| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/usher_matutils/usher_matutils/0.2.1+galaxy0 (this tool) |
| usher_matutils |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| usher | 0.2.1 | package |
| Additional information about this tool |
matUtils
$matutils_mode.options_mode
--input-mat $mutation_annotation_file
#if $matutils_mode.options_mode == 'extract'
#if $matutils_mode.operation_mode.operation == 'samples'
#if $matutils_mode.operation_mode.samples
--samples '${matutils_mode.operation_mode.samples}'
#end if
$matutils_mode.operation_mode.prune
#elif $matutils_mode.operation_mode.operation == 'clade'
--clade '${matutils_mode.operation_mode.clade}'
$matutils_mode.operation_mode.prune
#elif $matutils_mode.operation_mode.operation == 'mutation'
--mutation '${matutils_mode.operation_mode.mutation}'
$matutils_mode.operation_mode.prune
#elif $matutils_mode.operation_mode.operation == 'max-epps'
--max-epps $matutils_mode.operation_mode.max_epps
$matutils_mode.operation_mode.prune
#elif $matutils_mode.operation_mode.operation == 'max-parsimony'
--max-parsimony $matutils_mode.operation_mode.max_parsimony
$matutils_mode.operation_mode.prune
#elif $matutils_mode.operation_mode.operation == 'nearest-k'
--nearest-k '${matutils_mode.operation_mode.nearest_k}'
$matutils_mode.operation_mode.prune
#elif $matutils_mode.operation_mode.operation == 'max-branch-length'
--max-branch-length $matutils_mode.operation_mode.max_branch_length
#end if
$matutils_mode.get_representative
$matutils_mode.resolve_polytomies
#if 'used-samples' in $matutils_mode.outputs_extract
--used-samples selected_samples.txt ##$selected_samples
#end if
#if 'sample-paths' in $matutils_mode.outputs_extract
--sample-paths path_mutations.tabular ##$path_mutations
#end if
#if 'clade-paths' in $matutils_mode.outputs_extract
--clade-paths path_clades.tabular ##$path_clades
#end if
#if 'all-paths' in $matutils_mode.outputs_extract
--all-paths all_paths.txt ##$all_paths
#end if
#if 'write-vcf' in $matutils_mode.outputs_extract
--write-vcf subtree_vcf.vcf ##$subtree_vcf
#end if
#if 'write-vcf-no-genotypes' in $matutils_mode.outputs_extract and 'write-vcf' not in $matutils_mode.outputs_extract
--write-vcf subtree_vcf_no_genotypes.vcf --no-genotypes
#end if
#if 'write-mat' in $matutils_mode.outputs_extract
--write-mat mutation_annotated.pb ##$mutation_annotated
#end if
#if 'write-mat-collapsed' in $matutils_mode.outputs_extract and 'write-mat' not in $matutils_mode.outputs_extract
--write-mat mutation_annotated_collapsed.pb --collapsed-tree
#end if
#if 'write-json' in $matutils_mode.outputs_extract
--write-json subtree_json.json ##$subtree_json
#end if
#if 'write-tree' in $matutils_mode.outputs_extract
--write-tree tree_newick.nh ##$tree_newick
#end if
#if 'write-tree-retain-branch' in $matutils_mode.outputs_extract and 'write-tree' not in $matutils_mode.outputs_extract
--write-tree tree_newick_retain_branch.nh --retain-branch-length
#end if
#elif $matutils_mode.options_mode == 'summary'
#if 'samples' in $matutils_mode.summary_options
--samples samples_stats.tabular
#end if
#if 'clades' in $matutils_mode.summary_options
--clades clades_stats.tabular
#end if
#if 'mutations' in $matutils_mode.summary_options
--mutations mutations_stats.tabular
#end if
#if 'aberrant' in $matutils_mode.summary_options
--aberrant aberrant_stats.tabular
#end if
--output-directory ./
#elif $matutils_mode.options_mode == 'annotate'
#if $matutils_mode.clade_names
--clade-names '${matutils_mode.clade_names}'
#if $matutils_mode.allele_frequency
--allele-frequency $matutils_mode.allele_frequency
#end if
#if $matutils_mode.set_overlap
--set-overlap $matutils_mode.set_overlap
#end if
#if $matutils_mode.mask_frequency
--mask-frequency $matutils_mode.mask_frequency
#end if
#if $matutils_mode.clip_sample_frequency
--clip-sample-frequency $matutils_mode.clip_sample_frequency
#end if
#end if
#if $matutils_mode.clade_to_nid
--clade-to-nid '${matutils_mode.clade_to_nid}'
#end if
$matutils_mode.clear_current
--output-mat output_mat.pb ##$output_mat
#elif $matutils_mode.options_mode == 'uncertainty'
--samples '${matutils_mode.samples}'
#if 'get-parsimony' in $matutils_mode.uncertainty_options
--get-parsimony
#end if
#if 'find-epps' in $matutils_mode.uncertainty_options
--find-epps equally_parsimonious.tabular
#end if
#if 'find-neighborhood' in $matutils_mode.uncertainty_options
--find-neighborhood neighborhood.tabular
#end if
#elif $matutils_mode.options_mode == 'mask'
#if $matutils_mode.restricted_samples
--restricted-samples '${matutils_mode.restricted_samples}'
#end if
#if $matutils_mode.rename_samples
--rename-samples '${matutils_mode.rename_samples}'
#end if
$$matutils_mode.simplify
--output-mat output_mat.pb ##$output_mat
#end if
--threads \${GALAXY_SLOTS:-1} > output_stdout.txt
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
mutation_annotation_file: mutation_annotation.pb matutils_mode|operation_mode|samples: sample_names.txt matutils_mode|operation_mode|prune: True matutils_mode|operation_mode|operation: samples matutils_mode|resolve_polytomies: True matutils_mode|outputs_extract: ['used-samples', 'sample-paths', 'clade-paths'] matutils_mode|options_mode: extract |
name: value name: value name: value |
mutation_annotation.pb sample_names.txt value |
| Test-2 |
mutation_annotation_file: mutation_annotation.pb matutils_mode|operation_mode|samples: sample_names.txt matutils_mode|operation_mode|operation: samples matutils_mode|outputs_extract: ['used-samples', 'sample-paths', 'clade-paths', 'all-paths', 'write-vcf'] matutils_mode|options_mode: extract |
name: value name: value name: value name: value name: value |
mutation_annotation.pb sample_names.txt value |
| Test-3 |
mutation_annotation_file: mutation_annotation.pb matutils_mode|operation_mode|mutation: C241T matutils_mode|operation_mode|operation: mutation matutils_mode|outputs_extract: ['write-vcf-no-genotypes', 'write-mat', 'write-json', 'write-tree'] matutils_mode|options_mode: extract |
name: value name: value name: value name: value |
mutation_annotation.pb value |
| Test-4 |
mutation_annotation_file: mutation_annotation.pb matutils_mode|outputs_extract: ['used-samples', 'sample-paths', 'write-vcf'] matutils_mode|options_mode: extract |
name: value name: value name: value |
mutation_annotation.pb value |
| Test-5 |
mutation_annotation_file: mutation_annotation.pb matutils_mode|operation_mode|max_epps: 0 matutils_mode|operation_mode|operation: max-epps matutils_mode|outputs_extract: ['used-samples', 'sample-paths', 'clade-paths', 'all-paths', 'write-vcf'] matutils_mode|options_mode: extract |
name: value name: value name: value name: value name: value |
mutation_annotation.pb value |
| Test-6 |
mutation_annotation_file: mutation_annotation.pb matutils_mode|operation_mode|max_parsimony: 1 matutils_mode|operation_mode|operation: max-parsimony matutils_mode|outputs_extract: ['used-samples', 'sample-paths', 'clade-paths', 'all-paths', 'write-vcf'] matutils_mode|options_mode: extract |
name: value name: value name: value name: value name: value |
mutation_annotation.pb value |
| Test-7 |
mutation_annotation_file: mutation_annotation.pb matutils_mode|operation_mode|max_branch_length: 2 matutils_mode|operation_mode|operation: max-branch-length matutils_mode|outputs_extract: ['used-samples', 'sample-paths', 'clade-paths'] matutils_mode|options_mode: extract |
name: value name: value name: value |
mutation_annotation.pb value |
| Test-8 |
mutation_annotation_file: mutation_annotation.pb matutils_mode|summary_options: general matutils_mode|options_mode: summary |
name: value |
mutation_annotation.pb value |
| Test-9 |
mutation_annotation_file: mutation_annotation.pb matutils_mode|summary_options: ['samples', 'clades', 'mutations', 'aberrant'] matutils_mode|options_mode: summary |
name: value name: value name: value name: value |
mutation_annotation.pb value |
| Test-10 |
mutation_annotation_file: mutation_annotation.pb matutils_mode|samples: sample_names.txt matutils_mode|uncertainty_options: get-parsimony matutils_mode|options_mode: uncertainty |
name: value |
mutation_annotation.pb sample_names.txt value |
| Test-11 |
mutation_annotation_file: mutation_annotation.pb matutils_mode|samples: sample_names.txt matutils_mode|uncertainty_options: ['find-epps', 'find-neighborhood'] matutils_mode|options_mode: uncertainty |
name: value name: value |
mutation_annotation.pb sample_names.txt value |
| Test-12 |
mutation_annotation_file: mutation_annotation.pb matutils_mode|restricted_samples: sample_names.txt matutils_mode|simplify: True matutils_mode|options_mode: mask |
name: value |
mutation_annotation.pb sample_names.txt value |
| Test-13 |
mutation_annotation_file: mutation_annotation.pb matutils_mode|rename_samples: rename_samples.tabular matutils_mode|options_mode: mask |
name: value |
mutation_annotation.pb rename_samples.tabular value |