usher: usher.xml annotate

annotate usher.xml @ 0:524cb8f7a69a draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"

author	iuc
date	Tue, 11 May 2021 17:53:49 +0000
parents
children	335665e15630

rev	line source
0 524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	1 <tool id='usher' name='UShER' version='@TOOL_VERSION@+@GALAXY_TOOL_VERSION@' profile='20.01'>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	2 <description>ultrafast sample placement on existing trees</description>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	3 <macros>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	4 <import>macros.xml</import>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	5 </macros>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	6 <expand macro='edam_ontology' />
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	7 <expand macro='requirements' />
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	8 <version_command>usher --version</version_command>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	9 <command detect_errors='exit_code'><![CDATA[
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	10 #if $vcf.ext == 'vcf_bgzip':
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	11 ln -s '$vcf' input.vcf.gz &&
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	12 ln -s '$vcf.metadata.tabix_index' input.vcf.gz.tbi &&
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	13 #set $input_vcf = 'input.vcf.gz'
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	14 #else:
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	15 ln -s '$vcf' input.vcf &&
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	16 #set $input_vcf = 'input.vcf'
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	17 #end if
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	18
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	19 usher
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	20 -v '$input_vcf'
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	21 #if $tree
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	22 -t '${tree}'
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	23 #end if
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	24 #if $load_mutation_annotated_tree
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	25 -i '${load_mutation_annotated_tree}'
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	26 #end if
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	27 $output_options.save_mutation_annotated_tree
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	28 $sort_mode
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	29 $collapse_options.collapse_tree
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	30 $collapse_options.collapse_output_tree
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	31 #if $max_uncertainty_per_sample
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	32 -e $max_uncertainty_per_sample
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	33 #end if
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	34 $output_options.write_uncondensed_final_tree
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	35 #if $output_options.write_subtrees_size
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	36 -k $output_options.write_subtrees_size
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	37 #end if
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	38 #if $output_options.write_single_subtree
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	39 -K $output_options.write_single_subtree
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	40 #end if
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	41 $output_options.write_parsimony_scores_per_node
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	42 #if $output_options.multiple_placements
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	43 -M $output_options.multiple_placements
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	44 #end if
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	45 #if $retain_input_branch_lengths
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	46 $retain_input_branch_lengths
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	47 #end if
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	48 -T \${GALAXY_SLOTS:-1}
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	49 -d ./
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	50 #if $output_options.write_subtrees_size
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	51 && mkdir -p out_subtrees out_subtrees_expanded out_subtrees_mutations
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	52 && mv subtree*expanded.txt ./out_subtrees_expanded
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	53 && mv subtree*mutations.txt ./out_subtrees_mutations
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	54 && mv subtree*.nh ./out_subtrees
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	55 #end if
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	56 ]]> </command>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	57 <inputs>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	58 <param name="vcf" type="data" format="vcf,vcf_bgzip" label="VCF file" help="Input VCF file."/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	59 <param name="tree" type="data" format="newick" optional="True" label="Tree file" help="Input tree file in Newick format."/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	60 <param argument="--load-mutation-annotated-tree" type="data" format="protobuf3" optional="True" label="Mutation-annotated tree object" help="Load a mutation annotated tree file, in protocol-buffers format (protobuf3)."/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	61 <param name="sort_mode" type="select" label="Mode of sorting new samples">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	62 <option value="">Default sorting</option>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	63 <option value="--sort-before-placement-1">Sort based on computed parsimony score and then number of optimal placements before the actual placement (-s)</option>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	64 <option value="--sort-before-placement-1 --reverse-sort">Sort based on computed parsimony score and then number of optimal placements before the actual placement [reversed] (-s -r)</option>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	65 <option value="--sort-before-placement-2">Sort based on the number of optimal placements and then the parsimony score before the actual placement (-S)</option>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	66 <option value="--sort-before-placement-2 --reverse-sort">Sort based on the number of optimal placements and then the parsimony score before the actual placement [reversed] (-S -r)</option>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	67 <option value="--sort-before-placement-3">Sort based on the number of ambiguous bases (-A)</option>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	68 </param>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	69 <param argument="--max-uncertainty-per-sample" type="integer" optional="True" min="0" max="10000000" value="" label="Maximum number of equally parsimonious placements" help="Maximum number of equally parsimonious placements allowed per sample beyond which the sample is ignored." />
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	70 <param argument="--retain-input-branch-lengths" type="boolean" truevalue="--retain-input-branch-lengths" falsevalue="" label="Retain the branch lengths" help="Retain the branch lengths from the input tree in out newick files instead of using number of mutations for the branch lengths." />
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	71 <section name="collapse_options" title="Collapse options" expanded="True">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	72 <param argument="--collapse-tree" type="boolean" truevalue="--collapse-tree" falsevalue="" label="Collapse internal nodes of the input tree" help="Collapse internal nodes of the input tree with no mutations and condense identical sequences in polytomies into a single node and the save the tree to file condensed-tree.nh in outdir." />
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	73 <param argument="--collapse-output-tree" type="boolean" truevalue="--collapse-output-tree" falsevalue="" label="Collapse internal nodes of the output tree" help="Collapse internal nodes of the output tree with no mutations before the saving the tree to file final-tree.nh in outdir." />
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	74 </section>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	75 <section name="output_options" title="Output tree options" expanded="True">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	76 <param argument="--save-mutation-annotated-tree" type="boolean" truevalue="--save-mutation-annotated-tree annotated-tree.pb" falsevalue="" label="Save the new mutation-annotated tree object" help="Save output mutation-annotated tree object to the file new_global_assignments.pb." />
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	77 <param argument="--write-uncondensed-final-tree" type="boolean" truevalue="--write-uncondensed-final-tree" falsevalue="" label="Uncondensed final tree" help="Write the final tree in uncondensed format and save to file uncondensed-final-tree.nh in outdir." />
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	78 <param argument="--write-subtrees-size" type="integer" optional="True" min="0" max="100" value="" label="Generate multiple subtrees" help="Write minimum set of subtrees covering the newly added samples of size equal to this value." />
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	79 <param argument="--write-single-subtree" type="integer" optional="True" min="0" max="100" value="" label="Generate a single subtree" help="Similar to write-subtrees-size but produces a single subtree with all newly added samples along with random samples up to the value specified by this argument." />
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	80 <param argument="--write-parsimony-scores-per-node" type="boolean" truevalue="--write-parsimony-scores-per-node" falsevalue="" label="Generate parsimony scores per node" help="Write the parsimony scores for adding new samples at each existing node in the tree without modifying the tree in a file names parsimony-scores.tsv in outdir." />
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	81 <param argument="--multiple-placements" type="integer" optional="True" min="0" max="100" value="" label="Multiple placements" help="Create a new tree up to this limit for each possibility of parsimony-optimal placement." />
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	82 </section>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	83 </inputs>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	84 <outputs>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	85 <data name="annotated_tree" format="protobuf3" from_work_dir="annotated-tree.pb" label="${tool.name} on ${on_string}: mutation annotated tree">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	86 <filter>output_options['save_mutation_annotated_tree'] is True</filter>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	87 </data>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	88 <data name="condensed_tree" format="newick" from_work_dir="condensed-tree.nh" label="${tool.name} on ${on_string}: condensed tree">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	89 <filter>collapse_options['collapse_tree'] is True</filter>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	90 </data>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	91 <data name="final_tree" format="newick" from_work_dir="final-tree.nh" label="${tool.name} on ${on_string}: final tree">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	92 <filter>output_options['write_uncondensed_final_tree'] is False and output_options['write_parsimony_scores_per_node'] is False</filter>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	93 </data>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	94 <data name="uncondensed_tree" format="newick" from_work_dir="uncondensed-final-tree.nh" label="${tool.name} on ${on_string}: uncondensed tree">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	95 <filter>output_options['write_uncondensed_final_tree'] is True</filter>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	96 </data>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	97 <data name="mutation_paths" format="txt" from_work_dir="mutation-paths.txt" label="${tool.name} on ${on_string}: mutation paths">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	98 <filter>output_options['save_mutation_annotated_tree'] is False and output_options['write_parsimony_scores_per_node'] is False</filter>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	99 </data>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	100 <data name="clades" format="txt" from_work_dir="clades.txt" label="${tool.name} on ${on_string}: clades">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	101 <filter>output_options['save_mutation_annotated_tree'] is False and output_options['write_parsimony_scores_per_node'] is False</filter>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	102 </data>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	103 <collection name='subtrees' type='list' label='${tool.name} on ${on_string}: subtrees'>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	104 <discover_datasets pattern='__designation_and_ext__' format="newick" directory='out_subtrees'/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	105 <filter>output_options['write_subtrees_size']</filter>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	106 </collection>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	107 <collection name='subtrees_expanded' type='list' label='${tool.name} on ${on_string}: subtrees expanded'>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	108 <discover_datasets pattern='__designation_and_ext__' format='txt' directory='out_subtrees_expanded'/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	109 <filter>output_options['write_subtrees_size']</filter>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	110 </collection>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	111 <collection name='subtrees_mutations' type='list' label='${tool.name} on ${on_string}: subtrees mutations'>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	112 <discover_datasets pattern='__designation_and_ext__' format='txt' directory='out_subtrees_mutations'/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	113 <filter>output_options['write_subtrees_size']</filter>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	114 </collection>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	115 <data name="current_tree" format="newick" from_work_dir="current-tree.nh" label="${tool.name} on ${on_string}: current tree">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	116 <filter>output_options['write_parsimony_scores_per_node'] is True</filter>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	117 </data>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	118 <data name="parsimony_scores" format="tabular" from_work_dir="parsimony-scores.tsv" label="${tool.name} on ${on_string}: parsimony scores per node">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	119 <filter>output_options['write_parsimony_scores_per_node'] is True</filter>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	120 </data>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	121 <data name="single_subtree" format="newick" from_work_dir="single-subtree.nh" label="${tool.name} on ${on_string}: single subtree">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	122 <filter>output_options['write_single_subtree']</filter>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	123 </data>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	124 <data name="single_subtree_expanded" format="txt" from_work_dir="single-subtree-expanded.txt" label="${tool.name} on ${on_string}: single subtree expanded">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	125 <filter>output_options['write_single_subtree']</filter>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	126 </data>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	127 <data name="single_subtree_mutations" format="txt" from_work_dir="single-subtree-mutations.txt" label="${tool.name} on ${on_string}: single subtree mutations">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	128 <filter>output_options['write_single_subtree']</filter>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	129 </data>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	130 </outputs>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	131 <tests>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	132 <test expect_num_outputs="3">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	133 <param name="vcf" value="global_samples.vcf.gz" ftype="vcf_bgzip" />
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	134 <param name="tree" value="global_phylo.nh"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	135 <section name="collapse_options">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	136 <param name="collapse_tree" value="true"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	137 </section>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	138 <section name="output_options">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	139 <param name="save_mutation_annotated_tree" value="true"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	140 </section>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	141 <output name="annotated_tree" file="test_01_annotated_tree.pb" ftype="protobuf3">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	142 <assert_contents>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	143 <has_size value="26100" delta="100"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	144 </assert_contents>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	145 </output>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	146 <output name="condensed_tree" file="test_01_condensed_tree.nh" ftype="newick"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	147 <output name="final_tree" file="test_01_final_tree.nh" ftype="newick"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	148 </test>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	149 <test expect_num_outputs="3">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	150 <param name="vcf" value="new_samples.vcf.gz"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	151 <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	152 <section name="output_options">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	153 <param name="write_uncondensed_final_tree" value="true"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	154 </section>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	155 <output name="uncondensed_tree" file="test_02_uncondensed_tree.nh" ftype="newick"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	156 <output name="mutation_paths" file="test_02_mutation_path.nh" ftype="txt"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	157 <output name="clades" ftype="txt">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	158 <assert_contents>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	159 <has_size value="0" delta="0"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	160 </assert_contents>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	161 </output>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	162 </test>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	163 <test expect_num_outputs="4">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	164 <param name="vcf" value="global_samples.vcf.gz" ftye="vcf_bgzip" />
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	165 <param name="tree" value="global_phylo.nh"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	166 <param name="sort_mode" value="--sort-before-placement-1"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	167 <section name="collapse_options">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	168 <param name="collapse_tree" value="true"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	169 </section>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	170 <output name="condensed_tree" file="test_03_condensed_tree.nh" ftype="newick"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	171 <output name="final_tree" file="test_03_final_tree.nh" ftype="newick"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	172 <output name="mutation_paths" ftype="txt">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	173 <assert_contents>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	174 <has_size value="0"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	175 </assert_contents>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	176 </output>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	177 <output name="clades" ftype="txt">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	178 <assert_contents>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	179 <has_size value="0"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	180 </assert_contents>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	181 </output>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	182 </test>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	183 <test expect_num_outputs="6">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	184 <param name="vcf" value="new_samples.vcf.gz"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	185 <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	186 <section name="output_options">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	187 <param name="write_uncondensed_final_tree" value="true"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	188 <param name="write_subtrees_size" value="20"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	189 </section>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	190 <output name="uncondensed_tree" file="test_04_uncondensed_tree.nh" ftype="newick"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	191 <output name="mutation_paths" file="test_04_mutation_paths.txt" ftype="txt"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	192 <output name="clades" ftype="txt">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	193 <assert_contents>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	194 <has_size value="0"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	195 </assert_contents>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	196 </output>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	197 <output_collection name="subtrees" type="list" count="1">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	198 <element name="subtree-1" file="test_04_subtree_1.nh"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	199 </output_collection>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	200 <output_collection name="subtrees_expanded" type="list" count="1">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	201 <element name="subtree-1-expanded" file="test_04_subtree_1_expanded.txt" ftype="txt"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	202 </output_collection>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	203 <output_collection name="subtrees_mutations" type="list" count="1">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	204 <element name="subtree-1-mutations" file="test_04_subtree_1_mutations.txt" ftype="txt"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	205 </output_collection>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	206 </test>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	207 <test expect_num_outputs="2">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	208 <param name="vcf" value="new_samples.vcf.gz"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	209 <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	210 <section name="output_options">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	211 <param name="write_parsimony_scores_per_node" value="true"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	212 </section>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	213 <output name="current_tree" file="test_05_current_tree.nw" ftype="newick"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	214 <output name="parsimony_scores" file="test_05_parsimony_scores.tabular" ftype="tabular"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	215 </test>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	216 <test expect_num_outputs="3">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	217 <param name="vcf" value="new_samples.vcf.gz"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	218 <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	219 <section name="output_options">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	220 <param name="multiple_placements" value="2"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	221 </section>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	222 <output name="final_tree" file="test_06_final_tree.nh" ftype="newick"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	223 <output name="mutation_paths" file="test_06_mutation_paths.txt" ftype="txt"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	224 <output name="clades" ftype="txt">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	225 <assert_contents>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	226 <has_size value="0"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	227 </assert_contents>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	228 </output>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	229 </test>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	230 <test expect_num_outputs="6">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	231 <param name="vcf" value="new_samples.vcf.gz"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	232 <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	233 <section name="output_options">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	234 <param name="write_single_subtree" value="2"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	235 </section>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	236 <output name="final_tree" file="test_06_final_tree.nh" ftype="newick"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	237 <output name="mutation_paths" file="test_06_mutation_paths.txt" ftype="txt"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	238 <output name="clades" ftype="txt">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	239 <assert_contents>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	240 <has_size value="0"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	241 </assert_contents>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	242 </output>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	243 <output name="single_subtree" file="test_07_single_subtree.nh" ftype="newick"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	244 <output name="single_subtree_mutations" file="test_07_single_subtree_mutations.txt" ftype="txt"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	245 <output name="single_subtree_expanded" ftype="txt">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	246 <assert_contents>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	247 <has_size value="0"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	248 </assert_contents>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	249 </output>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	250 </test>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	251 <test expect_num_outputs="3">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	252 <param name="vcf" value="new_samples.vcf.gz"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	253 <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	254 <param name="sort_mode" value="--sort-before-placement-2"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	255 <output name="final_tree" file="test_08_final_tree.nh" ftype="newick"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	256 <output name="mutation_paths" file="test_08_mutation_path.nh" ftype="txt"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	257 <output name="clades" ftype="txt">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	258 <assert_contents>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	259 <has_size value="0"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	260 </assert_contents>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	261 </output>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	262 </test>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	263 <test expect_num_outputs="3">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	264 <param name="vcf" value="new_samples.vcf.gz"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	265 <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	266 <param name="sort_mode" value="--sort-before-placement-3"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	267 <output name="final_tree" file="test_09_final_tree.nh" ftype="newick"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	268 <output name="mutation_paths" file="test_09_mutation_path.nh" ftype="txt"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	269 <output name="clades" ftype="txt">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	270 <assert_contents>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	271 <has_size value="0"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	272 </assert_contents>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	273 </output>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	274 </test>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	275 <test expect_num_outputs="3">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	276 <param name="vcf" value="new_samples.vcf.gz"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	277 <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	278 <param name="sort_mode" value="--sort-before-placement-1 --reverse-sort"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	279 <output name="final_tree" file="test_10_final_tree.nh" ftype="newick"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	280 <output name="mutation_paths" file="test_10_mutation_path.nh" ftype="txt"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	281 <output name="clades" ftype="txt">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	282 <assert_contents>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	283 <has_size value="0"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	284 </assert_contents>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	285 </output>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	286 </test>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	287 <test expect_num_outputs="3">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	288 <param name="vcf" value="new_samples.vcf.gz"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	289 <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	290 <param name="sort_mode" value="--sort-before-placement-2 --reverse-sort"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	291 <output name="final_tree" file="test_11_final_tree.nh" ftype="newick"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	292 <output name="mutation_paths" file="test_11_mutation_path.nh" ftype="txt"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	293 <output name="clades" ftype="txt">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	294 <assert_contents>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	295 <has_size value="0"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	296 </assert_contents>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	297 </output>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	298 </test>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	299 <test expect_num_outputs="3">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	300 <param name="vcf" value="new_samples.vcf.gz" ftype="vcf_bgzip"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	301 <param name="load_mutation_annotated_tree" value="test_01_annotated_tree.pb"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	302 <param name="retain_input_branch" value="true"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	303 <output name="final_tree" file="test_12_final_tree.nh" ftype="newick" lines_diff="2"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	304 <output name="mutation_paths" file="test_12_mutation_path.nh" ftype="txt"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	305 <output name="clades" ftype="txt">
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	306 <assert_contents>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	307 <has_size value="0"/>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	308 </assert_contents>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	309 </output>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	310 </test>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	311 </tests>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	312 <help><![CDATA[
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	313 .. class:: infomark
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	314
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	315 Purpose
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	316
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	317 UShER is a program for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods, and is being widely used by several SARS-CoV-2 research groups, including the UCSC Genome Browser team and Rob Lanfear’s global phylogeny releases.
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	318
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	319 ----
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	320
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	321 .. class:: infomark
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	322
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	323 How UShER works?
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	324
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	325 Given existing samples, whose genotypes and phylogenetic tree is known, and the genotypes of new samples, UShER aims to incorporate new samples into the phylogenetic tree while preserving the topology of existing samples and maximizing parsimony. UShER’s algorithm consists of two phases: (i) the pre-processing phase and (ii) the placement phase.
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	326
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	327 In the pre-processing phase, UShER accepts the phylogenetic tree of existing samples in a Newick format and their genotypes, specified as a set of single-nucleotide variants with respect to a reference sequence (UShER currently ignores indels), in a VCF format. For each site in the VCF, UShER uses `Fitch-Sankoff algorithm <https://evolution.gs.washington.edu/gs541/2010/lecture1.pdf>`_ to find the most parsimonious nucleotide assignment for every node of the tree (UShER automatically labels internal tree nodes).
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	328
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	329 When a sample contains ambiguous genotypes, multiple nucleotides may be most parsimonious at a node. To resolve these, UShER assigns it any one of the most parsimonious nucleotides with preference, when possible, given to the reference base. UShER also allows the VCF to specify ambiguous bases in samples using `IUPAC format <https://www.bioinformatics.org/sms/iupac.html>`_, which are also resolved to a unique base using the above strategy. When a node is found to carry a mutation, i.e. the base assigned to the node differs from its parent, the mutation gets added to a list of mutations corresponding to that node. Finally, UShER uses `protocol buffers <https://developers.google.com/protocol-buffers>`_ to store in a file, the Newick string corresponding to the input tree and a list of lists of node mutation, which we refer to as mutation-annotated tree object.
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	330
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	331 The mutation-annotated tree object carries sufficient information to derive parsimony-resolved genotypes for any tip of the tree using the sequence of mutations from the root to that tip. Compared to other tools that use full multiple-sequence alignment (MSA) to guide the placement, UShER's mutation-annotated tree object is compact and is what helps make it fast.
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	332
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	333 In the placement phase, UShER loads the pre-processed mutation-annotated tree object and the genotypes of new samples in a VCF format and sequentially adds the new samples to the tree. For each new sample, UShER computes the additional parsimony score required for placing it at every node in the current tree while considering the full path of mutations from the root of the tree to that node.
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	334
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	335 Next, UShER places the new sample at the node that results in the smallest additional parsimony score. When multiple node placements are equally parsimonious, UShER picks the node with a greater number of descendant leaves for placement. If the choice is between a parent and its child node, the parent node would always be selected by this rule. However, a more accurate placement should reflect the number of leaves uniquely attributable to the child versus parent node. Therefore, in these cases, UShER picks the parent node if the number of descendant leaves of the parent that are not shared with the child node exceed the number of descendant leaves of the child.
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	336
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	337 UShER also automatically imputes and reports ambiguous genotypes for the newly added samples and ignores missing bases, such as 'N' or '.' (i.e. missing bases never contribute to the parsimony score).
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	338
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	339 At the end of the placement phase, UShER allows the user to create another protocol-buffer (protobuf) file containing the mutation-annotated tree object for the newly generated tree including added samples. This allows for another round of placements to be carried out over and above the newly added samples.
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	340
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	341
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	342 ]]> </help>
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	343 <expand macro="citations" />
524cb8f7a69a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1" iuc parents: diff changeset	344 </tool>

Mercurial > repos > iuc > usher

annotate usher.xml @ 0:524cb8f7a69a draft