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comparison small_rna_maps.xml @ 22:29f03c13c7a2 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit da30f7ecca2dff1124a0c14c60f5ddb7731ccd37
author artbio
date Mon, 24 Dec 2018 18:55:36 -0500
parents b585cb347a26
children 3ca8113cc758
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21:b585cb347a26 22:29f03c13c7a2
1 <tool id="small_rna_maps" name="small_rna_maps" version="2.10.1"> 1 <tool id="small_rna_maps" name="small_rna_maps" version="2.11.0">
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>
11 </requirements> 11 </requirements>
12 <stdio> 12 <stdio>
13 <exit_code range="1:" level="fatal" description="Tool exception" /> 13 <exit_code range="1:" level="fatal" description="Tool exception" />
14 </stdio> 14 </stdio>
15 <command detect_errors="exit_code"><![CDATA[ 15 <command detect_errors="exit_code"><![CDATA[
16 #for $file in $series 16 #import json
17 sambamba view -t \${GALAXY_SLOTS} -F "not unmapped and sequence_length >= ${minsize} and sequence_length <= ${maxsize}" -f bam '$file.inputs' >'$file.inputs.name' && 17 #import os
18 samtools index '$file.inputs.name' && 18 #for $file in $inputs
19 sambamba view -t \${GALAXY_SLOTS} -F "not unmapped and sequence_length >= ${minsize} and sequence_length <= ${maxsize}" -f bam '$file' -o '$file.element_identifier' &&
20 samtools index '$file.element_identifier' &&
19 #end for 21 #end for
22 ls -la ./ &&
20 python '$__tool_directory__'/small_rna_maps.py 23 python '$__tool_directory__'/small_rna_maps.py
21 --inputs 24 --inputs ${ ' '.join(['"%s"' % x.element_identifier for x in $inputs]) }
22 #for $file in $series 25 #set $labels = list()
23 '$file.inputs.name' 26 #for $file in $inputs:
27 $labels.append(str($file.element_identifier))
24 #end for 28 #end for
25 --sample_names 29 --sample_names ${ ' '.join(['"%s"' % x for x in $labels]) }
26 #for $sample in $series
27 '$sample.inputs.name'
28 #end for
29 --minsize $minsize 30 --minsize $minsize
30 --maxsize $maxsize 31 --maxsize $maxsize
31 #if str($plots_options.plots_options_selector ) == "two_plot": 32 #if str($plots_options.plots_options_selector ) == "two_plot":
32 --plot_methods '${plots_options.first_plot}' '${plots_options.extra_plot}' 33 --plot_methods '${plots_options.first_plot}' '${plots_options.extra_plot}'
33 --outputs '$output_tab' '$extra_output_tab' && 34 --outputs '$output_tab' '$extra_output_tab' &&
50 51
51 52
52 Rscript '$__tool_directory__'/small_rna_maps.r 53 Rscript '$__tool_directory__'/small_rna_maps.r
53 --first_dataframe '$output_tab' 54 --first_dataframe '$output_tab'
54 --extra_dataframe '$extra_output_tab' 55 --extra_dataframe '$extra_output_tab'
55 --normalization 56 #if len(str($normalization)) != 1:
56 #set $norm = "" 57 --normalization "${ ' '.join( [factor for factor in $normalization.split()]) }"
57 #for $file in $series 58 #else:
58 #set $norm += str($file.normalization)+' ' 59 --normalization "${ ' '.join( ["1" for factor in $inputs] )}"
59 #end for 60 #end if
60 #set $norm = $norm[:-1]
61 '$norm'
62 #if $ylimits_cond.ylimits == "no": 61 #if $ylimits_cond.ylimits == "no":
63 --ymin '' --ymax '' 62 --ymin '' --ymax ''
64 #else: 63 #else:
65 --ymin '${ylimits_cond.ymin}' --ymax '${ylimits_cond.ymax}' 64 --ymin '${ylimits_cond.ymin}' --ymax '${ylimits_cond.ymax}'
66 #end if 65 #end if
76 --extra_plot_method '' 75 --extra_plot_method ''
77 #end if 76 #end if
78 --output_pdf '$output_pdf' 77 --output_pdf '$output_pdf'
79 ]]></command> 78 ]]></command>
80 <inputs> 79 <inputs>
81 <repeat name="series" title="Input" min="1"> 80 <param name="inputs" type="data" format="bam" label="Select a alignment files to parse" multiple="true"
82 <param name="inputs" type="data" format="bam" label="Select a single alignment file to parse" multiple="false" 81 help="maps from these bam inputs will be collected in a single pdf output" />
83 help="If 'multiple datasets' method is used, the same normalization factor will be applied to each dataset. Please refer to the help section for more information." /> 82 <param name="normalization" type="text" label="Enter a size/normalization factor."
84 <param name="normalization" type="float" label="Enter a size/normalization factor." 83 help="Enter normalisation factors separated by space eg [0.75 1.23 1.1], no normalization if no values" value="1"/>
85 help="Enter only one value e.g. '0.75' or '1.23'" value="1.0"/>
86 </repeat>
87 <param name="minsize" type="integer" label="Minimal size of reads for inclusion in analysis" 84 <param name="minsize" type="integer" label="Minimal size of reads for inclusion in analysis"
88 value="0" help="default value: 0" /> 85 value="0" help="default value: 0" />
89 <param name="maxsize" type="integer" label="Maximal size of reads for inclusion in analysis" 86 <param name="maxsize" type="integer" label="Maximal size of reads for inclusion in analysis"
90 value="10000" help="default value: 10000" /> 87 value="10000" help="default value: 10000" />
91 <conditional name="plots_options"> 88 <conditional name="plots_options">
164 <data format="pdf" name="output_pdf" label="small RNA maps" /> 161 <data format="pdf" name="output_pdf" label="small RNA maps" />
165 </outputs> 162 </outputs>
166 163
167 <tests> 164 <tests>
168 <test> <!-- 0 --> 165 <test> <!-- 0 -->
169 <repeat name="series"> 166 <param name="inputs" value="input1.bam,input_new2.bam" ftype="bam" />
170 <param name="inputs" value="input1.bam" ftype="bam" /> 167 <param name="normalization" value="1 2" />
171 <param name="normalization" value="1.0" />
172 </repeat>
173 <repeat name="series">
174 <param name="inputs" value="input_new2.bam" ftype="bam" />
175 <param name="normalization" value="2.0" />
176 </repeat>
177 <param name="minsize" value="0" /> 168 <param name="minsize" value="0" />
178 <param name="maxsize" value="10000" /> 169 <param name="maxsize" value="10000" />
179 <param name="plots_options_selector" value="one_plot" /> 170 <param name="plots_options_selector" value="one_plot" />
180 <param name="first_plot" value="Counts" /> 171 <param name="first_plot" value="Counts" />
181 <output file="input1_input2new_norm_1_2_counts.tab" name="output_tab" /> 172 <output file="input1_input2new_norm_1_2_counts.tab" name="output_tab" />
182 <output file="input1_input2new_norm_1_2_single_plot_counts.pdf" name="output_pdf" /> 173 <output file="input1_input2new_norm_1_2_single_plot_counts.pdf" name="output_pdf" />
183 </test> 174 </test>
184 <test> <!-- 1 --> 175 <test> <!-- 1 -->
185 <repeat name="series"> 176 <param name="inputs" value="input1.bam" ftype="bam" />
186 <param name="inputs" value="input1.bam" ftype="bam" /> 177 <param name="normalization" value="1.0" />
187 <param name="normalization" value="1.0" />
188 </repeat>
189 <param name="minsize" value="0" /> 178 <param name="minsize" value="0" />
190 <param name="maxsize" value="10000" /> 179 <param name="maxsize" value="10000" />
191 <param name="ylimits" value="yes" /> 180 <param name="ylimits" value="yes" />
192 <param name="ymin" value="-5" /> 181 <param name="ymin" value="-5" />
193 <param name="ymax" value="5" /> 182 <param name="ymax" value="5" />
195 <param name="first_plot" value="Counts" /> 184 <param name="first_plot" value="Counts" />
196 <output file="input1_counts_yminneg5_5.tab" name="output_tab" /> 185 <output file="input1_counts_yminneg5_5.tab" name="output_tab" />
197 <output file="input1_yminneg5_5_single_plot_counts.pdf" name="output_pdf" /> 186 <output file="input1_yminneg5_5_single_plot_counts.pdf" name="output_pdf" />
198 </test> 187 </test>
199 <test> <!-- 2 --> 188 <test> <!-- 2 -->
200 <repeat name="series"> 189 <param name="inputs" value="input1.bam" ftype="bam" />
201 <param name="inputs" value="input1.bam" ftype="bam" /> 190 <param name="normalization" value="1.0" />
202 <param name="normalization" value="1.0" />
203 </repeat>
204 <param name="minsize" value="0" /> 191 <param name="minsize" value="0" />
205 <param name="maxsize" value="10000" /> 192 <param name="maxsize" value="10000" />
206 <param name="plots_options_selector" value="cluster" /> 193 <param name="plots_options_selector" value="cluster" />
207 <param name="first_plot" value="Counts" /> 194 <param name="first_plot" value="Counts" />
208 <param name="cluster" value="5" /> 195 <param name="cluster" value="5" />
211 <output file="clustering.tab" name="output_tab" /> 198 <output file="clustering.tab" name="output_tab" />
212 <output file="clustering.pdf" name="output_pdf" /> 199 <output file="clustering.pdf" name="output_pdf" />
213 <output file="bed1.bed" name="output_bed" /> 200 <output file="bed1.bed" name="output_bed" />
214 </test> 201 </test>
215 <test> <!-- 3 --> 202 <test> <!-- 3 -->
216 <repeat name="series"> 203 <param name="inputs" value="input1.bam" ftype="bam" />
217 <param name="inputs" value="input1.bam" ftype="bam" /> 204 <param name="normalization" value="1.0" />
218 <param name="normalization" value="1.0" />
219 </repeat>
220 <param name="minsize" value="0" /> 205 <param name="minsize" value="0" />
221 <param name="maxsize" value="10000" /> 206 <param name="maxsize" value="10000" />
222 <param name="plots_options_selector" value="cluster" /> 207 <param name="plots_options_selector" value="cluster" />
223 <param name="first_plot" value="Counts" /> 208 <param name="first_plot" value="Counts" />
224 <param name="cluster" value="5" /> 209 <param name="cluster" value="5" />
227 <output file="clustering_unstranded.tab" name="output_tab" /> 212 <output file="clustering_unstranded.tab" name="output_tab" />
228 <output file="clustering_unstranded.pdf" name="output_pdf" /> 213 <output file="clustering_unstranded.pdf" name="output_pdf" />
229 <output file="bed2.bed" name="output_bed" /> 214 <output file="bed2.bed" name="output_bed" />
230 </test> 215 </test>
231 <test> <!-- 4 --> 216 <test> <!-- 4 -->
232 <repeat name="series"> 217 <param name="inputs" value="input1.bam" ftype="bam" />
233 <param name="inputs" value="input1.bam" ftype="bam" /> 218 <param name="normalization" value="1.0" />
234 <param name="normalization" value="1.0" />
235 </repeat>
236 <param name="minsize" value="0" /> 219 <param name="minsize" value="0" />
237 <param name="maxsize" value="10000" /> 220 <param name="maxsize" value="10000" />
238 <param name="plots_options_selector" value="cluster" /> 221 <param name="plots_options_selector" value="cluster" />
239 <param name="first_plot" value="Counts" /> 222 <param name="first_plot" value="Counts" />
240 <param name="cluster" value="5" /> 223 <param name="cluster" value="5" />
243 <output file="clustering.tab" name="output_tab" /> 226 <output file="clustering.tab" name="output_tab" />
244 <output file="clustering.pdf" name="output_pdf" /> 227 <output file="clustering.pdf" name="output_pdf" />
245 <output file="bed3.bed" name="output_bed" /> 228 <output file="bed3.bed" name="output_bed" />
246 </test> 229 </test>
247 <test> <!-- 5 --> 230 <test> <!-- 5 -->
248 <repeat name="series"> 231 <param name="inputs" value="input1.bam" ftype="bam" />
249 <param name="inputs" value="input1.bam" ftype="bam" /> 232 <param name="normalization" value="1.0" />
250 <param name="normalization" value="1.0" />
251 </repeat>
252 <param name="minsize" value="0" /> 233 <param name="minsize" value="0" />
253 <param name="maxsize" value="10000" /> 234 <param name="maxsize" value="10000" />
254 <param name="plots_options_selector" value="cluster" /> 235 <param name="plots_options_selector" value="cluster" />
255 <param name="first_plot" value="Counts" /> 236 <param name="first_plot" value="Counts" />
256 <param name="cluster" value="5" /> 237 <param name="cluster" value="5" />
261 <output file="clustering.tab" name="output_tab" /> 242 <output file="clustering.tab" name="output_tab" />
262 <output file="clustering.pdf" name="output_pdf" /> 243 <output file="clustering.pdf" name="output_pdf" />
263 <output file="bed4.bed" name="output_bed" /> 244 <output file="bed4.bed" name="output_bed" />
264 </test> 245 </test>
265 <test> <!-- 6 --> 246 <test> <!-- 6 -->
266 <repeat name="series"> 247 <param name="inputs" value="input1.bam" ftype="bam" />
267 <param name="inputs" value="input1.bam" ftype="bam" /> 248 <param name="normalization" value="1.0" />
268 <param name="normalization" value="1.0" />
269 </repeat>
270 <param name="minsize" value="0" /> 249 <param name="minsize" value="0" />
271 <param name="maxsize" value="10000" /> 250 <param name="maxsize" value="10000" />
272 <param name="plots_options_selector" value="cluster" /> 251 <param name="plots_options_selector" value="cluster" />
273 <param name="first_plot" value="Counts" /> 252 <param name="first_plot" value="Counts" />
274 <param name="cluster" value="5" /> 253 <param name="cluster" value="5" />
279 <output file="clustering_unstranded.tab" name="output_tab" /> 258 <output file="clustering_unstranded.tab" name="output_tab" />
280 <output file="clustering_unstranded.pdf" name="output_pdf" /> 259 <output file="clustering_unstranded.pdf" name="output_pdf" />
281 <output file="bed5.bed" name="output_bed" /> 260 <output file="bed5.bed" name="output_bed" />
282 </test> 261 </test>
283 <test> <!-- 7 --> 262 <test> <!-- 7 -->
284 <repeat name="series"> 263 <param name="inputs" value="input1.bam" ftype="bam" />
285 <param name="inputs" value="input1.bam" ftype="bam" /> 264 <param name="normalization" value="1.0" />
286 <param name="normalization" value="1.0" />
287 </repeat>
288 <param name="minsize" value="20" /> 265 <param name="minsize" value="20" />
289 <param name="maxsize" value="30" /> 266 <param name="maxsize" value="30" />
290 <param name="plots_options_selector" value="one_plot" /> 267 <param name="plots_options_selector" value="one_plot" />
291 <param name="first_plot" value="Size" /> 268 <param name="first_plot" value="Size" />
292 <output file="input1_min20_max30_size.tab" name="output_tab" /> 269 <output file="input1_min20_max30_size.tab" name="output_tab" />
293 <output file="input1_min20_max30_single_plot_size.pdf" name="output_pdf" /> 270 <output file="input1_min20_max30_single_plot_size.pdf" name="output_pdf" />
294 </test> 271 </test>
295 <test> <!-- 8 --> 272 <test> <!-- 8 -->
296 <repeat name="series"> 273 <param name="inputs" value="input1.bam" ftype="bam" />
297 <param name="inputs" value="input1.bam" ftype="bam" /> 274 <param name="normalization" value="1.0" />
298 <param name="normalization" value="1.0" />
299 </repeat>
300 <param name="minsize" value="0" /> 275 <param name="minsize" value="0" />
301 <param name="maxsize" value="10000" /> 276 <param name="maxsize" value="10000" />
302 <param name="plots_options_selector" value="one_plot" /> 277 <param name="plots_options_selector" value="one_plot" />
303 <param name="first_plot" value="Mean" /> 278 <param name="first_plot" value="Mean" />
304 <output file="input1_mean.tab" name="output_tab" /> 279 <output file="input1_mean.tab" name="output_tab" />
305 <output file="input1__single_plot_mean.pdf" name="output_pdf" /> 280 <output file="input1__single_plot_mean.pdf" name="output_pdf" />
306 </test> 281 </test>
307 <test> <!-- 9 --> 282 <test> <!-- 9 -->
308 <repeat name="series"> 283 <param name="inputs" value="input1.bam" ftype="bam" />
309 <param name="inputs" value="input1.bam" ftype="bam" /> 284 <param name="normalization" value="1.0" />
310 <param name="normalization" value="1.0" />
311 </repeat>
312 <param name="minsize" value="0" /> 285 <param name="minsize" value="0" />
313 <param name="maxsize" value="10000" /> 286 <param name="maxsize" value="10000" />
314 <param name="plots_options_selector" value="one_plot" /> 287 <param name="plots_options_selector" value="one_plot" />
315 <param name="first_plot" value="Median" /> 288 <param name="first_plot" value="Median" />
316 <output file="input1_median.tab" name="output_tab" /> 289 <output file="input1_median.tab" name="output_tab" />
317 <output file="input1_single_plot_median.pdf" name="output_pdf" /> 290 <output file="input1_single_plot_median.pdf" name="output_pdf" />
318 </test> 291 </test>
319 <test> <!-- 10 --> 292 <test> <!-- 10 -->
320 <repeat name="series"> 293 <param name="inputs" value="input1.bam,input2.bam" ftype="bam" />
321 <param name="inputs" value="input1.bam" ftype="bam" /> 294 <param name="normalization" value="1.0 2.0" />
322 <param name="normalization" value="1.0" />
323 </repeat>
324 <repeat name="series">
325 <param name="inputs" value="input2.bam" ftype="bam" />
326 <param name="normalization" value="2.0" />
327 </repeat>
328 <param name="minsize" value="0" /> 295 <param name="minsize" value="0" />
329 <param name="maxsize" value="10000" /> 296 <param name="maxsize" value="10000" />
330 <param name="plots_options_selector" value="one_plot" /> 297 <param name="plots_options_selector" value="one_plot" />
331 <param name="first_plot" value="Counts" /> 298 <param name="first_plot" value="Counts" />
332 <output file="input1_input2_norm_1_2_counts.tab" name="output_tab" /> 299 <output file="input1_input2_norm_1_2_counts.tab" name="output_tab" />
333 <output file="input1_input2_norm_1_2_single_plot_counts.pdf" name="output_pdf" /> 300 <output file="input1_input2_norm_1_2_single_plot_counts.pdf" name="output_pdf" />
334 </test> 301 </test>
335 <test> <!-- 11 --> 302 <test> <!-- 11 -->
336 <repeat name="series"> 303 <param name="inputs" value="input1.bam,input2.bam" ftype="bam" />
337 <param name="inputs" value="input1.bam" ftype="bam" /> 304 <param name="normalization" value="1.0 1.0" />
338 <param name="normalization" value="1.0" />
339 </repeat>
340 <repeat name="series">
341 <param name="inputs" value="input2.bam" ftype="bam" />
342 <param name="normalization" value="1.0" />
343 </repeat>
344 <param name="minsize" value="0" /> 305 <param name="minsize" value="0" />
345 <param name="maxsize" value="10000" /> 306 <param name="maxsize" value="10000" />
346 <param name="ylimits" value="yes" /> 307 <param name="ylimits" value="yes" />
347 <param name="ymin" value="-5" /> 308 <param name="ymin" value="-5" />
348 <param name="ymax" value="5" /> 309 <param name="ymax" value="5" />
352 <output file="input1_input2_counts.tab" name="output_tab" /> 313 <output file="input1_input2_counts.tab" name="output_tab" />
353 <output file="input1_input2_size.tab" name="extra_output_tab" /> 314 <output file="input1_input2_size.tab" name="extra_output_tab" />
354 <output file="input1_input2_double_plot_counts_size_ylimneg5_5.pdf" name="output_pdf" /> 315 <output file="input1_input2_double_plot_counts_size_ylimneg5_5.pdf" name="output_pdf" />
355 </test> 316 </test>
356 <test> <!-- 12 --> 317 <test> <!-- 12 -->
357 <repeat name="series"> 318 <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" />
358 <param name="inputs" value="input_single_chr.bam" ftype="bam" /> 319 <param name="normalization" value="1.0 1.0 1.0 1.0 1.0 1.0" />
359 <param name="normalization" value="1.0" />
360 </repeat>
361 <repeat name="series">
362 <param name="inputs" value="input_single_chr.bam" ftype="bam" />
363 <param name="normalization" value="1.0" />
364 </repeat>
365 <repeat name="series">
366 <param name="inputs" value="input_single_chr.bam" ftype="bam" />
367 <param name="normalization" value="1.0" />
368 </repeat>
369 <repeat name="series">
370 <param name="inputs" value="input_single_chr.bam" ftype="bam" />
371 <param name="normalization" value="1.0" />
372 </repeat>
373 <repeat name="series">
374 <param name="inputs" value="input_single_chr.bam" ftype="bam" />
375 <param name="normalization" value="1.0" />
376 </repeat>
377 <repeat name="series">
378 <param name="inputs" value="input_single_chr.bam" ftype="bam" />
379 <param name="normalization" value="1.0" />
380 </repeat>
381 <param name="minsize" value="0" /> 320 <param name="minsize" value="0" />
382 <param name="maxsize" value="10000" /> 321 <param name="maxsize" value="10000" />
383 <param name="plots_options_selector" value="one_plot" /> 322 <param name="plots_options_selector" value="one_plot" />
384 <param name="first_plot" value="Coverage" /> 323 <param name="first_plot" value="Coverage" />
385 <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.tab" name="output_tab" />
386 <output file="input_single_chr_x_6_single_plot_coverage.pdf" name="output_pdf" /> 325 <output file="input_single_chr_x_6_single_plot_coverage.pdf" name="output_pdf" />
387 </test> 326 </test>
388 <test> <!-- 13 --> 327 <test> <!-- 13 -->
389 <repeat name="series"> 328 <param name="inputs" value="input1.bam,input2.bam" ftype="bam" />
390 <param name="inputs" value="input1.bam" ftype="bam" /> 329 <param name="normalization" value="1.0 1.0" />
391 <param name="normalization" value="1.0" />
392 </repeat>
393 <repeat name="series">
394 <param name="inputs" value="input2.bam" ftype="bam" />
395 <param name="normalization" value="1.0" />
396 </repeat>
397 <param name="minsize" value="0" /> 330 <param name="minsize" value="0" />
398 <param name="maxsize" value="10000" /> 331 <param name="maxsize" value="10000" />
399 <param name="plots_options_selector" value="global" /> 332 <param name="plots_options_selector" value="global" />
400 <param name="mergestrands" value="nomerge" /> 333 <param name="mergestrands" value="nomerge" />
401 <param name="first_plot" value="Size" /> 334 <param name="first_plot" value="Size" />
402 <output file="size.tab" name="output_tab" /> 335 <output file="size.tab" name="output_tab" />
403 <output file="global_nomerge.pdf" name="output_pdf" /> 336 <output file="global_nomerge.pdf" name="output_pdf" />
404 </test> 337 </test>
405 <test> <!-- 14 --> 338 <test> <!-- 14 -->
406 <repeat name="series"> 339 <param name="inputs" value="input1.bam,input2.bam" ftype="bam" />
407 <param name="inputs" value="input1.bam" ftype="bam" /> 340 <param name="normalization" value="1.0 1.0" />
408 <param name="normalization" value="1.0" />
409 </repeat>
410 <repeat name="series">
411 <param name="inputs" value="input2.bam" ftype="bam" />
412 <param name="normalization" value="1.0" />
413 </repeat>
414 <param name="minsize" value="0" /> 341 <param name="minsize" value="0" />
415 <param name="maxsize" value="10000" /> 342 <param name="maxsize" value="10000" />
416 <param name="plots_options_selector" value="global" /> 343 <param name="plots_options_selector" value="global" />
417 <param name="mergestrands" value="merge" /> 344 <param name="mergestrands" value="merge" />
418 <param name="first_plot" value="Size" /> 345 <param name="first_plot" value="Size" />