Mercurial > repos > bgruening > gfastats
comparison gfastats.xml @ 7:3ef480892a9f draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 70ba23af483a5a7edc5d5b4205b32ff77773f87a
author | bgruening |
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date | Fri, 23 Dec 2022 20:00:51 +0000 |
parents | 690c2caa367e |
children |
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6:690c2caa367e | 7:3ef480892a9f |
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33 #if $mode_condition.homopolymer_compress | 33 #if $mode_condition.homopolymer_compress |
34 --homopolymer-compress $mode_condition.homopolymer_compress | 34 --homopolymer-compress $mode_condition.homopolymer_compress |
35 #end if | 35 #end if |
36 $mode_condition.discover_paths | 36 $mode_condition.discover_paths |
37 -o dataset.$mode_condition.output_condition.out_format | 37 -o dataset.$mode_condition.output_condition.out_format |
38 #if $mode_condition.output_condition.out_format == 'fasta' | 38 #if $mode_condition.output_condition.out_format in ['fasta','fasta.gz'] |
39 #if $mode_condition.output_condition.line_length | 39 #if $mode_condition.output_condition.line_length |
40 --line-length $mode_condition.output_condition.line_length | 40 --line-length $mode_condition.output_condition.line_length |
41 #end if | 41 #end if |
42 #else if $mode_condition.output_condition.out_format == 'fasta.gz' | 42 #end if |
43 #if $mode_condition.output_condition.line_length | 43 #if $mode_condition.output_condition.out_format in ['gfa','gfa.gz'] |
44 --line-length $mode_condition.output_condition.line_length | 44 #if $mode_condition.output_condition.terminal_overlaps_condition.terminal_overlaps_select == 'yes': |
45 --discover-terminal-overlaps $mode_condition.output_condition.terminal_overlaps_condition.terminal_overlaps_length | |
45 #end if | 46 #end if |
46 #end if | 47 #end if |
47 #else if $mode_condition.selector == "statistics" | 48 #else if $mode_condition.selector == "statistics" |
48 #if $mode_condition.statistics_condition.selector == 'size' | 49 #if $mode_condition.statistics_condition.selector == 'size' |
49 --out-size $mode_condition.statistics_condition.out_size | 50 --out-size $mode_condition.statistics_condition.out_size |
53 --nstar-report | 54 --nstar-report |
54 #else | 55 #else |
55 --seq-report | 56 --seq-report |
56 $mode_condition.statistics_condition.out_sequence | 57 $mode_condition.statistics_condition.out_sequence |
57 #end if | 58 #end if |
59 $mode_condition.locale | |
58 $mode_condition.discover_paths | 60 $mode_condition.discover_paths |
59 $mode_condition.tabular > '$stats' | 61 $mode_condition.tabular > '$stats' |
60 #else | 62 #else |
61 --agp-to-path $mode_condition.agp_to_path | 63 --agp-to-path $mode_condition.agp_to_path |
62 $mode_condition.discover_paths | 64 $mode_condition.discover_paths |
91 <validator type="regex">[0-9A-Za-z:-_| ]+</validator> | 93 <validator type="regex">[0-9A-Za-z:-_| ]+</validator> |
92 </param> | 94 </param> |
93 <param argument="--include-bed" type="data" optional="true" | 95 <param argument="--include-bed" type="data" optional="true" |
94 format="bed" label="Include specific intervals" | 96 format="bed" label="Include specific intervals" |
95 help="Generates output on a subset list of headers or coordinates | 97 help="Generates output on a subset list of headers or coordinates |
96 in 0-based bed format. It can be combined with --exclude-bed. Optional"/> | 98 in 0-based bed format. It can be combined with --exclude-bed. Optional."/> |
97 <param argument="--exclude-bed" type="data" format="bed" optional="true" | 99 <param argument="--exclude-bed" type="data" format="bed" optional="true" |
98 label="Exclude specific intervals" | 100 label="Exclude specific intervals" |
99 help="Exclude a subset of headers or coordinates in 0-base bed format. It can be conmbined with --include-bed Optional"/> | 101 help="Exclude a subset of headers or coordinates in 0-base bed format. It can be conmbined with --include-bed. Optional."/> |
100 </when> | 102 </when> |
101 <when value="false"/> | 103 <when value="false"/> |
102 </conditional> | 104 </conditional> |
103 <conditional name="mode_condition"> | 105 <conditional name="mode_condition"> |
104 <param name="selector" type="select" label="Tool mode"> | 106 <param name="selector" type="select" label="Tool mode"> |
126 <when value="fasta.gz"> | 128 <when value="fasta.gz"> |
127 <expand macro="length_macro"/> | 129 <expand macro="length_macro"/> |
128 </when> | 130 </when> |
129 <when value="fastq"/> | 131 <when value="fastq"/> |
130 <when value="fastq.gz"/> | 132 <when value="fastq.gz"/> |
131 <when value="gfa"/> | 133 <when value="gfa"> |
132 <when value="gfa.gz"/> | 134 <expand macro="terminal_overlaps_macro"/> |
133 </conditional> | 135 </when> |
134 <param argument="--discover-paths" type="boolean" truevalue="--discover-paths" falsevalue="" checked="false" label="Generates the initial set of paths" help="In the graph space an assembly | 136 <when value="gfa.gz"> |
135 is a collection of segment and edges/gaps between these segments. A path defines a potential walk through the segments and edges/gaps that corresponds to a hypothesis of the actual linear sequence" /> | 137 <expand macro="terminal_overlaps_macro"/> |
136 <param argument="--sort" type="select" label="Sort sequences" help="Specify how to sort the sequences. Ascending/descending used the sequence/path header."> | 138 </when> |
139 </conditional> | |
140 <param argument="--discover-paths" type="boolean" truevalue="--discover-paths" falsevalue="" checked="false" label="Generates the initial set of paths" help="In the graph space, an assembly | |
141 is a collection of segments and edges/gaps between these segments. A path defines a potential walk through the segments and edges/gaps that corresponds to a hypothesis of the actual linear sequence." /> | |
142 <param argument="--sort" type="select" label="Sort sequences" help="Specify how to sort the sequences. Ascending/descending uses the sequence/path header."> | |
137 <option value="" selected="true">Disabled</option> | 143 <option value="" selected="true">Disabled</option> |
138 <option value="ascending">Ascending</option> | 144 <option value="ascending">Ascending</option> |
139 <option value="descending">Descending</option> | 145 <option value="descending">Descending</option> |
140 <option value="largest">Largest</option> | 146 <option value="largest">Largest</option> |
141 <option value="smallest">Smallest</option> | 147 <option value="smallest">Smallest</option> |
142 </param> | 148 </param> |
143 <param argument="--homopolymer-compress" type="integer" min="0" value="" optional="true" label="Homopolymer compression" help="Compress all the homopolymers in the input above the given threshhold" /> | 149 <param argument="--homopolymer-compress" type="integer" min="0" value="" optional="true" label="Homopolymer compression" help="Compress all the homopolymers in the input above the given threshold." /> |
144 </when> | 150 </when> |
145 <when value="statistics"> | 151 <when value="statistics"> |
146 <conditional name="statistics_condition"> | 152 <conditional name="statistics_condition"> |
147 <param name="selector" type="select" label="Report mode"> | 153 <param name="selector" type="select" label="Report mode"> |
148 <option value="assembly" selected="true">Genome assembly statistics (--nstar-report)</option> | 154 <option value="assembly" selected="true">Genome assembly statistics (--nstar-report)</option> |
173 <when value="sequence"> | 179 <when value="sequence"> |
174 <param argument="--out-sequence" type="boolean" truevalue="--out-sequence" falsevalue="" checked="false" | 180 <param argument="--out-sequence" type="boolean" truevalue="--out-sequence" falsevalue="" checked="false" |
175 label="Report actual sequence" help="It reports also the actual sequence"/> | 181 label="Report actual sequence" help="It reports also the actual sequence"/> |
176 </when> | 182 </when> |
177 </conditional> | 183 </conditional> |
184 <param argument="--locale" type="boolean" truevalue="--locale en_US.UTF-8" falsevalue="" checked="true" | |
185 label="Thousands separator in output" help="Use commas for thousands separator in output?"/> | |
178 <param argument="--tabular" type="boolean" truevalue="--tabular" falsevalue="" checked="true" | 186 <param argument="--tabular" type="boolean" truevalue="--tabular" falsevalue="" checked="true" |
179 label="Tabular-format output" help="Generate output in tabular format"/> | 187 label="Tabular-format output" help="Generate output in tabular format"/> |
180 <param argument="--discover-paths" type="boolean" truevalue="--discover-paths" falsevalue="" checked="false" label="Generates the initial set of paths" help="In the graph space an assembly | 188 <param argument="--discover-paths" type="boolean" truevalue="--discover-paths" falsevalue="" checked="false" label="Generates the initial set of paths" help="In the graph space an assembly |
181 is a collection of segment and edges/gaps between these segments. A path defines a potential walk through the segments and edges/gaps that corresponds to a hypothesis of the actual linear sequence" /> | 189 is a collection of segment and edges/gaps between these segments. A path defines a potential walk through the segments and edges/gaps that corresponds to a hypothesis of the actual linear sequence" /> |
182 </when> | 190 </when> |
209 </outputs> | 217 </outputs> |
210 <tests> | 218 <tests> |
211 <!--Test 01 --> | 219 <!--Test 01 --> |
212 <test expect_num_outputs="1"> | 220 <test expect_num_outputs="1"> |
213 <param name="input_file" value="dataset_01.fastq.gz"/> | 221 <param name="input_file" value="dataset_01.fastq.gz"/> |
214 <conditional name="target_condition"> | |
215 <param name="target_condition" value="true"/> | |
216 <param name="target_sequence" value="S1_1"/> | |
217 </conditional> | |
218 <conditional name="mode_condition"> | 222 <conditional name="mode_condition"> |
219 <param name="selector" value="manipulation"/> | 223 <param name="selector" value="manipulation"/> |
220 <param name="swiss_army_knife" value="swiss_army.sak"/> | 224 <param name="swiss_army_knife" value="swiss_army.sak"/> |
221 <conditional name="output_condition"> | 225 <conditional name="output_condition"> |
222 <param name="out_format" value="fasta.gz"/> | 226 <param name="out_format" value="fasta.gz"/> |
235 <param name="selector" value="statistics"/> | 239 <param name="selector" value="statistics"/> |
236 <conditional name="statistics_condition"> | 240 <conditional name="statistics_condition"> |
237 <param name="selector" value="size"/> | 241 <param name="selector" value="size"/> |
238 <param name="out_size" value="c"/> | 242 <param name="out_size" value="c"/> |
239 </conditional> | 243 </conditional> |
244 <param name="locale" value="false"/> | |
240 </conditional> | 245 </conditional> |
241 <output name="stats" ftype="tabular"> | 246 <output name="stats" ftype="tabular"> |
242 <assert_contents> | 247 <assert_contents> |
243 <has_text text="S1_76.1	9445" /> | 248 <has_text text="S1_1.1	8550" /> |
244 </assert_contents> | 249 </assert_contents> |
245 </output> | 250 </output> |
246 </test> | 251 </test> |
247 <!--Test 03 --> | 252 <!--Test 03 --> |
248 <test expect_num_outputs="1"> | 253 <test expect_num_outputs="1"> |
250 <conditional name="mode_condition"> | 255 <conditional name="mode_condition"> |
251 <param name="selector" value="statistics"/> | 256 <param name="selector" value="statistics"/> |
252 <conditional name="statistics_condition"> | 257 <conditional name="statistics_condition"> |
253 <param name="selector" value="sequence"/> | 258 <param name="selector" value="sequence"/> |
254 </conditional> | 259 </conditional> |
260 <param name="locale" value="false"/> | |
255 </conditional> | 261 </conditional> |
256 <output name="stats" ftype="tabular"> | 262 <output name="stats" ftype="tabular"> |
257 <assert_contents> | 263 <assert_contents> |
258 <has_text text="23029444-6c7d-4f19-ac8e-4c0a478589d0.1		476	198	68	93	117	33.82	0" /> | 264 <has_text text="23029444-6c7d-4f19-ac8e-4c0a478589d0.1		476	198	68	93	117	33.82	0" /> |
259 </assert_contents> | 265 </assert_contents> |
266 <param name="selector" value="statistics"/> | 272 <param name="selector" value="statistics"/> |
267 <conditional name="statistics_condition"> | 273 <conditional name="statistics_condition"> |
268 <param name="selector" value="assembly"/> | 274 <param name="selector" value="assembly"/> |
269 <param name="expected_genomesize" value="600000"/> | 275 <param name="expected_genomesize" value="600000"/> |
270 </conditional> | 276 </conditional> |
277 <param name="locale" value="false"/> | |
271 </conditional> | 278 </conditional> |
272 <output name="stats" value="test_04_stats.tabular" ftype="tabular"/> | 279 <output name="stats" value="test_04_stats.tabular" ftype="tabular"/> |
273 </test> | 280 </test> |
274 <!--Test 05 --> | 281 <!--Test 05 --> |
275 <test expect_num_outputs="1"> | 282 <test expect_num_outputs="1"> |
278 <param name="selector" value="statistics"/> | 285 <param name="selector" value="statistics"/> |
279 <conditional name="statistics_condition"> | 286 <conditional name="statistics_condition"> |
280 <param name="selector" value="coordinates"/> | 287 <param name="selector" value="coordinates"/> |
281 <param name="out_coord" value="a"/> | 288 <param name="out_coord" value="a"/> |
282 </conditional> | 289 </conditional> |
290 <param name="locale" value="false"/> | |
283 </conditional> | 291 </conditional> |
284 <output name="stats" value="test_05_stats.tabular" ftype="tabular"/> | 292 <output name="stats" value="test_05_stats.tabular" ftype="tabular"/> |
285 </test> | 293 </test> |
286 <!--Test 06 --> | 294 <!--Test 06 --> |
287 <test expect_num_outputs="1"> | 295 <test expect_num_outputs="1"> |
300 <conditional name="mode_condition"> | 308 <conditional name="mode_condition"> |
301 <param name="selector" value="statistics"/> | 309 <param name="selector" value="statistics"/> |
302 <conditional name="statistics_condition"> | 310 <conditional name="statistics_condition"> |
303 <param name="selector" value="assembly"/> | 311 <param name="selector" value="assembly"/> |
304 </conditional> | 312 </conditional> |
313 <param name="locale" value="false"/> | |
305 <param name="tabular" value="false"/> | 314 <param name="tabular" value="false"/> |
306 </conditional> | 315 </conditional> |
307 <output name="stats" value="test_07_stats.tabular" ftype="tabular"/> | 316 <output name="stats" value="test_07_stats.tabular" ftype="tabular"/> |
308 </test> | 317 </test> |
309 <!--Test 08 --> | 318 <!--Test 08 --> |
345 <param name="input_file" value="dataset_03.fasta"/> | 354 <param name="input_file" value="dataset_03.fasta"/> |
346 <conditional name="target_condition"> | 355 <conditional name="target_condition"> |
347 <param name="target_option" value="true"/> | 356 <param name="target_option" value="true"/> |
348 <param name="include_bed" value="regions.bed"/> | 357 <param name="include_bed" value="regions.bed"/> |
349 </conditional> | 358 </conditional> |
359 <conditional name="mode_condition"> | |
360 <param name="locale" value="false"/> | |
361 </conditional> | |
350 <output name="stats" value="test_11_stats.tabular" ftype="tabular"/> | 362 <output name="stats" value="test_11_stats.tabular" ftype="tabular"/> |
351 </test> | 363 </test> |
352 <!--Test 12 --> | 364 <!--Test 12 --> |
353 <test expect_num_outputs="1"> | 365 <test expect_num_outputs="1"> |
354 <param name="input_file" value="dataset_04.gfa"/> | 366 <param name="input_file" value="dataset_04.gfa"/> |
355 <conditional name="mode_condition"> | 367 <conditional name="mode_condition"> |
356 <param name="selector" value="statistics"/> | 368 <param name="selector" value="statistics"/> |
357 <conditional name="statistics_condition"> | 369 <conditional name="statistics_condition"> |
358 <param name="selector" value="assembly"/> | 370 <param name="selector" value="assembly"/> |
359 </conditional> | 371 </conditional> |
372 <param name="locale" value="false"/> | |
360 <param name="tabular" value="false"/> | 373 <param name="tabular" value="false"/> |
361 <param name="discover_paths" value="true"/> | 374 <param name="discover_paths" value="true"/> |
362 </conditional> | 375 </conditional> |
363 <output name="stats" value="test_12_stats.tabular" ftype="tabular"/> | 376 <output name="stats" value="test_12_stats.tabular" ftype="tabular"/> |
364 </test> | 377 </test> |