Mercurial > repos > iuc > usher_matutils
comparison matutils.xml @ 0:79e2ee4e6ebb draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/usher commit c1531745ea5f5c4fbd22ad18e290b47fdcb01bb1"
author | iuc |
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date | Tue, 11 May 2021 17:54:51 +0000 |
parents | |
children | 52fd1d491417 |
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-1:000000000000 | 0:79e2ee4e6ebb |
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1 <tool id='usher_matutils' name='UShER matUtils' version='@TOOL_VERSION@+@GALAXY_TOOL_VERSION@' profile='20.01'> | |
2 <description>analyze, edit, and manipulate mutation annotated tree files</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro='edam_ontology' /> | |
7 <expand macro='requirements' /> | |
8 <version_command>usher --version</version_command> | |
9 <command detect_errors='exit_code'><![CDATA[ | |
10 matUtils | |
11 $matutils_mode.options_mode | |
12 --input-mat $mutation_annotation_file | |
13 #if $matutils_mode.options_mode == 'extract' | |
14 #if $matutils_mode.operation_mode.operation == 'samples' | |
15 #if $matutils_mode.operation_mode.samples | |
16 --samples '${matutils_mode.operation_mode.samples}' | |
17 #end if | |
18 $matutils_mode.operation_mode.prune | |
19 #elif $matutils_mode.operation_mode.operation == 'clade' | |
20 --clade '${matutils_mode.operation_mode.clade}' | |
21 $matutils_mode.operation_mode.prune | |
22 #elif $matutils_mode.operation_mode.operation == 'mutation' | |
23 --mutation '${matutils_mode.operation_mode.mutation}' | |
24 $matutils_mode.operation_mode.prune | |
25 #elif $matutils_mode.operation_mode.operation == 'max-epps' | |
26 --max-epps $matutils_mode.operation_mode.max_epps | |
27 $matutils_mode.operation_mode.prune | |
28 #elif $matutils_mode.operation_mode.operation == 'max-parsimony' | |
29 --max-parsimony $matutils_mode.operation_mode.max_parsimony | |
30 $matutils_mode.operation_mode.prune | |
31 #elif $matutils_mode.operation_mode.operation == 'nearest-k' | |
32 --nearest-k '${matutils_mode.operation_mode.nearest_k}' | |
33 $matutils_mode.operation_mode.prune | |
34 #elif $matutils_mode.operation_mode.operation == 'max-branch-length' | |
35 --max-branch-length $matutils_mode.operation_mode.max_branch_length | |
36 #end if | |
37 $matutils_mode.get_representative | |
38 $matutils_mode.resolve_polytomies | |
39 #if 'used-samples' in $matutils_mode.outputs_extract | |
40 --used-samples selected_samples.txt ##$selected_samples | |
41 #end if | |
42 #if 'sample-paths' in $matutils_mode.outputs_extract | |
43 --sample-paths path_mutations.tabular ##$path_mutations | |
44 #end if | |
45 #if 'clade-paths' in $matutils_mode.outputs_extract | |
46 --clade-paths path_clades.tabular ##$path_clades | |
47 #end if | |
48 #if 'all-paths' in $matutils_mode.outputs_extract | |
49 --all-paths all_paths.txt ##$all_paths | |
50 #end if | |
51 #if 'write-vcf' in $matutils_mode.outputs_extract | |
52 --write-vcf subtree_vcf.vcf ##$subtree_vcf | |
53 #end if | |
54 #if 'write-vcf-no-genotypes' in $matutils_mode.outputs_extract and 'write-vcf' not in $matutils_mode.outputs_extract | |
55 --write-vcf subtree_vcf_no_genotypes.vcf --no-genotypes | |
56 #end if | |
57 #if 'write-mat' in $matutils_mode.outputs_extract | |
58 --write-mat mutation_annotated.pb ##$mutation_annotated | |
59 #end if | |
60 #if 'write-mat-collapsed' in $matutils_mode.outputs_extract and 'write-mat' not in $matutils_mode.outputs_extract | |
61 --write-mat mutation_annotated_collapsed.pb --collapsed-tree | |
62 #end if | |
63 #if 'write-json' in $matutils_mode.outputs_extract | |
64 --write-json subtree_json.json ##$subtree_json | |
65 #end if | |
66 #if 'write-tree' in $matutils_mode.outputs_extract | |
67 --write-tree tree_newick.nh ##$tree_newick | |
68 #end if | |
69 #if 'write-tree-retain-branch' in $matutils_mode.outputs_extract and 'write-tree' not in $matutils_mode.outputs_extract | |
70 --write-tree tree_newick_retain_branch.nh --retain-branch-length | |
71 #end if | |
72 #elif $matutils_mode.options_mode == 'summary' | |
73 #if 'samples' in $matutils_mode.summary_options | |
74 --samples samples_stats.tabular | |
75 #end if | |
76 #if 'clades' in $matutils_mode.summary_options | |
77 --clades clades_stats.tabular | |
78 #end if | |
79 #if 'mutations' in $matutils_mode.summary_options | |
80 --mutations mutations_stats.tabular | |
81 #end if | |
82 #if 'aberrant' in $matutils_mode.summary_options | |
83 --aberrant aberrant_stats.tabular | |
84 #end if | |
85 --output-directory ./ | |
86 #elif $matutils_mode.options_mode == 'annotate' | |
87 #if $matutils_mode.clade_names | |
88 --clade-names '${matutils_mode.clade_names}' | |
89 #if $matutils_mode.allele_frequency | |
90 --allele-frequency $matutils_mode.allele_frequency | |
91 #end if | |
92 #if $matutils_mode.set_overlap | |
93 --set-overlap $matutils_mode.set_overlap | |
94 #end if | |
95 #if $matutils_mode.mask_frequency | |
96 --mask-frequency $matutils_mode.mask_frequency | |
97 #end if | |
98 #if $matutils_mode.clip_sample_frequency | |
99 --clip-sample-frequency $matutils_mode.clip_sample_frequency | |
100 #end if | |
101 #end if | |
102 #if $matutils_mode.clade_to_nid | |
103 --clade-to-nid '${matutils_mode.clade_to_nid}' | |
104 #end if | |
105 $matutils_mode.clear_current | |
106 --output-mat output_mat.pb ##$output_mat | |
107 #elif $matutils_mode.options_mode == 'uncertainty' | |
108 --samples '${matutils_mode.samples}' | |
109 #if 'get-parsimony' in $matutils_mode.uncertainty_options | |
110 --get-parsimony | |
111 #end if | |
112 #if 'find-epps' in $matutils_mode.uncertainty_options | |
113 --find-epps equally_parsimonious.tabular | |
114 #end if | |
115 #if 'find-neighborhood' in $matutils_mode.uncertainty_options | |
116 --find-neighborhood neighborhood.tabular | |
117 #end if | |
118 #elif $matutils_mode.options_mode == 'mask' | |
119 #if $matutils_mode.restricted_samples | |
120 --restricted-samples '${matutils_mode.restricted_samples}' | |
121 #end if | |
122 #if $matutils_mode.rename_samples | |
123 --rename-samples '${matutils_mode.rename_samples}' | |
124 #end if | |
125 $$matutils_mode.simplify | |
126 --output-mat output_mat.pb ##$output_mat | |
127 #end if | |
128 --threads \${GALAXY_SLOTS:-1} > output_stdout.txt | |
129 | |
130 ]]> </command> | |
131 <inputs> | |
132 <param name="mutation_annotation_file" type="data" format="protobuf3" label="Mutation-annotated tree object" help="Load a mutation annotated tree file, in protocol-buffers format (protobuf3)."/> | |
133 <conditional name="matutils_mode"> | |
134 <param name="options_mode" type="select" label="matUtils mode"> | |
135 <option value="extract">Extract: subsetting and converting a MAT pb to other file formats</option> | |
136 <option value="summary">Summary: get basic statistics and attribute information about the MAT</option> | |
137 <option value="annotate">Annotate: adding clade annotation information to the MAT</option> | |
138 <option value="uncertainty">Uncertainty: calculates two specific metrics for sample placement certainty</option> | |
139 <option value="mask">Mask: mask specific samples out of the MAT, removing their mutations from visibility</option> | |
140 </param> | |
141 <when value="extract"> | |
142 <conditional name="operation_mode"> | |
143 <param name="operation" type="select" label="Operation mode"> | |
144 <option value="samples">Select samples by naming them</option> | |
145 <option value="clade">Select samples by clade(s)</option> | |
146 <option value="mutation">Select samples by mutation</option> | |
147 <option value="max-epps">Select samples by parsimonious placements</option> | |
148 <option value="max-parsimony">Select samples by parsimonious score</option> | |
149 <option value="nearest-k">Select samples by sample and context</option> | |
150 <option value="max-branch-length">Remove samples by branch length</option> | |
151 </param> | |
152 <when value="samples"> | |
153 <param argument="--samples" type="data" format="txt" optional="True" label="Select samples by explicitly naming them, one per line in a plain text file" /> | |
154 <param argument="--prune" type="boolean" truevalue="--prune" falsevalue="" label="Remove the selected samples" help="Remove the selected samples instead of keeping them in the output files" /> | |
155 </when> | |
156 <when value="clade"> | |
157 <param argument="--clade" type="text" value="" label="Select samples by membership in any of the indicated clade(s), comma delimited- e.g. -c clade1,clade2"> | |
158 <expand macro="sanitize_string" /> | |
159 </param> | |
160 <param argument="--prune" type="boolean" truevalue="--prune" falsevalue="" label="Remove the selected samples" help="Remove the selected samples instead of keeping them in the output files" /> | |
161 </when> | |
162 <when value="mutation"> | |
163 <param argument="--mutation" type="text" value="" label="Select samples by whether they contain any of the indicated mutation(s), comma delimited- e.g. -m mutation1,mutation2"> | |
164 <expand macro="sanitize_string" /> | |
165 </param> | |
166 <param argument="--prune" type="boolean" truevalue="--prune" falsevalue="" label="Remove the selected samples" help="Remove the selected samples instead of keeping them in the output files" /> | |
167 </when> | |
168 <when value="max-epps"> | |
169 <param argument="--max-epps" type="integer" min="0" max="1000" value="" label="Select samples by whether they have less than or equal to the maximum number of indicated equally parsimonious placements" /> | |
170 <param argument="--prune" type="boolean" truevalue="--prune" falsevalue="" label="Remove the selected samples" help="Remove the selected samples instead of keeping them in the output files" /> | |
171 </when> | |
172 <when value="max-parsimony"> | |
173 <param argument="--max-parsimony" type="integer" min="0" max="1000" value="" label="Select samples by whether they have less than or equal to the indicated maximum parsimony score (terminal branch length)" /> | |
174 <param argument="--prune" type="boolean" truevalue="--prune" falsevalue="" label="Remove the selected samples" help="Remove the selected samples instead of keeping them in the output files" /> | |
175 </when> | |
176 <when value="nearest-k"> | |
177 <param argument="--nearest-k" type="text" value="" label="Select a specific sample and X context samples, formatted as 'sample_name:X'"> | |
178 <expand macro="sanitize_string" /> | |
179 </param> | |
180 <param argument="--prune" type="boolean" truevalue="--prune" falsevalue="" label="Remove the selected samples" help="Remove the selected samples instead of keeping them in the output files" /> | |
181 </when> | |
182 <when value="max-branch-length"> | |
183 <param argument="--max-branch-length" type="integer" min="0" max="1000" value="" label="Remove samples which have branches of greater than the indicated length in their ancestry" /> | |
184 </when> | |
185 </conditional> | |
186 <param argument="--get-representative" type="boolean" truevalue="--get-representative" falsevalue="" label="Select two representative samples per clade" help=" Toggle to automatically select two representative samples per clade currently included in the tree, pruning all other samples from the tree. Applies after other selection steps" /> | |
187 <param argument="--resolve-polytomies" type="boolean" truevalue="--resolve-polytomies" falsevalue="" label="Resolve all polytomies" help="Resolve all polytomies by assigning branch length 0 relationships arbitrarily. Applied after selection; prevents recondensing of the MAT" /> | |
188 <param name="outputs_extract" type="select" display="checkboxes" multiple="true" label="Select the desired output"> | |
189 <option value="used-samples">Write a simple text file containing selected sample names (--used-samples)</option> | |
190 <option value="sample-paths">Write the path of mutations defining each sample in the subtree (--sample-paths)</option> | |
191 <option value="clade-paths">Write the path of mutations defining each clade in the subtree (--clade-paths)</option> | |
192 <option value="all-paths">Write mutations assigned to each node in the subtree in depth-first traversal order (--all-paths)</option> | |
193 <option value="write-vcf">Output VCF file representing selected subtree (--write-vcf)</option> | |
194 <option value="write-vcf-no-genotypes">Output VCF file representing selected subtree without including genotype column (--write-vcf --no-genotypes) </option> | |
195 <option value="write-mat">Write the selected subtree as a mutation annotated tree (--write-math)</option> | |
196 <option value="write-mat-collapsed">Write the selected subtree as a collapsed mutation annotated tree (--write-mat --collapsed)</option> | |
197 <option value="write-json">Write an Auspice-compatbile json representing the selected subtree (--write-json)</option> | |
198 <option value="write-tree"> Write a newick string representing the selected subtree (--write-tree)</option> | |
199 <option value="write-tree-retain-branch"> Write a newick string representing the selected subtree without recalculating branch lengths (--write-tree --retain-branch)</option> | |
200 </param> | |
201 </when> | |
202 <when value="summary"> | |
203 <param name="summary_options" type="select" display="checkboxes" multiple="true" label="Select statistics and attribute information"> | |
204 <option value="general">Number of nodes, number of samples, number of condensed nodes, and total tree parsimony</option> | |
205 <option value="samples">Samples in the tree and their parsimony score (--samples)</option> | |
206 <option value="clades">Clades and the count of associated samples in the tree (--clades)</option> | |
207 <option value="mutations">Mutations in the tree and their occurrence count (--mutations)</option> | |
208 <option value="aberrant">Potentially problematic nodes (--aberrant)</option> | |
209 </param> | |
210 </when> | |
211 <when value="annotate"> | |
212 <param argument="--clade-names" type="data" format="tabular" optional="True" label="File containing clade asssignments of samples" help="An algorithm automatically locates and annotates clade root nodes."/> | |
213 <param argument="--clade-to-nid" type="data" format="tabular" optional="True" label="File mapping clades to their respective internal node identifiers" help="Internal node names are not maintained when saving and loading from a .pb file. It is not guaranteed that internal node names will correspond directly between two .pb files, so use the direct assignment method with caution."/> | |
214 <param argument="--set-overlap" type="float" min="0" max="1" value="" optional="True" label="Minimum fraction of the lineage samples" help="Minimum fraction of the lineage samples that should be desecendants of the assigned clade root. Used only with --clade-names" /> | |
215 <param argument="--clear-current" type="boolean" truevalue="--clear-current" falsevalue="" label="Remove current annotations" help="Use to remove current annotations before applying new annotations." /> | |
216 <param argument="--allele-frequency" type="float" min="0" max="1" value="" optional="True" label="Minimum allele frequency for finding the best clade root" help="Minimum allele frequency in input samples for finding the best clade root. Used only with 'remove current annotation'. Used only with --clade-names" /> | |
217 <param argument="--mask-frequency" type="float" min="0" max="1" value="" optional="True" label="Minimum allele frequency for being masked" help="Minimum allele frequency in input samples that should be masked for finding the best clade root. Used only with --clade-names" /> | |
218 <param argument="--clip-sample-frequency" type="float" min="0" max="1" value="" optional="True" label="Clip sample frequency" help="Maximum proportion of samples in a branch that are exemplars from --clade-names to consider when sorting candidate clade root nodes." /> | |
219 </when> | |
220 <when value="uncertainty"> | |
221 <param argument="--samples" type="data" format="txt" label="Select samples by explicitly naming them, one per line in a plain text file" /> | |
222 <param name="uncertainty_options" type="select" display="checkboxes" multiple="true" label="Metrics for sample placement certainty"> | |
223 <option value="get-parsimony">Total tree parsimony score (--get-parsimony)</option> | |
224 <option value="find-epps">Number of equally parsimonious placements for each sample (--find-epps)</option> | |
225 <option value="find-neighborhood">Neighborhood size scores (--find-neighborhood)</option> | |
226 </param> | |
227 </when> | |
228 <when value="mask"> | |
229 <param argument="--restricted-samples" type="data" format="txt" optional="True" label="Select samples by explicitly naming them, one per line in a plain text file" help="Sample names to restrict. Use to perform masking"/> | |
230 <param argument="--rename-samples" type="data" format="tabular" optional="True" label="TSV file containing names of the samples to be renamed and their new names"/> | |
231 <param argument="--simplify" type="boolean" truevalue="--simplify" falsevalue="" label="Use to automatically remove identifying information from the tree, including all sample names and private mutations" /> | |
232 </when> | |
233 </conditional> | |
234 </inputs> | |
235 <outputs> | |
236 <data name="selected_samples" format="txt" from_work_dir='selected_samples.txt' label="${tool.name} on ${on_string}: selected samples"> | |
237 <filter>matutils_mode['options_mode'] == 'extract' and 'used-samples' in matutils_mode['outputs_extract'] </filter> | |
238 </data> | |
239 <data name="path_mutations" format="tabular" from_work_dir='path_mutations.tabular' label="${tool.name} on ${on_string}: sample mutations"> | |
240 <filter>matutils_mode['options_mode'] == 'extract' and 'sample-paths' in matutils_mode['outputs_extract']</filter> | |
241 </data> | |
242 <data name="path_clades" format="tabular" from_work_dir='path_clades.tabular' label="${tool.name} on ${on_string}: clade mutations"> | |
243 <filter>matutils_mode['options_mode'] == 'extract' and 'clade-paths' in matutils_mode['outputs_extract']</filter> | |
244 </data> | |
245 <data name="all_paths" format="txt" from_work_dir='all_paths.txt' label="${tool.name} on ${on_string}: node mutations"> | |
246 <filter>matutils_mode['options_mode'] == 'extract' and 'all-paths' in matutils_mode['outputs_extract']</filter> | |
247 </data> | |
248 <data name="subtree_vcf" format="vcf" from_work_dir='subtree_vcf.vcf' label="${tool.name} on ${on_string}: subtree"> | |
249 <filter>matutils_mode['options_mode'] == 'extract' and 'write-vcf' in matutils_mode['outputs_extract']</filter> | |
250 </data> | |
251 <data name="subtree_no_genotype_vcf" format="vcf" from_work_dir='subtree_vcf_no_genotypes.vcf' label="${tool.name} on ${on_string}: subtree without genotype"> | |
252 <filter>matutils_mode['options_mode'] == 'extract' and 'write-vcf-no-genotypes' in matutils_mode['outputs_extract'] and 'write-vcf' not in matutils_mode['outputs_extract']</filter> | |
253 </data> | |
254 <data name="mutation_annotated" format="protobuf3" from_work_dir='mutation_annotated.pb' label="${tool.name} on ${on_string}: mutation annotated tree"> | |
255 <filter>matutils_mode['options_mode'] == 'extract' and 'write-mat' in matutils_mode['outputs_extract'] </filter> | |
256 </data> | |
257 <data name="mutation_annotated_collapsed" format="protobuf3" from_work_dir='mutation_annotated_collapsed.pb' label="${tool.name} on ${on_string}: mutation annotated tree collapsed"> | |
258 <filter>matutils_mode['options_mode'] == 'extract' and 'write-mat-collapse' in matutils_mode['outputs_extract'] and 'write-mat' not in matutils_mode['outputs_extract']</filter> | |
259 </data> | |
260 <data name="subtree_json" format="json" from_work_dir='subtree_json.json' label="${tool.name} on ${on_string}: subtree (json)"> | |
261 <filter>matutils_mode['options_mode'] == 'extract' and 'write-json' in matutils_mode['outputs_extract']</filter> | |
262 </data> | |
263 <data name="tree_newick" format="newick" from_work_dir='tree_newick.nh' label="${tool.name} on ${on_string}: subtree (newick)"> | |
264 <filter>matutils_mode['options_mode'] == 'extract' and 'write-tree' in matutils_mode['outputs_extract']</filter> | |
265 </data> | |
266 <data name="tree_newick_retain_branch" format="newick" from_work_dir='tree_newick_retain_branch.nh' label="${tool.name} on ${on_string}: subtree retain branch (newick)"> | |
267 <filter>matutils_mode['options_mode'] == 'extract' and 'write-tree-retain-branch' in matutils_mode['outputs_extract'] and 'write-tree' not in matutils_mode['outputs_extract']</filter> | |
268 </data> | |
269 <data name="general_stats" format="txt" from_work_dir='output_stdout.txt' label="${tool.name} on ${on_string}: general stats"> | |
270 <filter>matutils_mode['options_mode'] == 'summary' and 'general' in matutils_mode['summary_options']</filter> | |
271 </data> | |
272 <data name="samples_stats" format="tabular" from_work_dir='samples_stats.tabular' label="${tool.name} on ${on_string}: samples stats"> | |
273 <filter>matutils_mode['options_mode'] == 'summary' and 'samples' in matutils_mode['summary_options']</filter> | |
274 </data> | |
275 <data name="clades_stats" format="tabular" from_work_dir='clades_stats.tabular' label="${tool.name} on ${on_string}: clades stats"> | |
276 <filter>matutils_mode['options_mode'] == 'summary' and 'clades' in matutils_mode['summary_options']</filter> | |
277 </data> | |
278 <data name="mutations_stats" format="tabular" from_work_dir='mutations_stats.tabular' label="${tool.name} on ${on_string}: mutations stats"> | |
279 <filter>matutils_mode['options_mode'] == 'summary' and 'mutations' in matutils_mode['summary_options']</filter> | |
280 </data> | |
281 <data name="aberrant_stats" format="tabular" from_work_dir='aberrant_stats.tabular' label="${tool.name} on ${on_string}: aberrant stats"> | |
282 <filter>matutils_mode['options_mode'] == 'summary' and 'aberrant' in matutils_mode['summary_options']</filter> | |
283 </data> | |
284 <data name="output_mat" format="protobuf3" from_work_dir='output_mat.pb' label="${tool.name} on ${on_string}: mutation annotated tree"> | |
285 <filter>matutils_mode['options_mode'] == 'annotate' or matutils_mode['options_mode'] == 'mask'</filter> | |
286 </data> | |
287 <data name="total_parsimony_tree" format="txt" from_work_dir='output_stdout.txt' label="${tool.name} on ${on_string}: parsimony tree"> | |
288 <filter>matutils_mode['options_mode'] == 'uncertainty' and 'get-parsimony' in matutils_mode['uncertainty_options']</filter> | |
289 </data> | |
290 <data name="equally_parsimonious" from_work_dir='equally_parsimonious.tabular' format="tabular" label="${tool.name} on ${on_string}: equally parsimonious placements"> | |
291 <filter>matutils_mode['options_mode'] == 'uncertainty' and 'find-epps' in matutils_mode['uncertainty_options']</filter> | |
292 </data> | |
293 <data name="neighbourhood" format="tabular" from_work_dir='neighborhood.tabular' label="${tool.name} on ${on_string}: neighborhood size scores"> | |
294 <filter>matutils_mode['options_mode'] == 'uncertainty' and 'find-neighborhood' in matutils_mode['uncertainty_options']</filter> | |
295 </data> | |
296 </outputs> | |
297 <tests> | |
298 <test expect_num_outputs="3"> | |
299 <param name="mutation_annotation_file" value="mutation_annotation.pb"/> | |
300 <conditional name="matutils_mode"> | |
301 <param name="options_mode" value="extract"/> | |
302 <param name="resolve_polytomies" value="true"/> | |
303 <param name="outputs_extract" value="used-samples,sample-paths,clade-paths"/> | |
304 <conditional name="operation_mode"> | |
305 <param name="operation" value="samples"/> | |
306 <param name="samples" value="sample_names.txt"/> | |
307 <param name="prune" value="true"/> | |
308 </conditional> | |
309 </conditional> | |
310 <output name="selected_samples" file="test_13_sample_names.txt" ftype="txt"/> | |
311 <output name="path_mutations" file="test_13_path_mutations.tabular" ftype="tabular"/> | |
312 <output name="path_clades" file="test_13_path_clades.tabular" ftype="tabular"/> | |
313 </test> | |
314 <test expect_num_outputs="5"> | |
315 <param name="mutation_annotation_file" value="mutation_annotation.pb"/> | |
316 <conditional name="matutils_mode"> | |
317 <param name="options_mode" value="extract"/> | |
318 <param name="outputs_extract" value="used-samples,sample-paths,clade-paths,all-paths,write-vcf"/> | |
319 <conditional name="operation_mode"> | |
320 <param name="operation" value="samples"/> | |
321 <param name="samples" value="sample_names.txt"/> | |
322 </conditional> | |
323 </conditional> | |
324 <output name="selected_samples" file="test_14_sample_names.txt" ftype="txt"/> | |
325 <output name="path_mutations" file="test_14_path_mutations.tabular" ftype="tabular"/> | |
326 <output name="path_clades" file="test_14_path_clades.tabular" ftype="tabular"/> | |
327 <output name="all_paths" file="test_14_all_paths.txt" ftype="txt"/> | |
328 <output name="subtree_vcf" ftype="vcf"> | |
329 <assert_contents> | |
330 <has_size value="7219100" delta="300"/> | |
331 </assert_contents> | |
332 </output> | |
333 </test> | |
334 <test expect_num_outputs="4"> | |
335 <param name="mutation_annotation_file" value="mutation_annotation.pb"/> | |
336 <conditional name="matutils_mode"> | |
337 <param name="options_mode" value="extract"/> | |
338 <param name="outputs_extract" value="write-vcf-no-genotypes,write-mat,write-json,write-tree"/> | |
339 <conditional name="operation_mode"> | |
340 <param name="operation" value="mutation"/> | |
341 <param name="mutation" value="C241T"/> | |
342 </conditional> | |
343 </conditional> | |
344 <output name="subtree_no_genotype_vcf" file="test_15_subtree_no_genotype.vcf" ftype="vcf"/> | |
345 <output name="mutation_annotated" file="test_15_mutation_annotated_tree.pb" ftype="protobuf3"/> | |
346 <output name="subtree_json" file="test_15_subtree.json" ftype="json"/> | |
347 <output name="tree_newick" file="test_15_tree.nh" ftype="newick"/> | |
348 </test> | |
349 <test expect_num_outputs="3"> | |
350 <param name="mutation_annotation_file" value="mutation_annotation.pb"/> | |
351 <conditional name="matutils_mode"> | |
352 <param name="options_mode" value="extract"/> | |
353 <param name="outputs_extract" value="used-samples,sample-paths,write-vcf"/> | |
354 <conditional name="operation_mode"> | |
355 <param name="operation" value="clades"/> | |
356 <param name="clade" value="B.1.160.7, B.1.258.4"/> | |
357 </conditional> | |
358 </conditional> | |
359 <output name="selected_samples" file="test_16_sample_names.txt" ftype="txt"/> | |
360 <output name="path_mutations" file="test_16_path_mutations.tabular" ftype="tabular"/> | |
361 <output name="subtree_vcf" ftype="vcf"> | |
362 <assert_contents> | |
363 <has_size value="8999600" delta="300"/> | |
364 </assert_contents> | |
365 </output> | |
366 </test> | |
367 <test expect_num_outputs="5"> | |
368 <param name="mutation_annotation_file" value="mutation_annotation.pb"/> | |
369 <conditional name="matutils_mode"> | |
370 <param name="options_mode" value="extract"/> | |
371 <param name="outputs_extract" value="used-samples,sample-paths,clade-paths,all-paths,write-vcf"/> | |
372 <conditional name="operation_mode"> | |
373 <param name="operation" value="max-epps"/> | |
374 <param name="max_epps" value="0"/> | |
375 </conditional> | |
376 </conditional> | |
377 <output name="selected_samples" file="test_17_sample_names.txt" ftype="txt"/> | |
378 <output name="path_mutations" file="test_17_path_mutations.tabular" ftype="tabular"/> | |
379 <output name="path_clades" file="test_17_path_clades.tabular" ftype="tabular"/> | |
380 <output name="all_paths" file="test_17_all_paths.txt" ftype="txt"/> | |
381 <output name="subtree_vcf" ftype="vcf"> | |
382 <assert_contents> | |
383 <has_size value="8999600" delta="300"/> | |
384 </assert_contents> | |
385 </output> | |
386 </test> | |
387 <test expect_num_outputs="5"> | |
388 <param name="mutation_annotation_file" value="mutation_annotation.pb"/> | |
389 <conditional name="matutils_mode"> | |
390 <param name="options_mode" value="extract"/> | |
391 <param name="outputs_extract" value="used-samples,sample-paths,clade-paths,all-paths,write-vcf"/> | |
392 <conditional name="operation_mode"> | |
393 <param name="operation" value="max-parsimony"/> | |
394 <param name="max_parsimony" value="1"/> | |
395 </conditional> | |
396 </conditional> | |
397 <output name="selected_samples" file="test_18_sample_names.txt" ftype="txt"/> | |
398 <output name="path_mutations" file="test_18_path_mutations.tabular" ftype="tabular"/> | |
399 <output name="path_clades" file="test_18_path_clades.tabular" ftype="tabular"/> | |
400 <output name="all_paths" file="test_18_all_paths.txt" ftype="txt"/> | |
401 <output name="subtree_vcf" ftype="vcf"> | |
402 <assert_contents> | |
403 <has_size value="1183300" delta="300"/> | |
404 </assert_contents> | |
405 </output> | |
406 </test> | |
407 <test expect_num_outputs="3"> | |
408 <param name="mutation_annotation_file" value="mutation_annotation.pb"/> | |
409 <conditional name="matutils_mode"> | |
410 <param name="options_mode" value="extract"/> | |
411 <param name="outputs_extract" value="used-samples,sample-paths,clade-paths"/> | |
412 <conditional name="operation_mode"> | |
413 <param name="operation" value="max-branch-length"/> | |
414 <param name="max_branch_length" value="2"/> | |
415 </conditional> | |
416 </conditional> | |
417 <output name="selected_samples" file="test_19_sample_names.txt" ftype="txt"/> | |
418 <output name="path_mutations" file="test_19_path_mutations.tabular" ftype="tabular"/> | |
419 <output name="path_clades" file="test_19_path_clades.tabular" ftype="tabular"/> | |
420 </test> | |
421 <test expect_num_outputs="1"> | |
422 <param name="mutation_annotation_file" value="mutation_annotation.pb"/> | |
423 <conditional name="matutils_mode"> | |
424 <param name="options_mode" value="summary"/> | |
425 <param name="summary_options" value="general"/> | |
426 </conditional> | |
427 <output name="general_stats" file="test_20_general_stats.txt" ftype="txt"/> | |
428 </test> | |
429 <test expect_num_outputs="4"> | |
430 <param name="mutation_annotation_file" value="mutation_annotation.pb"/> | |
431 <conditional name="matutils_mode"> | |
432 <param name="options_mode" value="summary"/> | |
433 <param name="summary_options" value="samples,clades,mutations,aberrant"/> | |
434 </conditional> | |
435 <output name="samples_stats" file="test_21_sample_stats.tabular" ftype="tabular"/> | |
436 <output name="clades_stats" file="test_21_clades_stats.tabular" ftype="tabular"/> | |
437 <output name="mutations_stats" file="test_21_mutations_stats.tabular" ftype="tabular"/> | |
438 <output name="aberrant_stats" file="test_21_aberrant_stats.tabular" ftype="tabular"/> | |
439 </test> | |
440 <test expect_num_outputs="1"> | |
441 <param name="mutation_annotation_file" value="mutation_annotation.pb"/> | |
442 <conditional name="matutils_mode"> | |
443 <param name="options_mode" value="uncertainty"/> | |
444 <param name="samples" value="sample_names.txt"/> | |
445 <param name="uncertainty_options" value="get-parsimony"/> | |
446 </conditional> | |
447 <output name="total_parsimony_tree" file="test_22_total_parsimony_tree.txt" ftype="txt"/> | |
448 </test> | |
449 <test expect_num_outputs="2"> | |
450 <param name="mutation_annotation_file" value="mutation_annotation.pb"/> | |
451 <conditional name="matutils_mode"> | |
452 <param name="options_mode" value="uncertainty"/> | |
453 <param name="samples" value="sample_names.txt"/> | |
454 <param name="uncertainty_options" value="find-epps,find-neighborhood"/> | |
455 </conditional> | |
456 <output name="equally_parsimonious" file="test_23_equally_parsimoniou.tabular" ftype="tabular"/> | |
457 <output name="neighbourhood" file="test_23_neighbourhood.tabular" ftype="tabular"/> | |
458 </test> | |
459 <test expect_num_outputs="1"> | |
460 <param name="mutation_annotation_file" value="mutation_annotation.pb"/> | |
461 <conditional name="matutils_mode"> | |
462 <param name="options_mode" value="mask"/> | |
463 <param name="restricted_samples" value="sample_names.txt"/> | |
464 <param name="simplify" value="true"/> | |
465 </conditional> | |
466 <output name="output_mat" file="test_24_restricted.pb" ftype="protobuf3"/> | |
467 </test> | |
468 <test expect_num_outputs="1"> | |
469 <param name="mutation_annotation_file" value="mutation_annotation.pb"/> | |
470 <conditional name="matutils_mode"> | |
471 <param name="options_mode" value="mask"/> | |
472 <param name="rename_samples" value="rename_samples.tabular"/> | |
473 </conditional> | |
474 <output name="output_mat" file="test_25_renamed.pb" ftype="protobuf3"/> | |
475 </test> | |
476 </tests> | |
477 <help><![CDATA[ | |
478 | |
479 .. class:: infomark | |
480 | |
481 **Purpose** | |
482 | |
483 matUtils is a suite of tools used to analyze, edit, and manipulate mutation annotated tree (.pb) files. | |
484 | |
485 ---- | |
486 | |
487 .. class:: infomark | |
488 | |
489 **matUtils Common Options** | |
490 | |
491 **Extract**: matUtils extract serves as a flexible prebuilt pipeline, and serves as the primary tool for subsetting and converting a MAT pb to other file formats. | |
492 **Sumary**: matUtils summary is used to get basic statistics and attribute information about the mat. | |
493 **Annotate**: matUtils annotate is a function for adding clade annotation information to the pb. | |
494 **Uncertainly**: matUtils uncertainty calculates two specific metrics for sample placement certainty. These metrics can be very important to support contact tracing and reliable identification of the origin of a newly placed sample. | |
495 **Mask**: matUtils mask is used to mask specific samples out of the pb, removing their mutations from visibility. | |
496 | |
497 You can find more information in the `matUtils official documentation page <https://usher-wiki.readthedocs.io/en/latest/matUtils.html>`_. | |
498 | |
499 ]]> </help> | |
500 <expand macro="citations" /> | |
501 </tool> |