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comparison small_rna_maps.xml @ 20:de7fbcb1348c draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 44599c93586bc909f405ac6b745230563b290ee2
author artbio
date Sun, 25 Nov 2018 06:56:40 -0500
parents f33afecac67a
children b585cb347a26
comparison
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19:f33afecac67a 20:de7fbcb1348c
1 <tool id="small_rna_maps" name="small_rna_maps" version="2.9.1"> 1 <tool id="small_rna_maps" name="small_rna_maps" version="2.10.0">
2 <description></description> 2 <description></description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.11.2=py27_0">numpy</requirement> 4 <requirement type="package" version="1.11.2=py27_0">numpy</requirement>
5 <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement> 5 <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement>
6 <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement> 6 <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement>
37 #elif str($plots_options.plots_options_selector ) == "cluster": 37 #elif str($plots_options.plots_options_selector ) == "cluster":
38 --plot_methods 'Counts' 38 --plot_methods 'Counts'
39 --outputs '$output_tab' 39 --outputs '$output_tab'
40 --cluster ${plots_options.cluster} 40 --cluster ${plots_options.cluster}
41 --bed '$output_bed' 41 --bed '$output_bed'
42 --bed_skipcluster ${plots_options.skip_cluster} 42 --bed_skipsize ${plots_options.skip_size}
43 --bed_skipcounts ${plots_options.skip_counts}
44 --bed_skipdensity ${plots_options.skip_density}
43 ${plots_options.strandness} && 45 ${plots_options.strandness} &&
44 #else: 46 #else:
45 --plot_methods '${plots_options.first_plot}' 47 --plot_methods '${plots_options.first_plot}'
46 --outputs '$output_tab' && 48 --outputs '$output_tab' &&
47 #end if 49 #end if
125 <option value="merge">Merge forward and reverse reads</option> 127 <option value="merge">Merge forward and reverse reads</option>
126 </param> 128 </param>
127 </when> 129 </when>
128 <when value="cluster"> 130 <when value="cluster">
129 <param name="first_plot" type="hidden" value="Counts"/> 131 <param name="first_plot" type="hidden" value="Counts"/>
130 <param name="cluster" type="integer" label="Aggregation distance in nucleotides" value="1" 132 <param name="cluster" type="integer" label="Clustering distance in nucleotides" value="1"
131 help="Sets the distance (in nt) below which reads are clustered to a single median position" /> 133 help="Sets the distance (in nt) below which reads are clustered to a single median position" />
132 <param name="strandness" argument="--nostrand" type="boolean" truevalue="--nostrand" falsevalue="" checked="false" 134 <param name="strandness" argument="--nostrand" type="boolean" truevalue="--nostrand" falsevalue="" checked="false"
133 label="Ignore polarity of reads ?" help="Set if you wish to cluster reads regardless of whether they are forward or reverse"/> 135 label="Ignore polarity of reads ?" help="Set if you wish to cluster reads regardless of whether they are forward or reverse"/>
134 <param name="skip_cluster" type="integer" label="do not report cluster equal or less than the specified number of nucleotides" value="0" 136 <param name="skip_size" type="integer" label="do not report clusters whose size is less than the specified value" value="1"
135 help="Set the number of nucleotides in the cluster for which and below which a cluster is not reported in the bed output. Set to 0 (default) reports all including singlets" /> 137 help="Cluster size threshod (in nucleotides) for reporting. Set to 1 (default) reports all clusters, including singlets" />
138 <param name="skip_counts" type="integer" label="do not report cluster with a number of reads lower than the specified value" value="1"
139 help="Number-of-reads threshod (in nucleotides) for cluster reporting. Set to 1 (default) reports all clusters, irrespective of their counts" />
140 <param name="skip_density" type="float" label="do not report cluster with density equal or less than the specified value" value="0"
141 help="Density threshod (in reads per nucleotides) for reporting. Set to 0 (default) reports all cluster densities" />
136 </when> 142 </when>
137 </conditional> 143 </conditional>
138 <conditional name="ylimits_cond"> 144 <conditional name="ylimits_cond">
139 <param name="ylimits" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Do you wish to set an y axis limit to the plots?" 145 <param name="ylimits" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Do you wish to set an y axis limit to the plots?"
140 help="This limit won't be applied to size distribution plots"/> 146 help="This limit won't be applied to size distribution plots"/>
198 <param name="minsize" value="0" /> 204 <param name="minsize" value="0" />
199 <param name="maxsize" value="10000" /> 205 <param name="maxsize" value="10000" />
200 <param name="plots_options_selector" value="cluster" /> 206 <param name="plots_options_selector" value="cluster" />
201 <param name="first_plot" value="Counts" /> 207 <param name="first_plot" value="Counts" />
202 <param name="cluster" value="5" /> 208 <param name="cluster" value="5" />
203 <param name="skip_cluster" value="0" /> 209 <param name="skip_size" value="1" />
204 <param name="strandness" value="false" /> 210 <param name="strandness" value="false" />
205 <output file="clustering.tab" name="output_tab" /> 211 <output file="clustering.tab" name="output_tab" />
206 <output file="clustering.pdf" name="output_pdf" /> 212 <output file="clustering.pdf" name="output_pdf" />
207 <output file="bed1.bed" name="output_bed" /> 213 <output file="bed1.bed" name="output_bed" />
208 </test> 214 </test>
214 <param name="minsize" value="0" /> 220 <param name="minsize" value="0" />
215 <param name="maxsize" value="10000" /> 221 <param name="maxsize" value="10000" />
216 <param name="plots_options_selector" value="cluster" /> 222 <param name="plots_options_selector" value="cluster" />
217 <param name="first_plot" value="Counts" /> 223 <param name="first_plot" value="Counts" />
218 <param name="cluster" value="5" /> 224 <param name="cluster" value="5" />
219 <param name="skip_cluster" value="0" /> 225 <param name="skip_size" value="1" />
220 <param name="strandness" value="true" /> 226 <param name="strandness" value="true" />
221 <output file="clustering_unstranded.tab" name="output_tab" /> 227 <output file="clustering_unstranded.tab" name="output_tab" />
222 <output file="clustering_unstranded.pdf" name="output_pdf" /> 228 <output file="clustering_unstranded.pdf" name="output_pdf" />
223 <output file="bed2.bed" name="output_bed" /> 229 <output file="bed2.bed" name="output_bed" />
224 </test> 230 </test>
225 <test> <!-- 3.1 --> 231 <test> <!-- 4 -->
226 <repeat name="series"> 232 <repeat name="series">
227 <param name="inputs" value="input1.bam" ftype="bam" /> 233 <param name="inputs" value="input1.bam" ftype="bam" />
228 <param name="normalization" value="1.0" /> 234 <param name="normalization" value="1.0" />
229 </repeat> 235 </repeat>
230 <param name="minsize" value="0" /> 236 <param name="minsize" value="0" />
231 <param name="maxsize" value="10000" /> 237 <param name="maxsize" value="10000" />
232 <param name="plots_options_selector" value="cluster" /> 238 <param name="plots_options_selector" value="cluster" />
233 <param name="first_plot" value="Counts" /> 239 <param name="first_plot" value="Counts" />
234 <param name="cluster" value="5" /> 240 <param name="cluster" value="5" />
235 <param name="skip_cluster" value="1" /> 241 <param name="skip_size" value="2" />
236 <param name="strandness" value="false" /> 242 <param name="strandness" value="false" />
237 <output file="clustering.tab" name="output_tab" /> 243 <output file="clustering.tab" name="output_tab" />
238 <output file="clustering.pdf" name="output_pdf" /> 244 <output file="clustering.pdf" name="output_pdf" />
239 <output file="bed3.bed" name="output_bed" /> 245 <output file="bed3.bed" name="output_bed" />
240 </test> 246 </test>
241 <test> <!-- 4 --> 247 <test> <!-- 5 -->
248 <repeat name="series">
249 <param name="inputs" value="input1.bam" ftype="bam" />
250 <param name="normalization" value="1.0" />
251 </repeat>
252 <param name="minsize" value="0" />
253 <param name="maxsize" value="10000" />
254 <param name="plots_options_selector" value="cluster" />
255 <param name="first_plot" value="Counts" />
256 <param name="cluster" value="5" />
257 <param name="skip_size" value="2" />
258 <param name="skip_counts" value="3" />
259 <param name="skip_density" value="1.0" />
260 <param name="strandness" value="false" />
261 <output file="clustering.tab" name="output_tab" />
262 <output file="clustering.pdf" name="output_pdf" />
263 <output file="bed4.bed" name="output_bed" />
264 </test>
265 <test> <!-- 6 -->
266 <repeat name="series">
267 <param name="inputs" value="input1.bam" ftype="bam" />
268 <param name="normalization" value="1.0" />
269 </repeat>
270 <param name="minsize" value="0" />
271 <param name="maxsize" value="10000" />
272 <param name="plots_options_selector" value="cluster" />
273 <param name="first_plot" value="Counts" />
274 <param name="cluster" value="5" />
275 <param name="skip_size" value="2" />
276 <param name="skip_counts" value="2" />
277 <param name="skip_density" value="0.4" />
278 <param name="strandness" value="true" />
279 <output file="clustering_unstranded.tab" name="output_tab" />
280 <output file="clustering_unstranded.pdf" name="output_pdf" />
281 <output file="bed5.bed" name="output_bed" />
282 </test>
283 <test> <!-- 7 -->
242 <repeat name="series"> 284 <repeat name="series">
243 <param name="inputs" value="input1.bam" ftype="bam" /> 285 <param name="inputs" value="input1.bam" ftype="bam" />
244 <param name="normalization" value="1.0" /> 286 <param name="normalization" value="1.0" />
245 </repeat> 287 </repeat>
246 <param name="minsize" value="20" /> 288 <param name="minsize" value="20" />
248 <param name="plots_options_selector" value="one_plot" /> 290 <param name="plots_options_selector" value="one_plot" />
249 <param name="first_plot" value="Size" /> 291 <param name="first_plot" value="Size" />
250 <output file="input1_min20_max30_size.tab" name="output_tab" /> 292 <output file="input1_min20_max30_size.tab" name="output_tab" />
251 <output file="input1_min20_max30_single_plot_size.pdf" name="output_pdf" /> 293 <output file="input1_min20_max30_single_plot_size.pdf" name="output_pdf" />
252 </test> 294 </test>
253 <test> <!-- 5 --> 295 <test> <!-- 8 -->
254 <repeat name="series"> 296 <repeat name="series">
255 <param name="inputs" value="input1.bam" ftype="bam" /> 297 <param name="inputs" value="input1.bam" ftype="bam" />
256 <param name="normalization" value="1.0" /> 298 <param name="normalization" value="1.0" />
257 </repeat> 299 </repeat>
258 <param name="minsize" value="0" /> 300 <param name="minsize" value="0" />
260 <param name="plots_options_selector" value="one_plot" /> 302 <param name="plots_options_selector" value="one_plot" />
261 <param name="first_plot" value="Mean" /> 303 <param name="first_plot" value="Mean" />
262 <output file="input1_mean.tab" name="output_tab" /> 304 <output file="input1_mean.tab" name="output_tab" />
263 <output file="input1__single_plot_mean.pdf" name="output_pdf" /> 305 <output file="input1__single_plot_mean.pdf" name="output_pdf" />
264 </test> 306 </test>
265 <test> <!-- 6 --> 307 <test> <!-- 9 -->
266 <repeat name="series"> 308 <repeat name="series">
267 <param name="inputs" value="input1.bam" ftype="bam" /> 309 <param name="inputs" value="input1.bam" ftype="bam" />
268 <param name="normalization" value="1.0" /> 310 <param name="normalization" value="1.0" />
269 </repeat> 311 </repeat>
270 <param name="minsize" value="0" /> 312 <param name="minsize" value="0" />
272 <param name="plots_options_selector" value="one_plot" /> 314 <param name="plots_options_selector" value="one_plot" />
273 <param name="first_plot" value="Median" /> 315 <param name="first_plot" value="Median" />
274 <output file="input1_median.tab" name="output_tab" /> 316 <output file="input1_median.tab" name="output_tab" />
275 <output file="input1_single_plot_median.pdf" name="output_pdf" /> 317 <output file="input1_single_plot_median.pdf" name="output_pdf" />
276 </test> 318 </test>
277 <test> <!-- 7 --> 319 <test> <!-- 10 -->
278 <repeat name="series"> 320 <repeat name="series">
279 <param name="inputs" value="input1.bam" ftype="bam" /> 321 <param name="inputs" value="input1.bam" ftype="bam" />
280 <param name="normalization" value="1.0" /> 322 <param name="normalization" value="1.0" />
281 </repeat> 323 </repeat>
282 <repeat name="series"> 324 <repeat name="series">
288 <param name="plots_options_selector" value="one_plot" /> 330 <param name="plots_options_selector" value="one_plot" />
289 <param name="first_plot" value="Counts" /> 331 <param name="first_plot" value="Counts" />
290 <output file="input1_input2_norm_1_2_counts.tab" name="output_tab" /> 332 <output file="input1_input2_norm_1_2_counts.tab" name="output_tab" />
291 <output file="input1_input2_norm_1_2_single_plot_counts.pdf" name="output_pdf" /> 333 <output file="input1_input2_norm_1_2_single_plot_counts.pdf" name="output_pdf" />
292 </test> 334 </test>
293 <test> <!-- 8 --> 335 <test> <!-- 11 -->
294 <repeat name="series"> 336 <repeat name="series">
295 <param name="inputs" value="input1.bam" ftype="bam" /> 337 <param name="inputs" value="input1.bam" ftype="bam" />
296 <param name="normalization" value="1.0" /> 338 <param name="normalization" value="1.0" />
297 </repeat> 339 </repeat>
298 <repeat name="series"> 340 <repeat name="series">
309 <param name="extra_plot" value="Size" /> 351 <param name="extra_plot" value="Size" />
310 <output file="input1_input2_counts.tab" name="output_tab" /> 352 <output file="input1_input2_counts.tab" name="output_tab" />
311 <output file="input1_input2_size.tab" name="extra_output_tab" /> 353 <output file="input1_input2_size.tab" name="extra_output_tab" />
312 <output file="input1_input2_double_plot_counts_size_ylimneg5_5.pdf" name="output_pdf" /> 354 <output file="input1_input2_double_plot_counts_size_ylimneg5_5.pdf" name="output_pdf" />
313 </test> 355 </test>
314 <test> <!-- 9 --> 356 <test> <!-- 12 -->
315 <repeat name="series"> 357 <repeat name="series">
316 <param name="inputs" value="input_single_chr.bam" ftype="bam" /> 358 <param name="inputs" value="input_single_chr.bam" ftype="bam" />
317 <param name="normalization" value="1.0" /> 359 <param name="normalization" value="1.0" />
318 </repeat> 360 </repeat>
319 <repeat name="series"> 361 <repeat name="series">
341 <param name="plots_options_selector" value="one_plot" /> 383 <param name="plots_options_selector" value="one_plot" />
342 <param name="first_plot" value="Coverage" /> 384 <param name="first_plot" value="Coverage" />
343 <output file="input_single_chr_x_6_single_plot_coverage.tab" name="output_tab" /> 385 <output file="input_single_chr_x_6_single_plot_coverage.tab" name="output_tab" />
344 <output file="input_single_chr_x_6_single_plot_coverage.pdf" name="output_pdf" /> 386 <output file="input_single_chr_x_6_single_plot_coverage.pdf" name="output_pdf" />
345 </test> 387 </test>
346 <test> <!-- 10 --> 388 <test> <!-- 13 -->
347 <repeat name="series"> 389 <repeat name="series">
348 <param name="inputs" value="input1.bam" ftype="bam" /> 390 <param name="inputs" value="input1.bam" ftype="bam" />
349 <param name="normalization" value="1.0" /> 391 <param name="normalization" value="1.0" />
350 </repeat> 392 </repeat>
351 <repeat name="series"> 393 <repeat name="series">
358 <param name="mergestrands" value="nomerge" /> 400 <param name="mergestrands" value="nomerge" />
359 <param name="first_plot" value="Size" /> 401 <param name="first_plot" value="Size" />
360 <output file="size.tab" name="output_tab" /> 402 <output file="size.tab" name="output_tab" />
361 <output file="global_nomerge.pdf" name="output_pdf" /> 403 <output file="global_nomerge.pdf" name="output_pdf" />
362 </test> 404 </test>
363 <test> <!-- 11 --> 405 <test> <!-- 14 -->
364 <repeat name="series"> 406 <repeat name="series">
365 <param name="inputs" value="input1.bam" ftype="bam" /> 407 <param name="inputs" value="input1.bam" ftype="bam" />
366 <param name="normalization" value="1.0" /> 408 <param name="normalization" value="1.0" />
367 </repeat> 409 </repeat>
368 <repeat name="series"> 410 <repeat name="series">