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comparison gfastats.xml @ 7:3ef480892a9f draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 70ba23af483a5a7edc5d5b4205b32ff77773f87a
author bgruening
date Fri, 23 Dec 2022 20:00:51 +0000
parents 690c2caa367e
children
comparison
equal deleted inserted replaced
6:690c2caa367e 7:3ef480892a9f
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&#009;9445" /> 248 <has_text text="S1_1.1&#009;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&#009;&#009;476&#009;198&#009;68&#009;93&#009;117&#009;33.82&#009;0" /> 264 <has_text text="23029444-6c7d-4f19-ac8e-4c0a478589d0.1&#009;&#009;476&#009;198&#009;68&#009;93&#009;117&#009;33.82&#009;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>