Mercurial > repos > artbio > small_rna_maps

comparison small_rna_maps.xml @ 26:376fae7c9f32 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 32eba59fa52705ae74fd9fe65f6f55be783bfc74
author artbio
date Sun, 14 Apr 2019 14:43:44 -0400
parents 07aa8f928d4b
children fe1a9cfaf5c3
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25:07aa8f928d4b 26:376fae7c9f32
1 <tool id="small_rna_maps" name="small_rna_maps" version="2.13.0"> 1 <tool id="small_rna_maps" name="small_rna_maps" version="2.13.1">
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>
79 <param name="inputs" type="data" format="bam" label="Select a alignment files to parse" multiple="true" 79 <param name="inputs" type="data" format="bam" label="Select a alignment files to parse" multiple="true"
80 help="maps from these bam inputs will be collected in a single pdf output" /> 80 help="maps from these bam inputs will be collected in a single pdf output" />
81 <param name="normalization" type="text" label="Enter a size/normalization factor." 81 <param name="normalization" type="text" label="Enter a size/normalization factor."
82 help="Enter normalisation factors separated by space eg [0.75 1.23 1.1], no normalization if no values" value="1"/> 82 help="Enter normalisation factors separated by space eg [0.75 1.23 1.1], no normalization if no values" value="1"/>
83 <param name="minsize" type="integer" label="Minimal size of reads for inclusion in analysis" 83 <param name="minsize" type="integer" label="Minimal size of reads for inclusion in analysis"
84 value="0" help="default value: 0" /> 84 value="19" help="default value: 19" />
85 <param name="maxsize" type="integer" label="Maximal size of reads for inclusion in analysis" 85 <param name="maxsize" type="integer" label="Maximal size of reads for inclusion in analysis"
86 value="10000" help="default value: 10000" /> 86 value="29" help="default value: 29" />
87 <conditional name="plots_options"> 87 <conditional name="plots_options">
88 <param name="plots_options_selector" type="select" display="radio" label="Plot Options"> 88 <param name="plots_options_selector" type="select" display="radio" label="Plot Options">
89 <option value="one_plot">Just one plot per chromosome</option> 89 <option value="one_plot">Just one plot per chromosome</option>
90 <option value="two_plot" selected="True">Two plots per chromosome</option> 90 <option value="two_plot" selected="True">Two plots per chromosome</option>
91 <option value="global">Global read size distributions of aligned reads</option> 91 <option value="global">Global read size distributions of aligned reads</option>
162 162
163 <tests> 163 <tests>
164 <test> <!-- 0 --> 164 <test> <!-- 0 -->
165 <param name="inputs" value="input1.bam,input_new2.bam" ftype="bam" /> 165 <param name="inputs" value="input1.bam,input_new2.bam" ftype="bam" />
166 <param name="normalization" value="1 2" /> 166 <param name="normalization" value="1 2" />
167 <param name="minsize" value="0" />
168 <param name="maxsize" value="10000" />
169 <param name="plots_options_selector" value="one_plot" /> 167 <param name="plots_options_selector" value="one_plot" />
170 <param name="first_plot" value="Counts" /> 168 <param name="first_plot" value="Counts" />
171 <output file="input1_input2new_norm_1_2_counts.tab" name="output_tab" /> 169 <output file="input1_input2new_norm_1_2_counts.tab" name="output_tab" />
172 <output file="input1_input2new_norm_1_2_single_plot_counts.pdf" name="output_pdf" /> 170 <output file="input1_input2new_norm_1_2_single_plot_counts.pdf" name="output_pdf" />
173 </test> 171 </test>
174 <test> <!-- 1 --> 172 <test> <!-- 1 -->
175 <param name="inputs" value="input1.bam" ftype="bam" /> 173 <param name="inputs" value="input1.bam" ftype="bam" />
176 <param name="normalization" value="1.0" /> 174 <param name="normalization" value="1.0" />
177 <param name="minsize" value="0" />
178 <param name="maxsize" value="10000" />
179 <param name="ylimits" value="yes" /> 175 <param name="ylimits" value="yes" />
180 <param name="ymin" value="-5" /> 176 <param name="ymin" value="-5" />
181 <param name="ymax" value="5" /> 177 <param name="ymax" value="5" />
182 <param name="plots_options_selector" value="one_plot" /> 178 <param name="plots_options_selector" value="one_plot" />
183 <param name="first_plot" value="Counts" /> 179 <param name="first_plot" value="Counts" />
185 <output file="input1_yminneg5_5_single_plot_counts.pdf" name="output_pdf" /> 181 <output file="input1_yminneg5_5_single_plot_counts.pdf" name="output_pdf" />
186 </test> 182 </test>
187 <test> <!-- 2 --> 183 <test> <!-- 2 -->
188 <param name="inputs" value="input1.bam" ftype="bam" /> 184 <param name="inputs" value="input1.bam" ftype="bam" />
189 <param name="normalization" value="1.0" /> 185 <param name="normalization" value="1.0" />
190 <param name="minsize" value="0" />
191 <param name="maxsize" value="10000" />
192 <param name="plots_options_selector" value="cluster" /> 186 <param name="plots_options_selector" value="cluster" />
193 <param name="first_plot" value="Counts" /> 187 <param name="first_plot" value="Counts" />
194 <param name="cluster" value="5" /> 188 <param name="cluster" value="5" />
195 <param name="skip_size" value="1" /> 189 <param name="skip_size" value="1" />
196 <param name="strandness" value="false" /> 190 <param name="strandness" value="false" />
199 <output file="bed1.bed" name="output_bed" /> 193 <output file="bed1.bed" name="output_bed" />
200 </test> 194 </test>
201 <test> <!-- 3 --> 195 <test> <!-- 3 -->
202 <param name="inputs" value="input1.bam" ftype="bam" /> 196 <param name="inputs" value="input1.bam" ftype="bam" />
203 <param name="normalization" value="1.0" /> 197 <param name="normalization" value="1.0" />
204 <param name="minsize" value="0" />
205 <param name="maxsize" value="10000" />
206 <param name="plots_options_selector" value="cluster" /> 198 <param name="plots_options_selector" value="cluster" />
207 <param name="first_plot" value="Counts" /> 199 <param name="first_plot" value="Counts" />
208 <param name="cluster" value="5" /> 200 <param name="cluster" value="5" />
209 <param name="skip_size" value="1" /> 201 <param name="skip_size" value="1" />
210 <param name="strandness" value="true" /> 202 <param name="strandness" value="true" />
213 <output file="bed2.bed" name="output_bed" /> 205 <output file="bed2.bed" name="output_bed" />
214 </test> 206 </test>
215 <test> <!-- 4 --> 207 <test> <!-- 4 -->
216 <param name="inputs" value="input1.bam" ftype="bam" /> 208 <param name="inputs" value="input1.bam" ftype="bam" />
217 <param name="normalization" value="1.0" /> 209 <param name="normalization" value="1.0" />
218 <param name="minsize" value="0" />
219 <param name="maxsize" value="10000" />
220 <param name="plots_options_selector" value="cluster" /> 210 <param name="plots_options_selector" value="cluster" />
221 <param name="first_plot" value="Counts" /> 211 <param name="first_plot" value="Counts" />
222 <param name="cluster" value="5" /> 212 <param name="cluster" value="5" />
223 <param name="skip_size" value="2" /> 213 <param name="skip_size" value="2" />
224 <param name="strandness" value="false" /> 214 <param name="strandness" value="false" />
227 <output file="bed3.bed" name="output_bed" /> 217 <output file="bed3.bed" name="output_bed" />
228 </test> 218 </test>
229 <test> <!-- 5 --> 219 <test> <!-- 5 -->
230 <param name="inputs" value="input1.bam" ftype="bam" /> 220 <param name="inputs" value="input1.bam" ftype="bam" />
231 <param name="normalization" value="1.0" /> 221 <param name="normalization" value="1.0" />
232 <param name="minsize" value="0" />
233 <param name="maxsize" value="10000" />
234 <param name="plots_options_selector" value="cluster" /> 222 <param name="plots_options_selector" value="cluster" />
235 <param name="first_plot" value="Counts" /> 223 <param name="first_plot" value="Counts" />
236 <param name="cluster" value="5" /> 224 <param name="cluster" value="5" />
237 <param name="skip_size" value="2" /> 225 <param name="skip_size" value="2" />
238 <param name="skip_counts" value="3" /> 226 <param name="skip_counts" value="3" />
243 <output file="bed4.bed" name="output_bed" /> 231 <output file="bed4.bed" name="output_bed" />
244 </test> 232 </test>
245 <test> <!-- 6 --> 233 <test> <!-- 6 -->
246 <param name="inputs" value="input1.bam" ftype="bam" /> 234 <param name="inputs" value="input1.bam" ftype="bam" />
247 <param name="normalization" value="1.0" /> 235 <param name="normalization" value="1.0" />
248 <param name="minsize" value="0" />
249 <param name="maxsize" value="10000" />
250 <param name="plots_options_selector" value="cluster" /> 236 <param name="plots_options_selector" value="cluster" />
251 <param name="first_plot" value="Counts" /> 237 <param name="first_plot" value="Counts" />
252 <param name="cluster" value="5" /> 238 <param name="cluster" value="5" />
253 <param name="skip_size" value="2" /> 239 <param name="skip_size" value="2" />
254 <param name="skip_counts" value="2" /> 240 <param name="skip_counts" value="2" />
259 <output file="bed5.bed" name="output_bed" /> 245 <output file="bed5.bed" name="output_bed" />
260 </test> 246 </test>
261 <test> <!-- 7 --> 247 <test> <!-- 7 -->
262 <param name="inputs" value="input1.bam" ftype="bam" /> 248 <param name="inputs" value="input1.bam" ftype="bam" />
263 <param name="normalization" value="1.0" /> 249 <param name="normalization" value="1.0" />
264 <param name="minsize" value="20" />
265 <param name="maxsize" value="30" />
266 <param name="plots_options_selector" value="one_plot" /> 250 <param name="plots_options_selector" value="one_plot" />
267 <param name="first_plot" value="Size" /> 251 <param name="first_plot" value="Size" />
268 <output file="input1_min20_max30_size.tab" name="output_tab" /> 252 <output file="input1_min20_max30_size.tab" name="output_tab" />
269 <output file="input1_min20_max30_single_plot_size.pdf" name="output_pdf" /> 253 <output file="input1_min20_max30_single_plot_size.pdf" name="output_pdf" />
270 </test> 254 </test>
271 <test> <!-- 8 --> 255 <test> <!-- 8 -->
272 <param name="inputs" value="input1.bam" ftype="bam" /> 256 <param name="inputs" value="input1.bam" ftype="bam" />
273 <param name="normalization" value="1.0" /> 257 <param name="normalization" value="1.0" />
274 <param name="minsize" value="0" />
275 <param name="maxsize" value="10000" />
276 <param name="plots_options_selector" value="one_plot" /> 258 <param name="plots_options_selector" value="one_plot" />
277 <param name="first_plot" value="Mean" /> 259 <param name="first_plot" value="Mean" />
278 <output file="input1_mean.tab" name="output_tab" /> 260 <output file="input1_mean.tab" name="output_tab" />
279 <output file="input1__single_plot_mean.pdf" name="output_pdf" /> 261 <output file="input1__single_plot_mean.pdf" name="output_pdf" />
280 </test> 262 </test>
281 <test> <!-- 9 --> 263 <test> <!-- 9 -->
282 <param name="inputs" value="input1.bam" ftype="bam" /> 264 <param name="inputs" value="input1.bam" ftype="bam" />
283 <param name="normalization" value="1.0" /> 265 <param name="normalization" value="1.0" />
284 <param name="minsize" value="0" />
285 <param name="maxsize" value="10000" />
286 <param name="plots_options_selector" value="one_plot" /> 266 <param name="plots_options_selector" value="one_plot" />
287 <param name="first_plot" value="Median" /> 267 <param name="first_plot" value="Median" />
288 <output file="input1_median.tab" name="output_tab" /> 268 <output file="input1_median.tab" name="output_tab" />
289 <output file="input1_single_plot_median.pdf" name="output_pdf" /> 269 <output file="input1_single_plot_median.pdf" name="output_pdf" />
290 </test> 270 </test>
291 <test> <!-- 10 --> 271 <test> <!-- 10 -->
292 <param name="inputs" value="input1.bam,input2.bam" ftype="bam" /> 272 <param name="inputs" value="input1.bam,input2.bam" ftype="bam" />
293 <param name="normalization" value="1.0 2.0" /> 273 <param name="normalization" value="1.0 2.0" />
294 <param name="minsize" value="0" />
295 <param name="maxsize" value="10000" />
296 <param name="plots_options_selector" value="one_plot" /> 274 <param name="plots_options_selector" value="one_plot" />
297 <param name="first_plot" value="Counts" /> 275 <param name="first_plot" value="Counts" />
298 <output file="input1_input2_norm_1_2_counts.tab" name="output_tab" /> 276 <output file="input1_input2_norm_1_2_counts.tab" name="output_tab" />
299 <output file="input1_input2_norm_1_2_single_plot_counts.pdf" name="output_pdf" /> 277 <output file="input1_input2_norm_1_2_single_plot_counts.pdf" name="output_pdf" />
300 </test> 278 </test>
301 <test> <!-- 11 --> 279 <test> <!-- 11 -->
302 <param name="inputs" value="input1.bam,input2.bam" ftype="bam" /> 280 <param name="inputs" value="input1.bam,input2.bam" ftype="bam" />
303 <param name="normalization" value="1.0 1.0" /> 281 <param name="normalization" value="1.0 1.0" />
304 <param name="minsize" value="0" />
305 <param name="maxsize" value="10000" />
306 <param name="ylimits" value="yes" /> 282 <param name="ylimits" value="yes" />
307 <param name="ymin" value="-5" /> 283 <param name="ymin" value="-5" />
308 <param name="ymax" value="5" /> 284 <param name="ymax" value="5" />
309 <param name="plots_options_selector" value="two_plot" /> 285 <param name="plots_options_selector" value="two_plot" />
310 <param name="first_plot" value="Counts" /> 286 <param name="first_plot" value="Counts" />
314 <output file="input1_input2_double_plot_counts_size_ylimneg5_5.pdf" name="output_pdf" /> 290 <output file="input1_input2_double_plot_counts_size_ylimneg5_5.pdf" name="output_pdf" />
315 </test> 291 </test>
316 <test> <!-- 12 --> 292 <test> <!-- 12 -->
317 <param name="inputs" value="input_single_chr.bam,input_single_chr.bam,input_single_chr.bam,input_single_chr.bam,input_single_chr.bam,input_single_chr.bam" ftype="bam" /> 293 <param name="inputs" value="input_single_chr.bam,input_single_chr.bam,input_single_chr.bam,input_single_chr.bam,input_single_chr.bam,input_single_chr.bam" ftype="bam" />
318 <param name="normalization" value="1.0 1.0 1.0 1.0 1.0 1.0" /> 294 <param name="normalization" value="1.0 1.0 1.0 1.0 1.0 1.0" />
319 <param name="minsize" value="0" />
320 <param name="maxsize" value="10000" />
321 <param name="plots_options_selector" value="one_plot" /> 295 <param name="plots_options_selector" value="one_plot" />
322 <param name="first_plot" value="Coverage" /> 296 <param name="first_plot" value="Coverage" />
323 <output file="input_single_chr_x_6_single_plot_coverage.tab" name="output_tab" /> 297 <output file="input_single_chr_x_6_single_plot_coverage.tab" name="output_tab" />
324 <output file="input_single_chr_x_6_single_plot_coverage.pdf" name="output_pdf" /> 298 <output file="input_single_chr_x_6_single_plot_coverage.pdf" name="output_pdf" />
325 </test> 299 </test>
326 <test> <!-- 13 --> 300 <test> <!-- 13 -->
327 <param name="inputs" value="input1.bam,input2.bam" ftype="bam" /> 301 <param name="inputs" value="input1.bam,input2.bam" ftype="bam" />
328 <param name="normalization" value="1.0 1.0" /> 302 <param name="normalization" value="1.0 1.0" />
329 <param name="minsize" value="0" />
330 <param name="maxsize" value="10000" />
331 <param name="plots_options_selector" value="global" /> 303 <param name="plots_options_selector" value="global" />
332 <param name="mergestrands" value="nomerge" /> 304 <param name="mergestrands" value="nomerge" />
333 <param name="first_plot" value="Size" /> 305 <param name="first_plot" value="Size" />
334 <output file="size.tab" name="output_tab" /> 306 <output file="size.tab" name="output_tab" />
335 <output file="global_nomerge.pdf" name="output_pdf" /> 307 <output file="global_nomerge.pdf" name="output_pdf" />
336 </test> 308 </test>
337 <test> <!-- 14 --> 309 <test> <!-- 14 -->
338 <param name="inputs" value="input1.bam,input2.bam" ftype="bam" /> 310 <param name="inputs" value="input1.bam,input2.bam" ftype="bam" />
339 <param name="normalization" value="1.0 1.0" /> 311 <param name="normalization" value="1.0 1.0" />
340 <param name="minsize" value="0" />
341 <param name="maxsize" value="10000" />
342 <param name="plots_options_selector" value="global" /> 312 <param name="plots_options_selector" value="global" />
343 <param name="mergestrands" value="merge" /> 313 <param name="mergestrands" value="merge" />
344 <param name="first_plot" value="Size" /> 314 <param name="first_plot" value="Size" />
345 <output file="size.tab" name="output_tab" /> 315 <output file="size.tab" name="output_tab" />
346 <output file="global_merge.pdf" name="output_pdf" /> 316 <output file="global_merge.pdf" name="output_pdf" />