gubbins: gubbins.xml annotate

annotate gubbins.xml @ 1:96e6283e4745 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823

author	iuc
date	Wed, 24 Aug 2022 07:37:39 +0000
parents	637ec5d5368c
children

rev	line source
1 96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	1 <tool id="gubbins" name="Gubbins" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
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>
1 96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	3 <macros>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	4 <token name="@TOOL_VERSION@">3.2.1</token>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	5 <token name="@VERSION_SUFFIX@">0</token>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	6 </macros>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	7 <xrefs>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	8 <xref type="bio.tools">gubbins</xref>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	9 </xrefs>
0 637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	10 <requirements>
1 96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	11 <requirement type="package" version="@TOOL_VERSION@">gubbins</requirement>
0 637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	12 </requirements>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	13
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	14 <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	15
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	16 <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	17
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	18 ln -s '$alignment_file' foo.aln &&
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	19
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	20 run_gubbins.py
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	21
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	22 --threads \${GALAXY_SLOTS:-1}
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	23
1 96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	24 -i '$adv.iterations'
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	25 -z '$adv.converge_method'
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	26 $adv.extensive_search
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	27
0 637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	28 #if $adv.outgroup
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	29 -o '$adv.outgroup'
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	30 #end if
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	31
1 96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	32 -t '$really_adv.tree_builder'
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	33 -m '$really_adv.min_snps'
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	34 -f '$really_adv.filter_percentage'
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	35 -a '$really_adv.min_window_size'
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	36 -b '$really_adv.max_window_size'
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	37 -p '$really_adv.p_value'
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	38 --trimming-ratio '$really_adv.trimming_ratio'
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	39 $really_adv.remove_identical_sequences
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	40
0 637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	41 foo.aln
1 96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	42
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	43 ## Requited because the p-value is included as prefix
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	44
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	45 && mv *branch_base_reconstruction.embl branch_base_reconstruction.embl
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	46 && mv *filtered_polymorphic_sites.fasta filtered_polymorphic_sites.fasta
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	47 && mv *filtered_polymorphic_sites.phylip filtered_polymorphic_sites.phylip
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	48 && mv *node_labelled.final_tree.tre node_labelled.final_tree
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	49 && mv *final_tree.tre final_tree.tre
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	50 && mv *per_branch_statistics.csv per_branch_statistics.csv
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	51 && mv *recombination_predictions.embl recombination_predictions.embl
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	52 && mv *recombination_predictions.gff recombination_predictions.gff
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	53 && mv *summary_of_snp_distribution.vcf summary_of_snp_distribution.vcf
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	54
0 637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	55 ]]></command>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	56 <inputs>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	57 <!-- 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	58 <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	59
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	60 <!-- output file picker -->
1 96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	61 <param name="outfiles" type="select" 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">
0 637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	62 <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	63 <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	64 <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	65 <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	66 <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	67 <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	68 <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	69 <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	70 </param>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	71
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	72 <!-- 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	73 <section name="adv" title="Advanced options" expanded="True">
1 96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	74 <param argument="--iterations" type="integer" label="Iterations" min="0" value="5" help="Maximum No. of iterations, default is 5" />
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	75 <param argument="--converge-method" type="select" label="Model conversion Options" help="Criteria to use to know when to halt iterations">
0 637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	76 <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	77 <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	78 <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	79 </param>
1 96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	80 <param argument="--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.">
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	81 <sanitizer invalid_char="">
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	82 <valid initial="string.letters,string.digits">
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	83 <add value="+" />
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	84 <add value="-" />
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	85 <add value=" " />
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	86 <add value="_" />
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	87 </valid>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	88 </sanitizer>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	89 </param>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	90 <param argument="--extensive-search" type="boolean" truevalue="--extensive-search" falsevalue="" checked="false" label="Extensive search " help="Default: False" />
0 637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	91 </section>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	92
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	93 <!-- 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	94 <section name="really_adv" title="Really advanced options - change these if you really know what you are doing." expanded="false">
1 96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	95 <param argument="--tree-builder" type="select" label="Tree builder" help="Application to use for tree building, default RAxML">
0 637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	96 <option value="raxml" selected="true">RAxML</option>
1 96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	97 <option value="raxmlng">RAxML-NG</option>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	98 <option value="iqtree">IQ-TREE</option>
0 637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	99 <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	100 <option value="hybrid">Hybrid</option>
1 96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	101 <option value="rapidnj">RapidNJ</option>
0 637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	102 </param>
1 96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	103 <param argument="--min-snps" type="integer" label="Minimum SNPs" min="0" value="3" help="Min SNPs to identify a recombination block. Default: 3" />
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	104 <param argument="--filter-percentage" type="float" label="Filter percentage" min="0" value="25" help="Filter out taxa with more than this percentage of gaps. Default: 25" />
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	105 <param argument="--min-window-size" type="integer" label="Minimum window size" min="0" value="100" help="Minimum window size. Default: 100" />
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	106 <param argument="--max-window-size" type="integer" label="Maximum window size" min="0" value="10000" help="Maximum window size. Default: 10000" />
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	107 <param argument="--remove-identical-sequences" type="boolean" label="Remove identical sequences" falsevalue="" truevalue="-d" />
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	108 <param argument="--p-value" type="float" min="0" max="1" value="0.05" label="p-Value" help="p-Value for detecting recombinations. Default: 0.05" />
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	109 <param argument="--trimming_ratio" type="float" min="0" value="1" label="Trimming ration" help="Ratio of log probabilities used to trim recombinations. Default: 1" />
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	110
0 637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	111 </section>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	112
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	113 </inputs>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	114
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	115 <outputs>
1 96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	116 <data format="txt" name="final_tree" label="${tool.name} on ${on_string} Final Tree" from_work_dir="final_tree.tre" >
0 637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	117 <filter>outfiles and 'ftree' in outfiles</filter>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	118 </data>
1 96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	119 <data format="gff3" name="recomb_pred_gff" label="${tool.name} on ${on_string} Recombinations Prediction gff" from_work_dir="recombination_predictions.gff" >
0 637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	120 <filter>outfiles and 'gff' in outfiles</filter>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	121 </data>
1 96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	122 <data format="embl" name="recomb_pred_embl" label="${tool.name} on ${on_string} Recombinations Prediction embl" from_work_dir="recombination_predictions.embl" >
0 637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	123 <filter>outfiles and 'recomb_embl' in outfiles</filter>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	124 </data>
1 96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	125 <data format="fasta" name="filt_polymorph_fna" label="${tool.name} on ${on_string} Filtered Polymorphic Sites fasta" from_work_dir="filtered_polymorphic_sites.fasta" >
0 637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	126 <filter>outfiles and 'fpoly' in outfiles</filter>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	127 </data>
1 96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	128 <data format="phylip" name="filt_polymorph_phy" label="${tool.name} on ${on_string} Filtered Polymorphic Sites phylip" from_work_dir="filtered_polymorphic_sites.phylip" >
0 637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	129 <filter>outfiles and 'ppoly' in outfiles</filter>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	130 </data>
1 96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	131 <data format="csv" name="per_b_stat_csv" label="${tool.name} on ${on_string} Per Branch Statistics csv" from_work_dir="per_branch_statistics.csv" >
0 637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	132 <filter>outfiles and 'stats' in outfiles</filter>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	133 </data>
1 96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	134 <data format="vcf" name="sum_snp_vcf" label="${tool.name} on ${on_string} Summary of SNP Distribution vcf" from_work_dir="summary_of_snp_distribution.vcf" >
0 637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	135 <filter>outfiles and 'vcf' in outfiles</filter>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	136 </data>
1 96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	137 <data format="embl" name="base_branch_embl" label="${tool.name} on ${on_string} Branch Base Reconstruction embl" from_work_dir="branch_base_reconstruction.embl" >
0 637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	138 <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	139 </data>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	140 </outputs>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	141
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	142
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	143 <tests>
1 96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	144 <test expect_num_outputs="3">
0 637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	145 <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	146 <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	147 <assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	148 <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	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 </output>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	151 <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	152 <assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	153 <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	154 </assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	155 </output>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	156 </test>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	157
1 96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	158 <test expect_num_outputs="3">
0 637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	159 <param name="alignment_file" value="multiple_recombinations.aln" ftype="fasta" />
1 96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	160 <param name="iterations" value="3"/>
0 637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	161 <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	162 <assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	163 <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	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 </output>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	166 <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	167 <assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	168 <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	169 </assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	170 </output>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	171 </test>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	172
1 96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	173 <test expect_num_outputs="3">
0 637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	174 <param name="alignment_file" value="multiple_recombinations.aln" ftype="fasta" />
1 96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	175 <param name="converge_method" value="recombination" />
0 637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	176 <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	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 <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	179 </assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	180 </output>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	181 <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	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 <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	184 </assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	185 </output>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	186 </test>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	187
1 96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	188 <test expect_num_outputs="8">
0 637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	189 <param name="alignment_file" value="multiple_recombinations.aln" ftype="fasta" />
1 96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	190 <param name="converge_method" value="recombination" />
0 637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	191 <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	192 <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	193 <assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	194 <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	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 </output>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	197 <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	198 <assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	199 <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	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 </output>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	202 <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	203 <assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	204 <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	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 </output>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	207 <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	208 <assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	209 <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	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 </output>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	212 <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	213 <assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	214 <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	215 </assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	216 </output>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	217 <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	218 <assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	219 <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	220 </assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	221 </output>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	222 <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	223 <assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	224 <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	225 </assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	226 </output>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	227 <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	228 <assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	229 <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	230 </assert_contents>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	231 </output>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	232 </test>
1 96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	233 <!-- Test new options-->
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	234 <test expect_num_outputs="8" >
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	235 <param name="alignment_file" value="multiple_recombinations.aln" ftype="fasta" />
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	236 <param name="outfiles" value="ftree,gff,vcf,recomb_embl,fpoly,ppoly,stats,baseb"/>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	237 <section name="adv">
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	238 <param name="expensive_research" value="true"/>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	239 </section>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	240 <section name="really_adv">
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	241 <param name="tree_builder" value="fasttree"/>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	242 <param name="remove_identical_sequences" value="true"/>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	243 </section>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	244 <output name="recomb_pred_gff">
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	245 <assert_contents>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	246 <has_text text="##gff-version 3" />
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	247 <has_text text="sequence_4" />
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	248 </assert_contents>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	249 </output>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	250 <output name="sum_snp_vcf">
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	251 <assert_contents>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	252 <has_text text="##fileformat=VCFv4.2" />
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	253 </assert_contents>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	254 </output>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	255 <output name="base_branch_embl">
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	256 <assert_contents>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	257 <has_n_lines n="1638"/>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	258 <has_text text="sequence_8" />
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	259 </assert_contents>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	260 </output>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	261 <output name="final_tree">
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	262 <assert_contents>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	263 <has_n_lines n="1"/>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	264 <has_text text="sequence_10" />
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	265 </assert_contents>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	266 </output>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	267 <output name="recomb_pred_embl">
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	268 <assert_contents>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	269 <has_n_lines n="24"/>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	270 <has_text text="sequence_2" />
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	271 </assert_contents>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	272 </output>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	273 <output name="filt_polymorph_fna">
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	274 <assert_contents>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	275 <has_n_lines n="18"/>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	276 <has_text text="GAAAA" />
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	277 </assert_contents>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	278 </output>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	279 <output name="filt_polymorph_phy">
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	280 <assert_contents>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	281 <has_n_lines n="10"/>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	282 <has_text text="GAAAA" />
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	283 </assert_contents>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	284 </output>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	285 <output name="per_b_stat_csv">
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	286 <assert_contents>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	287 <has_n_lines n="18"/>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	288 <has_text text="Number of SNPs Inside Recombinations" />
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	289 </assert_contents>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	290 </output>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	291 <output name="sum_snp_vcf">
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	292 <assert_contents>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	293 <has_text text="ID=1,length=242" />
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	294 </assert_contents>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	295 </output>
96e6283e4745 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823 iuc parents: 0 diff changeset	296 </test>
0 637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	297 </tests>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	298
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	299
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	300 <help><![CDATA[
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	301 Gubbins
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	302
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	303 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	304
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	305 Running Gubbins
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	306
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	307 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	308
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	309 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	310
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	311 Other options
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	312
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	313 Advanced
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	314
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	315 Iterations, (-i)
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	316
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	317 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	318
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	319 Converge_method (-z)
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	320
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	321 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	322
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	323 Outgroup, (-o)
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	324
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	325 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	326
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	327 Really Advanced
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	328
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	329 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	330
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	331 Tree builder, (-t)
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	332
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	333 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	334
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	335 Filter Percentage, (-f)
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	336
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	337 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	338
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	339 Minimum snps, (-m)
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	340
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	341 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	342
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	343
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	344 And others...
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	345
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	346
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	347
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	348 Output files
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	349
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	350 * 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	351
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	352
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	353 * 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	354
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	355
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	356 * 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	357
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	358
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	359 * 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	360
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	361
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	362 * 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	363
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	364
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	365 * 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	366
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	367
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	368 * 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	369
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	370
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	371 * 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	372
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	373 ]]></help>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	374
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	375
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	376 <citations>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	377 <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	378 </citations>
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	379
637ec5d5368c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit 98be6edc2544513347149b50e0cfb530811f890a iuc parents: diff changeset	380 </tool>

Mercurial > repos > iuc > gubbins

annotate gubbins.xml @ 1:96e6283e4745 draft default tip