Mercurial > repos > iuc > gubbins

annotate gubbins.xml @ 0:637ec5d5368c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
author iuc
date Fri, 23 Jun 2017 08:29:43 -0400
parents
children 96e6283e4745
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
1 <tool id="gubbins" name="Gubbins" version="0.1.0">
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
2 <description>Recombination detection in Bacteria</description>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
3 <requirements>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
4 <requirement type="package" version="2.2.1">gubbins</requirement>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
5 </requirements>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
6
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
7 <version_command>run_gubbins.py --version</version_command>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
8
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
9 <command detect_errors="exit_code"><![CDATA[
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
10
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
11 ln -s '$alignment_file' foo.aln &&
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
12
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
13 run_gubbins.py
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
14
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
15 --threads \${GALAXY_SLOTS:-1}
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
16
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
17 #if $adv.iters
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
18 -i '$adv.iters'
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
19 #end if
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
20
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
21 #if $adv.conv_meth
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
22 -z '$adv.conv_meth'
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
23 #end if
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
24
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
25 #if $adv.outgroup
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
26 -o '$adv.outgroup'
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
27 #end if
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
28
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
29 #if $really_adv.tree_builder
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
30 -t '$really_adv.tree_builder'
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
31 #end if
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
32
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
33 #if $really_adv.min_snps
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
34 -m '$really_adv.min_snps'
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
35 #end if
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
36
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
37 #if $really_adv.filter_percentage
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
38 -f '$really_adv.filter_percentage'
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
39 #end if
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
40
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
41 #if $really_adv.min_window_size
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
42 -a '$really_adv.min_window_size'
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
43 #end if
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
44
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
45 #if $really_adv.max_window_size
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
46 -b '$really_adv.max_window_size'
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
47 #end if
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
48
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
49 $really_adv.remove_duplicates
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
50
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
51 foo.aln
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
52
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
53 ]]></command>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
54 <inputs>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
55 <!-- Just the data set.. -->
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
56 <param type="data" name="alignment_file" format="fasta" label="Whole genome alignment file" help="Whole genome alignment file in fasta format"/>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
57
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
58 <!-- output file picker -->
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
59 <param type="select" name="outfiles" multiple="true" display="checkboxes" label="Select the required output files" help="Default selections are the Final Tree in Newick format, the Recombination Predictions in gff3 format and the Summary of SNP Distribution">
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
60 <option value="ftree" selected="true">Final Tree in newick format</option>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
61 <option value="gff" selected="true">Recombination Predictions in gff3 format</option>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
62 <option value="vcf" selected="true">Summary of SNP Distribution in vcf format</option>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
63 <option value="recomb_embl">Recombination Predictions in embl format</option>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
64 <option value="fpoly">Filtered Polymorphic Sites in fasta format</option>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
65 <option value="ppoly">Filtered Polymorphic Sites in phylip format</option>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
66 <option value="stats">Per Branch Statistics in csv format</option>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
67 <option value="baseb">Base Branch Reconstruction in embl format</option>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
68 </param>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
69
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
70 <!-- A semi advanced section, really shouldn't have to change anything. -->
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
71 <section name="adv" title="Advanced options" expanded="True">
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
72 <param name="iters" type="integer" label="Iterations" value="5" help="Maximum No. of iterations, default is 5" />
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
73 <param name="conv_meth" type="select" label="Model Conversion Options" help="Criteria to use to know when to halt iterations">
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
74 <option value="weighted_robinson_foulds" selected="True">Weighted Robinson Foulds</option>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
75 <option value="robinson_foulds">Robinson Foulds</option>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
76 <option value="recombination">Recombination</option>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
77 </param>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
78 <param name="outgroup" type="text" label="Outgroup" value="" help="Outgroup name for rerooting. A list of comma separated names can be used if they form a clade."/>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
79 </section>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
80
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
81 <!-- a really advanced section, play with this at your peril! -->
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
82 <section name="really_adv" title="Really advanced options - change these if you really know what you are doing." expanded="false">
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
83 <param name="tree_builder" type="select" label="Tree builder" help="Application to use for tree building, default RAxML">
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
84 <option value="raxml" selected="true">RAxML</option>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
85 <option value="fasttree">FastTree</option>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
86 <option value="hybrid">Hybrid</option>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
87 </param>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
88 <param name="min_snps" type="integer" label="Minimum SNPS" value="3" help="Min SNPs to identify a recombination block, default is 3" />
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
89 <param name="filter_percentage" type="integer" label="Filter Percentage" value="25" help="Filter out taxa with more than this percentage of gaps, default is 25" />
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
90 <param name="min_window_size" type="integer" label="Minimum Window Size" value="100" help="Minimum window size, default 100" />
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
91 <param name="max_window_size" type="integer" label="Maximum Window Size" value="10000" help="Maximum window size, default 10000" />
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
92 <param name="remove_duplicates" type="boolean" label="Remove identical sequences" falsevalue="" truevalue="-d" />
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
93 </section>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
94
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
95 </inputs>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
96
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
97 <outputs>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
98 <data format="txt" name="final_tree" label="${tool.name} on ${on_string} Final Tree" from_work_dir="foo.final_tree.tre" >
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
99 <filter>outfiles and 'ftree' in outfiles</filter>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
100 </data>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
101 <data format="gff3" name="recomb_pred_gff" label="${tool.name} on ${on_string} Recombinations Prediction gff" from_work_dir="foo.recombination_predictions.gff" >
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
102 <filter>outfiles and 'gff' in outfiles</filter>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
103 </data>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
104 <data format="embl" name="recomb_pred_embl" label="${tool.name} on ${on_string} Recombinations Prediction embl" from_work_dir="foo.recombination_predictions.embl" >
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
105 <filter>outfiles and 'recomb_embl' in outfiles</filter>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
106 </data>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
107 <data format="fasta" name="filt_polymorph_fna" label="${tool.name} on ${on_string} Filtered Polymorphic Sites fasta" from_work_dir="foo.filtered_polymorphic_sites.fasta" >
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
108 <filter>outfiles and 'fpoly' in outfiles</filter>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
109 </data>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
110 <data format="phylip" name="filt_polymorph_phy" label="${tool.name} on ${on_string} Filtered Polymorphic Sites phylip" from_work_dir="foo.filtered_polymorphic_sites.phylip" >
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
111 <filter>outfiles and 'ppoly' in outfiles</filter>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
112 </data>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
113 <data format="csv" name="per_b_stat_csv" label="${tool.name} on ${on_string} Per Branch Statistics csv" from_work_dir="foo.per_branch_statistics.csv" >
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
114 <filter>outfiles and 'stats' in outfiles</filter>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
115 </data>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
116 <data format="vcf" name="sum_snp_vcf" label="${tool.name} on ${on_string} Summary of SNP Distribution vcf" from_work_dir="foo.summary_of_snp_distribution.vcf" >
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
117 <filter>outfiles and 'vcf' in outfiles</filter>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
118 </data>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
119 <data format="embl" name="base_branch_embl" label="${tool.name} on ${on_string} Branch Base Reconstruction embl" from_work_dir="foo.branch_base_reconstruction.embl" >
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
120 <filter>outfiles and 'baseb' in outfiles</filter>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
121 </data>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
122 </outputs>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
123
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
124
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
125 <tests>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
126 <test>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
127 <param name="alignment_file" value="multiple_recombinations.aln" ftype="fasta" />
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
128 <output name="recomb_pred_gff">
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
129 <assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
130 <has_text text="##gff-version 3" />
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
131 </assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
132 </output>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
133 <output name="sum_snp_vcf">
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
134 <assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
135 <has_text text="##fileformat=VCFv4.2" />
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
136 </assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
137 </output>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
138 </test>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
139
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
140 <test>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
141 <param name="alignment_file" value="multiple_recombinations.aln" ftype="fasta" />
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
142 <param name="iters" value="3"/>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
143 <output name="recomb_pred_gff">
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
144 <assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
145 <has_text text="##gff-version 3" />
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
146 </assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
147 </output>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
148 <output name="sum_snp_vcf">
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
149 <assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
150 <has_text text="##fileformat=VCFv4.2" />
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
151 </assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
152 </output>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
153 </test>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
154
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
155 <test>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
156 <param name="alignment_file" value="multiple_recombinations.aln" ftype="fasta" />
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
157 <param name="conv_meth" value="recombination" />
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
158 <output name="recomb_pred_gff">
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
159 <assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
160 <has_text text="##gff-version 3" />
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
161 </assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
162 </output>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
163 <output name="sum_snp_vcf">
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
164 <assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
165 <has_text text="##fileformat=VCFv4.2" />
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
166 </assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
167 </output>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
168 </test>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
169
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
170 <test>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
171 <param name="alignment_file" value="multiple_recombinations.aln" ftype="fasta" />
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
172 <param name="conv_meth" value="recombination" />
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
173 <param name="outfiles" value="gff,vcf,ftree,recomb_embl,fpoly,ppoly,stats,baseb"/>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
174 <output name="recomb_pred_gff">
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
175 <assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
176 <has_text text="##gff-version 3" />
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
177 </assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
178 </output>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
179 <output name="sum_snp_vcf">
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
180 <assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
181 <has_text text="##fileformat=VCFv4.2" />
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
182 </assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
183 </output>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
184 <output name="filt_polymorph_fna">
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
185 <assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
186 <has_text text=">sequence_1" />
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
187 </assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
188 </output>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
189 <output name="recomb_pred_embl">
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
190 <assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
191 <has_text text="FT" />
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
192 </assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
193 </output>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
194 <output name="filt_polymorph_phy">
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
195 <assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
196 <has_text text="sequence_1" />
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
197 </assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
198 </output>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
199 <output name="per_b_stat_csv">
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
200 <assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
201 <has_text text="Node" />
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
202 </assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
203 </output>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
204 <output name="base_branch_embl">
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
205 <assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
206 <has_text text="FT" />
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
207 </assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
208 </output>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
209 <output name="final_tree">
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
210 <assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
211 <has_text text="((sequence_" />
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
212 </assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
213 </output>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
214 </test>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
215 </tests>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
216
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
217
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
218 <help><![CDATA[
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
219 **Gubbins**
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
220
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
221 Since the introduction of high-throughput, second-generation DNA sequencing technologies, there has been an enormous increase in the size of datasets being used for estimating bacterial population phylodynamics. Although many phylogenetic techniques are scalable to hundreds of bacterial genomes, methods which have been used for mitigating the effect of mechanisms of horizontal sequence transfer on phylogenetic reconstructions cannot cope with these new datasets. Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. Simulations demonstrate the algorithm generates highly accurate reconstructions under realistic models of short-term bacterial evolution, and can be run in only a few hours on alignments of hundreds of bacterial genome sequences.
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
222
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
223 **Running Gubbins**
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
224
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
225 To run Gubbins with default settings:
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
226
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
227 Supply a "fasta" genome alignment file and press execute.
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
228
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
229 **Other options**
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
230
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
231 **Advanced**
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
232
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
233 *Iterations*, (-i)
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
234
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
235 The maximum number of iterations to perform; the algorithm will stop earlier than this if it converges on the same tree in two successive iterations. Default is 5.
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
236
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
237 *Converge_method* (-z)
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
238
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
239 Criteria to use to know when to halt iterations [weighted_robinson_foulds|robinson_foulds|recombination]. Default is weighted_robinson_foulds.
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
240
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
241 *Outgroup*, (-o)
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
242
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
243 The name of a sequence in the alignment on which to root the tree
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
244
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
245 **Really Advanced**
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
246
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
247 These options are here for completeness and you shouldn't need to change them from their defaults. You really need to know what you are doing before you use these.
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
248
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
249 *Tree builder*, (-t)
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
250
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
251 The algorithm to use in the construction of phylogenies in the analysis; can be ‘raxml’, to use RAxML, ‘fasttree’, to use Fasttree, or ‘hybrid’, to use Fasttree for the first iteration and RAxML in all subsequent iterations. Default is raxml
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
252
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
253 Filter Percentage, (-f)
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
254
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
255 Filter out taxa with more than this percentage of missing data. Default is 25%
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
256
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
257 *Minimum snps*, (-m)
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
258
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
259 The minimum number of base substitutions required to identify a recombination. Default is 3.
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
260
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
261
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
262 And others...
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
263
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
264
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
265
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
266 **Output files**
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
267
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
268 * Recombination predictions in EMBL tab file format.
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
269
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
270
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
271 * Recombination predictions in GFF3 format
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
272
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
273
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
274 * Base substitution reconstruction in EMBL tab format.
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
275
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
276
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
277 * VCF file summarising the distribution of SNPs
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
278
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
279
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
280 * Per branch reporting of the base substitutions inside and outside recombinations events.
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
281
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
282
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
283 * FASTA format alignment of filtered polymorphic sites used to generate the phylogeny in the final iteration.
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
284
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
285
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
286 * Phylip format alignment of filtered polymorphic sites used to generate the phylogeny in the final iteration.
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
287
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
288
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
289 * Final phylogenetic tree in newick format.
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
290
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
291 ]]></help>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
292
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
293
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
294 <citations>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
295 <citation type="doi">doi:10.1093/nar/gku1196</citation>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
296 </citations>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
297
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a
iuc
parents:
diff changeset
298 </tool>