746 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af"
iuc
parents: 6
diff changeset
709 <data name="mlrate" format="data" from_work_dir="*.mlrate" label="${tool.name} on ${on_string}: ML Rates">
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
710 <filter>modelling_parameters['rate_heterogeneity']['mlrate']</filter>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
711 </data>
7
cef78e63f746 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af"
iuc
parents: 6
diff changeset
712 <data name="timetree" format="nex" from_work_dir="PREF.timetree.nex" label="${tool.name} on ${on_string}: Tree labeled with dates">
cef78e63f746 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af"
iuc
parents: 6
diff changeset
713 <filter>time_tree['date_source']['select_source'] != 'none'</filter>
cef78e63f746 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af"
iuc
parents: 6
diff changeset
714 </data>
9
35129e963633 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 00ddca12cd441fab5c928f93c62fa8aa79160967"
iuc
parents: 8
diff changeset
715 <data name="lsd_report" format="txt" from_work_dir="PREF.timetree.lsd" label="${tool.name} on ${on_string}: LSD Report">
35129e963633 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 00ddca12cd441fab5c928f93c62fa8aa79160967"
iuc
parents: 8
diff changeset
716 <filter>time_tree['date_source']['select_source'] != 'none'</filter>
35129e963633 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 00ddca12cd441fab5c928f93c62fa8aa79160967"
iuc
parents: 8
diff changeset
717 </data>
18
09961138fcaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit ed98c907217fd95aa455f4f74de74e9b3893c1d3
iuc
parents: 17
diff changeset
718 <data name="ufboot_out" format="nhx" from_work_dir="*.ufboot" label="${tool.name} on ${on_string}: UFBoot Bootstrap trees">
09961138fcaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit ed98c907217fd95aa455f4f74de74e9b3893c1d3
iuc
parents: 17
diff changeset
719 <filter>bootstrap_parameters['ultrafast_bootstrap']['boot_trees'] </filter>
09961138fcaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit ed98c907217fd95aa455f4f74de74e9b3893c1d3
iuc
parents: 17
diff changeset
720 </data>
09961138fcaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit ed98c907217fd95aa455f4f74de74e9b3893c1d3
iuc
parents: 17
diff changeset
721
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
722 </outputs>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
723 <tests>
18
09961138fcaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit ed98c907217fd95aa455f4f74de74e9b3893c1d3
iuc
parents: 17
diff changeset
724 <test expect_num_outputs="6">
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
725 <param name="seed" value="1257" />
12
df8bf04acdb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3b1c44e42b042ccbbe2d9e01c77d18f109d4984f"
iuc
parents: 11
diff changeset
726 <param name="seqtype" value="DNA" />
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
727 <param name="s" value="example.phy" />
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
728 <param name="m" value="TEST" />
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
729 <param name="msub" value="nuclear" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
730 <param name="madd" value="LG4M,LG4X" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
731 <param name="merit" value="AICc" />
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
732 <param name="ufboot" value="1000" />
18
09961138fcaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit ed98c907217fd95aa455f4f74de74e9b3893c1d3
iuc
parents: 17
diff changeset
733 <param name="boot_trees" value="--boot-trees"/>
4
388a6d4a892b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
734 <output name="bionj">
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
735 <assert_contents>
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
736 <has_text_matching expression=".*Whale.*" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
737 <has_text_matching expression=".*Human.*" />
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
738 </assert_contents>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
739 </output>
4
388a6d4a892b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
740 <output name="iqtree">
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
741 <assert_contents>
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
742 <has_text_matching expression="GTR\+F(\s+((-|\d|\.)+))+" />
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
743 </assert_contents>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
744 </output>
4
388a6d4a892b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
745 <output name="mldist">
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
746 <assert_contents>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
747 <has_line_matching expression="^Frog(\s+((\d|\.)+))+\s+$" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
748 <has_line_matching expression="^Whale(\s+((\d|\.)+))+\s+$" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
749 <has_line_matching expression="^Cow(\s+((\d|\.)+))+\s+$" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
750 </assert_contents>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
751 </output>
4
388a6d4a892b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
752 <output name="treefile">
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
753 <assert_contents>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
754 <has_line_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
755 </assert_contents>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
756 </output>
11
d460875c806a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f"
iuc
parents: 10
diff changeset
757 <output name="consensus_tree">
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
758 <assert_contents>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
759 <has_line_matching
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
760 expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*\)\d+:(\d|\.)+,.*" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
761 </assert_contents>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
762 </output>
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
763 <output name="splits">
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
764 <assert_contents>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
765 <has_line line="BEGIN Splits;" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
766 <has_line line="END; [Splits]" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
767 </assert_contents>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
768 </output>
18
09961138fcaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit ed98c907217fd95aa455f4f74de74e9b3893c1d3
iuc
parents: 17
diff changeset
769 <output name="ufboot_out" >
09961138fcaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit ed98c907217fd95aa455f4f74de74e9b3893c1d3
iuc
parents: 17
diff changeset
770 <assert_contents>
09961138fcaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit ed98c907217fd95aa455f4f74de74e9b3893c1d3
iuc
parents: 17
diff changeset
771 <has_text text="(LngfishAu" />
09961138fcaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit ed98c907217fd95aa455f4f74de74e9b3893c1d3
iuc
parents: 17
diff changeset
772 <has_text text="(Platypus,Opossum)" />
09961138fcaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit ed98c907217fd95aa455f4f74de74e9b3893c1d3
iuc
parents: 17
diff changeset
773 </assert_contents>
09961138fcaf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit ed98c907217fd95aa455f4f74de74e9b3893c1d3
iuc
parents: 17
diff changeset
774 </output>
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
775 </test>
11
d460875c806a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f"
iuc
parents: 10
diff changeset
776 <test expect_num_outputs="5">
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
777 <!-- bootstrap sans model -->
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
778 <param name="seed" value="1257" />
12
df8bf04acdb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3b1c44e42b042ccbbe2d9e01c77d18f109d4984f"
iuc
parents: 11
diff changeset
779 <param name="seqtype" value="DNA" />
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
780 <param name="s" value="example.phy" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
781 <!-- <param name="m" value="TESTONLY" /> -->
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
782 <param name="msub" value="nuclear" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
783 <param name="cmin" value="2" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
784 <param name="cmax" value="10" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
785 <param name="merit" value="AICc" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
786 <param name="madd" value="LG4M,LG4X" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
787 <param name="ninit" value="100" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
788 <param name="ntop" value="20" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
789 <param name="nbest" value="5" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
790 <param name="nstop" value="100" />
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
791 <param name="radius" value="6" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
792 <param name="perturb" value="0.5" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
793 <param name="sup_min" value="0.0" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
794 <param name="nmax" value="1000" />
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
795 <param name="bcor" value="0.99" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
796 <param name="nstep" value="100" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
797 <param name="beps" value="0.5" />
13
9454e1c4f022 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 01204be0cb805c82785dcef994237b96a39ee40c
iuc
parents: 12
diff changeset
798 <param name="boot" value="2" />
4
388a6d4a892b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
799 <output name="iqtree">
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
800 <assert_contents>
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
801 <has_text_matching expression="GTR\+F\+I(\s+((-|\d|\.)+))+" />
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
802 </assert_contents>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
803 </output>
4
388a6d4a892b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
804 <output name="treefile">
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
805 <assert_contents>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
806 <has_line_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
807 </assert_contents>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
808 </output>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
809 </test>
11
d460875c806a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f"
iuc
parents: 10
diff changeset
810 <test expect_num_outputs="5">
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
811 <!-- model sans bootstrap -->
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
812 <param name="seed" value="1257" />
12
df8bf04acdb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3b1c44e42b042ccbbe2d9e01c77d18f109d4984f"
iuc
parents: 11
diff changeset
813 <param name="seqtype" value="DNA" />
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
814 <param name="s" value="example.phy" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
815 <param name="m" value="TESTONLY" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
816 <param name="msub" value="nuclear" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
817 <param name="cmin" value="2" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
818 <param name="cmax" value="10" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
819 <param name="merit" value="AICc" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
820 <param name="madd" value="LG4M,LG4X" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
821 <param name="ninit" value="100" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
822 <param name="ntop" value="20" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
823 <param name="nbest" value="5" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
824 <param name="nstop" value="100" />
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
825 <param name="radius" value="6" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
826 <param name="perturb" value="0.5" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
827 <param name="sup_min" value="0.0" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
828 <param name="nmax" value="1000" />
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
829 <param name="bcor" value="0.99" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
830 <param name="nstep" value="100" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
831 <param name="beps" value="0.5" />
4
388a6d4a892b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
832 <output name="iqtree">
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
833 <assert_contents>
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
834 <has_text_matching expression="GTR\+F\+I\+G4(\s+((-|\d|\.)+))+" />
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
835 </assert_contents>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
836 </output>
4
388a6d4a892b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
837 <output name="treefile">
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
838 <assert_contents>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
839 <has_line_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
840 </assert_contents>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
841 </output>
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
842 </test>
11
d460875c806a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f"
iuc
parents: 10
diff changeset
843 <test expect_num_outputs="5">
4
388a6d4a892b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
844 <param name="s" value="example.phy" />
388a6d4a892b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
845 <output name="iqtree">
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
846 <assert_contents>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
847 <has_text_matching expression=".*Human.*Whale.*" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
848 </assert_contents>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
849 </output>
4
388a6d4a892b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
850 <output name="treefile">
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
851 <assert_contents>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
852 <has_text_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
853 </assert_contents>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
854 </output>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
855 </test>
11
d460875c806a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f"
iuc
parents: 10
diff changeset
856 <test expect_num_outputs="5">
4
388a6d4a892b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
857 <param name="s" value="example.phy" />
388a6d4a892b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
858 <param name="opt_custommodel" value="true" />
388a6d4a892b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
859 <param name="m" value="GTR+G{0.9}" />
388a6d4a892b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
860 <output name="iqtree">
3
edc5004afbaf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 73ef23e40772952e5fde0576d66fa81de4916058"
iuc
parents: 2
diff changeset
861 <assert_contents>
edc5004afbaf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 73ef23e40772952e5fde0576d66fa81de4916058"
iuc
parents: 2
diff changeset
862 <has_text_matching expression=".*Human.*Whale.*" />
edc5004afbaf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 73ef23e40772952e5fde0576d66fa81de4916058"
iuc
parents: 2
diff changeset
863 </assert_contents>
edc5004afbaf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 73ef23e40772952e5fde0576d66fa81de4916058"
iuc
parents: 2
diff changeset
864 </output>
4
388a6d4a892b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
865 <output name="treefile">
3
edc5004afbaf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 73ef23e40772952e5fde0576d66fa81de4916058"
iuc
parents: 2
diff changeset
866 <assert_contents>
edc5004afbaf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 73ef23e40772952e5fde0576d66fa81de4916058"
iuc
parents: 2
diff changeset
867 <has_text_matching expression="\(LngfishAu:(\d|\..)+,\(LngfishSA:(\d.)+,.*" />
edc5004afbaf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 73ef23e40772952e5fde0576d66fa81de4916058"
iuc
parents: 2
diff changeset
868 </assert_contents>
edc5004afbaf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 73ef23e40772952e5fde0576d66fa81de4916058"
iuc
parents: 2
diff changeset
869 </output>
edc5004afbaf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 73ef23e40772952e5fde0576d66fa81de4916058"
iuc
parents: 2
diff changeset
870 </test>
11
d460875c806a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f"
iuc
parents: 10
diff changeset
871 <test expect_num_outputs="5">
4
388a6d4a892b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
872 <param name="s" value="short.fasta" />
388a6d4a892b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
873 <param name="short_alignments" value="true" />
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
874 <output name="treefile">
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
875 <assert_contents>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
876 <has_line_matching expression="\(NC_045512.+\(MT019531.+MT019532.+" />
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
877 </assert_contents>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
878 </output>
4
388a6d4a892b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit dc68d9064facc8da0024b4c2c41ef82150bdd386"
iuc
parents: 3
diff changeset
879 </test>
11
d460875c806a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 72a0164fcc4430240241ac057974f8bb87b4e04f"
iuc
parents: 10
diff changeset
880 <test expect_num_outputs="7">
7
cef78e63f746 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af"
iuc
parents: 6
diff changeset
881 <param name="s" value="dates.fa" />
cef78e63f746 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af"
iuc
parents: 6
diff changeset
882 <param name="n" value="100" />
cef78e63f746 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af"
iuc
parents: 6
diff changeset
883 <param name="seed" value="122125" />
cef78e63f746 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af"
iuc
parents: 6
diff changeset
884 <param name="select_source" value="dataset" />
cef78e63f746 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af"
iuc
parents: 6
diff changeset
885 <param name="date" value="dates.tabular" />
cef78e63f746 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af"
iuc
parents: 6
diff changeset
886 <output name="timetree">
cef78e63f746 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af"
iuc
parents: 6
diff changeset
887 <assert_contents>
cef78e63f746 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af"
iuc
parents: 6
diff changeset
888 <has_line_matching expression=".+222-3pu_03-28-01_985737600.+" />
cef78e63f746 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af"
iuc
parents: 6
diff changeset
889 </assert_contents>
cef78e63f746 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af"
iuc
parents: 6
diff changeset
890 </output>
9
35129e963633 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 00ddca12cd441fab5c928f93c62fa8aa79160967"
iuc
parents: 8
diff changeset
891 <output name="lsd_report">
35129e963633 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 00ddca12cd441fab5c928f93c62fa8aa79160967"
iuc
parents: 8
diff changeset
892 <assert_contents>
35129e963633 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 00ddca12cd441fab5c928f93c62fa8aa79160967"
iuc
parents: 8
diff changeset
893 <has_line_matching expression="^LEAST-SQUARE METHODS.+" />
35129e963633 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 00ddca12cd441fab5c928f93c62fa8aa79160967"
iuc
parents: 8
diff changeset
894 </assert_contents>
35129e963633 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 00ddca12cd441fab5c928f93c62fa8aa79160967"
iuc
parents: 8
diff changeset
895 </output>
7
cef78e63f746 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 255253945d747156f59c7834998725afdc7499af"
iuc
parents: 6
diff changeset
896 </test>
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
897 </tests>
2
b2fbfb61f019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 686710a7d313b828f1daed20c4055479727f2d91
iuc
parents: 1
diff changeset
898 <help><![CDATA[
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
899 IQ-TREE
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
900 =======
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
901
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
902 General Tutorial
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
903 ===================
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
904
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
905 Input data
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
906 ----------
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
907
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
908 IQ-TREE takes as input a *multiple sequence alignment* and will reconstruct an evolutionary tree that is best explained by the input data. The input alignment can be in various common formats. For example the PHYLIP_ format which may look like:
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
909
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
910 .. _PHYLIP: http://evolution.genetics.washington.edu/phylip/doc/sequence.html
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
911
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
912 ::
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
913
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
914 7 28
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
915 Frog AAATTTGGTCCTGTGATTCAGCAGTGAT
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
916 Turtle CTTCCACACCCCAGGACTCAGCAGTGAT
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
917 Bird CTACCACACCCCAGGACTCAGCAGTAAT
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
918 Human CTACCACACCCCAGGAAACAGCAGTGAT
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
919 Cow CTACCACACCCCAGGAAACAGCAGTGAC
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
920 Whale CTACCACGCCCCAGGACACAGCAGTGAT
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
921 Mouse CTACCACACCCCAGGACTCAGCAGTGAT
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
922
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
923 This tiny alignment contains 7 DNA sequences from several animals with the sequence length of 28 nucleotides. IQ-TREE also supports other file formats such as FASTA, NEXUS, CLUSTALW. The FASTA file for the above example may look like this:
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
924
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
925 ::
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
926
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
927 >Frog
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
928 AAATTTGGTCCTGTGATTCAGCAGTGAT
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
929 >Turtle
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
930 CTTCCACACCCCAGGACTCAGCAGTGAT
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
931 >Bird
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
932 CTACCACACCCCAGGACTCAGCAGTAAT
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
933 >Human
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
934 CTACCACACCCCAGGAAACAGCAGTGAT
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
935 >Cow
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
936 CTACCACACCCCAGGAAACAGCAGTGAC
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
937 >Whale
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
938 CTACCACGCCCCAGGACACAGCAGTGAT
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
939 >Mouse
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
940 CTACCACACCCCAGGACTCAGCAGTGAT
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
941
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
942 **NOTE**: If you have raw sequences, you need to first apply alignment programs like MAFFT_ or ClustalW_ to align the sequences, before feeding them into IQ-TREE.
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
943
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
944 .. _MAFFT: http://mafft.cbrc.jp/alignment/software/
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
945 .. _ClustalW: http://www.clustal.org
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
946
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
947
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
948 Running example
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
949 ---------------------
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
950
17
4e7fd03b0a13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit bfeaaf8691c2f88d4f6d888b4e739207afde1970
iuc
parents: 16
diff changeset
951 From the downloads there is an example alignment called `example.phy`
13
9454e1c4f022 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 01204be0cb805c82785dcef994237b96a39ee40c
iuc
parents: 12
diff changeset
952 in PHYLIP format. This example contains parts of the mitochondrial DNA sequences of several animals.
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
953
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
954 You can now start to reconstruct a maximum-likelihood tree
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
955 from this alignment by entering (assuming that you are now in the same folder with `example.phy`):
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
956
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
957 ::iqtree -s example.phy -st AA -seed 9999 -m TESTNEW -msub nuclear -madd LG4M,LG4x -merit AICc --ufboot 2000
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
958
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
959 * **-s** is the option to specify the name of the alignment file
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
960
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
961 * **-st** specifies the sequence type as amino-acid
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
962
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
963 * **-seed** ensures that the output files remain the same for subsequent runs
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
964
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
965 * **-m** sets the modelling parameter for standard model selection
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
966
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
967 * **-msub** determines the type sub-modelling
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
968
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
969 * **-madd** provides an additional selection mixed models
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
970
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
971 * **-merit** asserts the type of optimality criterion
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
972
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
973 * **-ufboot** defines the number of replicates
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
974
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
975
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
976 Each of these parameters are available under the relevant sub-sections in the main tool interface.
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
977
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
978 At the end of the run IQ-TREE will write several output files including:
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
979
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
980 * **example.phy.iqtree**: the main report file that is self-readable. You should look at this file to see the computational results. It also contains a textual representation of the final tree (see below).
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
981
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
982 * **example.phy.treefile**: the ML tree in NEWICK format, which can be visualized by any supported tree viewer programs like FigTree or iTOL.
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
983
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
984 **NOTE**: Starting with version 1.5.4, with this simple command IQ-TREE will by default perform ModelFinder to find the best-fit substitution model and then infer a phylogenetic tree using the selected model.
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
985
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
986 For this example data the resulting maximum-likelihood tree may look like this (extracted from **.iqtree** file):
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
987
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
988 **NOTE**: Tree is UNROOTED although outgroup taxon 'LngfishAu' is drawn at root
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
989
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
990 ::
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
991
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
992 +--------------LngfishAu
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
993 |
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
994 | +--------------LngfishSA
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
995 +--------|
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
996 | +--------------LngfishAf
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
997 |
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
998 | +-------------------Frog
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
999 +------|
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1000 | +-----------------Turtle
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1001 | +-----|
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1002 | | | +-----------------------Sphenodon
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1003 | | | +--|
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1004 | | | | +--------------------------Lizard
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1005 | | +---|
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1006 | | | +---------------------Crocodile
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1007 | | +------|
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1008 | | +------------------Bird
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1009 +---------|
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1010 | +----------------Human
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1011 | +--|
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1012 | | | +--------Seal
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1013 | | +--|
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1014 | | | +-------Cow
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1015 | | +---|
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1016 | | +---------Whale
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1017 | +----|
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1018 | | | +------Mouse
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1019 | | +---------|
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1020 | | +--------Rat
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1021 +----------|
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1022 | +----------------Platypus
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1023 +---|
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
1024 +-------------Opossum
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1025
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1026
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1027 This makes sense as the mammals (**Human** to **Opossum**) form a clade, whereas the reptiles **Turtle** to **Crocodile**) and **Bird** form a separate sister clade. Here the tree is drawn at the *outgroup* Lungfish which is more accient than other species in this example. However, please note that IQ-TREE always produces an **unrooted tree** as it knows nothing about this biological background; IQ-TREE simply draws the tree this way as **LngfishAu** is the first sequence occuring in the alignment.
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1028
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1029 Choosing the right substitution model
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1030 -------------------------------------
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1031
17
4e7fd03b0a13 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit bfeaaf8691c2f88d4f6d888b4e739207afde1970
iuc
parents: 16
diff changeset
1032 IQ-TREE will choose the best model for you automatically if specify any of the TEST models, but valid custom models can also be specified that conform to those found in Models page.
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1033
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1034
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1035
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1036 ------------------------------
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1037
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1038 Advanced Parameter Selection
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1039 ============================
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1040
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1041 Using codon models
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1042 ------------------
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1043
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1044 IQ-TREE supports a number of codon models. You need to input a protein-coding DNA alignment and specify codon data by option **-st CODON** (Otherwise, IQ-TREE applies DNA model because it detects that your alignment has DNA sequences):
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1045
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1046 ::
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1047
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
1048 iqtree -s coding_gene.phy -st CODON
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1049
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1050 If your alignment length is not divisible by 3, IQ-TREE will stop with an error message. IQ-TREE will group sites 1,2,3 into codon site 1; sites 4,5,6 to codon site 2; etc. Moreover, any codon, which has at least one gap/unknown/ambiguous nucleotide, will be treated as unknown codon character.
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1051
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1052 Note that the above command assumes the standard genetic code. If your sequences follow 'The Invertebrate Mitochondrial Code', then run:
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1053
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1054 ::
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
1055
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
1056 iqtree -s coding_gene.phy -st CODON5
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1057
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1058 Note that ModelFinder works for codon alignments. IQ-TREE version >= 1.5.4 will automatically invokes ModelFinder to find the best-fit codon model.
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1059
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1060
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1061 Assessing branch supports with ultrafast bootstrap approximation
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1062 ----------------------------------------------------------------
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1063
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1064 To overcome the computational burden required by the nonparametric bootstrap, IQ-TREE introduces an ultrafast bootstrap approximation (UFBoot) ([Minh et al., 2013]) that is orders of magnitude faster than the standard procedure and provides relatively unbiased branch support values. Citation for UFBoot:
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1065
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
1066 B.Q. Minh, M.A.T. Nguyen, and A. von Haeseler (2013) Ultrafast approximation for phylogenetic bootstrap. _Mol. Biol. Evol., 30:1188-1195.
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1067
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1068 ::
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1069
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
1070 iqtree -s example.phy -m TIM2+I+G --ufboot 1000
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1071
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
1072 **-ufboot** specifies the number of bootstrap replicates where 1000 is the minimum number recommended. The section **MAXIMUM LIKELIHOOD TREE** in **example.phy.iqtree** shows a textual representation of the maximum likelihood tree with branch support values in percentage. The NEWICK format of the tree is printed to the file **example.phy.treefile**. In addition, IQ-TREE writes the following files:
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1073
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1074 * **example.phy.contree**: the consensus tree with assigned branch supports where branch lengths are optimized on the original alignment.
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1075
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1076 * **example.phy.splits**: support values in percentage for all splits (bipartitions), computed as the occurence frequencies in the bootstrap trees. This file is in "star-dot" format.
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1077
13
9454e1c4f022 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 01204be0cb805c82785dcef994237b96a39ee40c
iuc
parents: 12
diff changeset
1078 * **example.phy.splits.nex**: has the same information as **example.phy.splits** but in NEXUS format, which can be viewed with the program IcyTree_ to explore the conflicting signals in the data. So it is more informative than consensus tree, e.g. you can see how highly supported the second best conflicting split is, which had no chance to enter the consensus tree.
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1079
13
9454e1c4f022 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 01204be0cb805c82785dcef994237b96a39ee40c
iuc
parents: 12
diff changeset
1080 .. _IcyTree: https://icytree.org
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1081
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1082 Reducing impact of severe model violations with UFBoot
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1083 ------------------------------------------------------
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1084
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1085 Starting with IQ-TREE version 1.6 we provide a new option **-bnni** to reduce the risk of overestimating branch supports with UFBoot due to severe model violations. With this option UFBoot will further optimize each bootstrap tree using a hill-climbing nearest neighbor interchange (NNI) search based directly on the corresponding bootstrap alignment.
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1086
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1087 Thus, if severe model violations are present in the data set at hand, users are advised to append **-bnni** to the regular UFBoot command:
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1088
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
1089 iqtree -s example.phy -m TIM2+I+G --ufboot 1000 -bnni
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1090
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1091 For more details see:
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1092
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1093 D.T. Hoang, O. Chernomor, A. von Haeseler, B.Q. Minh, L.S. Vinh (2017) UFBoot2: Improving the ultrafast bootstrap approximation.
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1094
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1095
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1096 Assessing branch supports with standard nonparametric bootstrap
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1097 ----------------------------------------------------------------
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1098
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1099 The standard nonparametric bootstrap is invoked by the **-b** option:
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1100
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1101 iqtree -s example.phy -m TIM2+I+G -b 100
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1102
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1103 **-b** specifies the number of bootstrap replicates where 100
1
f041f5a855cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit d4423a8641e86485dde733e8148c5bced4d8410c
iuc
parents: 0
diff changeset
1104 is the minimum recommended number. The output files are similar to those produced by the UFBoot procedure.
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1105
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1106
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1107
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1108 Assessing branch supports with single branch tests
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1109 --------------------------------------------------
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1110
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1111 IQ-TREE provides an implementation of the SH-like approximate likelihood ratio test ([Guindon et al., 2010]). To perform this test, run:
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1112
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1113 ::
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1114
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
1115 iqtree -s example.phy -m TIM2+I+G --alrt 1000
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1116
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
1117 **--alrt** specifies the number of bootstrap replicates for SH-aLRT where 1000 is the minimum number recommended.
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1118
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1119 IQ-TREE also supports other tests such as the aBayes test (Anisimova et al., 2011) and the local bootstrap test (Adachi and Hasegawa, 1996).
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1120
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1121 You can also perform both SH-aLRT and the ultrafast bootstrap within one single run:
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1122
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1123 ::
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1124
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
1125 iqtree -s example.phy -m TIM2+I+G --alrt 1000 --ufboot 1000
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1126
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1127 The branches of the resulting **.treefile** will be assigned with both SH-aLRT and UFBoot support values, which are readable by any tree viewer program like FigTree, Dendroscope or ETE. You can also look at the textual tree figure in **.iqtree** file:
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1128
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1129 **NOTE**: Tree is UNROOTED although outgroup taxon 'LngfishAu' is drawn at root
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1130 Numbers in parentheses are SH-aLRT support (%) / ultrafast bootstrap support (%)
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1131
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1132 ::
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1133
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1134 +-------------LngfishAu
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1135 |
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1136 | +--------------LngfishSA
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1137 +-------| (100/100)
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1138 | +------------LngfishAf
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1139 |
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1140 | +--------------------Frog
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1141 +------| (99.8/100)
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1142 | +-----------------Turtle
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1143 | +--| (85/72)
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1144 | | | +------------------------Crocodile
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1145 | | +----| (96.5/97)
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1146 | | +------------------Bird
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1147 | +--| (39/51)
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1148 | | +---------------------------Sphenodon
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1149 | +-----| (98.2/99)
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1150 | | +-------------------------------Lizard
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1151 +---------| (100/100)
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1152 | +--------------Human
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1153 | +--| (92.3/93)
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1154 | | | +------Seal
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1155 | | +--| (68.3/75)
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1156 | | | +-----Cow
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1157 | | +--| (99.7/100)
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1158 | | +-------Whale
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1159 | +----| (99.1/100)
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1160 | | | +---Mouse
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1161 | | +---------| (100/100)
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1162 | | +------Rat
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1163 +-----------| (100/100)
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1164 | +--------------Platypus
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1165 +--| (93/98)
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1166 +-----------Opossum
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1167
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1168
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1169 From this figure, the branching patterns within reptiles are poorly supported (e.g. **Sphenodon** with SH-aLRT: 39%, UFBoot: 51% and **Turtle** with SH-aLRT: 85%, UFBoot: 72%) as well as the phylogenetic position of **Seal** within mammals (SH-aLRT: 68.3%, UFBoot: 75%). Other branches appear to be well supported.
2
b2fbfb61f019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 686710a7d313b828f1daed20c4055479727f2d91
iuc
parents: 1
diff changeset
1170 ]]></help>
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1171 <citations>
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
1172 <citation type="doi">10.1038/nmeth.4285</citation>
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1173 <citation type="doi">10.1093/molbev/msu300</citation>
5
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
1174 <citation type="doi">10.1093/molbev/msx281</citation>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
1175 <citation type="doi">10.1093/sysbio/syx068</citation>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
1176 <citation type="doi">10.1093/sysbio/syw037</citation>
2f343cfa4aad "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3accba706168833bbe6d7774b8bf929608fbb559"
iuc
parents: 4
diff changeset
1177 <citation type="doi">10.1016/j.jtbi.2016.07.042</citation>
0
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1178 <citation type="doi">10.1093/molbev/mst024</citation>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1179 </citations>
72ef801e8d98 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 494efe4359ba046587dd2d5585464a3df05ba997
iuc
parents:
diff changeset
1180 </tool>