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comparison small_rna_maps.xml @ 16:600e2498bd21 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 82bb0971cde6ba1972588c9315c3007bc3a5a6a7-dirty
author artbio
date Tue, 13 Nov 2018 17:03:46 -0500
parents 82fedc576024
children b28dcd4051e8
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15:82fedc576024 16:600e2498bd21
1 <tool id="small_rna_maps" name="small_rna_maps" version="2.6.0"> 1 <tool id="small_rna_maps" name="small_rna_maps" version="2.7.0">
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>
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 #for $file in $series
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 sambamba view -t \${GALAXY_SLOTS} -F "not unmapped and sequence_length >= ${minsize} and sequence_length <= ${maxsize}" -f bam '$file.inputs' >'$file.inputs.name' &&
18 samtools index '$file.inputs.name'; 18 samtools index '$file.inputs.name' &&
19 #end for 19 #end for
20 python '$__tool_directory__'/small_rna_maps.py 20 python '$__tool_directory__'/small_rna_maps.py
21 --inputs 21 --inputs
22 #for $file in $series 22 #for $file in $series
23 '$file.inputs.name' 23 '$file.inputs.name'
24 #end for 24 #end for
25 --sample_names 25 --sample_names
26 #for $sample in $series 26 #for $sample in $series
27 '$sample.inputs.name' 27 '$sample.inputs.name'
28 #end for 28 #end for
29 --minsize $minsize 29 --minsize $minsize
30 --maxsize $maxsize 30 --maxsize $maxsize
31 --cluster $cluster 31 #if str($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' '$extra_output_tab'; 34 #elif str($plots_options.plots_options_selector ) == "global":
35 #elif str($plots_options.plots_options_selector ) == "global": 35 --plot_methods 'Size'
36 --plot_methods 'Size' 36 --outputs '$output_tab' &&
37 --outputs '$output_tab'; 37 #elif str($plots_options.plots_options_selector ) == "cluster":
38 #else: 38 --plot_methods 'Counts'
39 --plot_methods '${plots_options.first_plot}' 39 --outputs '$output_tab'
40 --outputs '$output_tab' ; 40 --cluster ${plots_options.cluster} &&
41 #end if 41 #else:
42 Rscript '$__tool_directory__'/small_rna_maps.r 42 --plot_methods '${plots_options.first_plot}'
43 --first_dataframe '$output_tab' 43 --outputs '$output_tab' &&
44 --extra_dataframe '$extra_output_tab' 44 #end if
45 --normalization 45
46 #set $norm = "" 46 Rscript '$__tool_directory__'/small_rna_maps.r
47 #for $file in $series 47 --first_dataframe '$output_tab'
48 #set $norm += str($file.normalization)+' ' 48 --extra_dataframe '$extra_output_tab'
49 #end for 49 --normalization
50 #set $norm = $norm[:-1] 50 #set $norm = ""
51 '$norm' 51 #for $file in $series
52 #if $ylimits_cond.ylimits == "no": 52 #set $norm += str($file.normalization)+' '
53 --ymin '' --ymax '' 53 #end for
54 #else: 54 #set $norm = $norm[:-1]
55 --ymin '${ylimits_cond.ymin}' --ymax '${ylimits_cond.ymax}' 55 '$norm'
56 #end if 56 #if $ylimits_cond.ylimits == "no":
57 #if str($plots_options.plots_options_selector ) == "two_plot": 57 --ymin '' --ymax ''
58 --first_plot_method '${plots_options.first_plot}' 58 #else:
59 --extra_plot_method '${plots_options.extra_plot}' 59 --ymin '${ylimits_cond.ymin}' --ymax '${ylimits_cond.ymax}'
60 #elif str($plots_options.plots_options_selector ) == "global": 60 #end if
61 --first_plot_method 'Size' 61 #if str($plots_options.plots_options_selector ) == "two_plot":
62 --extra_plot_method '' 62 --first_plot_method '${plots_options.first_plot}'
63 --global '${plots_options.mergestrands}' 63 --extra_plot_method '${plots_options.extra_plot}'
64 #else: 64 #elif str($plots_options.plots_options_selector ) == "global":
65 --first_plot_method '${plots_options.first_plot}' 65 --first_plot_method 'Size'
66 --extra_plot_method '' 66 --extra_plot_method ''
67 #end if 67 --global '${plots_options.mergestrands}'
68 #else:
69 --first_plot_method '${plots_options.first_plot}'
70 --extra_plot_method ''
71 #end if
68 --output_pdf '$output_pdf' 72 --output_pdf '$output_pdf'
69 ]]></command> 73 ]]></command>
70 <inputs> 74 <inputs>
71 <repeat name="series" title="Input" min="1"> 75 <repeat name="series" title="Input" min="1">
72 <param name="inputs" type="data" format="bam" label="Select a single alignment file to parse" multiple="false" 76 <param name="inputs" type="data" format="bam" label="Select a single alignment file to parse" multiple="false"
76 </repeat> 80 </repeat>
77 <param name="minsize" type="integer" label="Minimal size of reads for inclusion in analysis" 81 <param name="minsize" type="integer" label="Minimal size of reads for inclusion in analysis"
78 value="0" help="default value: 0" /> 82 value="0" help="default value: 0" />
79 <param name="maxsize" type="integer" label="Maximal size of reads for inclusion in analysis" 83 <param name="maxsize" type="integer" label="Maximal size of reads for inclusion in analysis"
80 value="10000" help="default value: 10000" /> 84 value="10000" help="default value: 10000" />
81 <param name="cluster" type="integer" label="Aggregation distance in nucleotides"
82 value="0" help="If not 0, sets the distance (in nt) below which data are clustered to a single median position" />
83 <conditional name="plots_options"> 85 <conditional name="plots_options">
84 <param name="plots_options_selector" type="select" display="radio" label="Plot Options"> 86 <param name="plots_options_selector" type="select" display="radio" label="Plot Options">
85 <option value="one_plot">Just one plot per chromosome</option> 87 <option value="one_plot">Just one plot per chromosome</option>
86 <option value="two_plot" selected="True">Two plots per chromosome</option> 88 <option value="two_plot" selected="True">Two plots per chromosome</option>
87 <option value="global">Global read size distributions of aligned reads</option> 89 <option value="global">Global read size distributions of aligned reads</option>
90 <option value="cluster">Map read clusters</option>
88 </param> 91 </param>
89 <when value="two_plot"> 92 <when value="two_plot">
90 <param name="first_plot" type="select" display="radio" label="Select the type of the top plot"> 93 <param name="first_plot" type="select" display="radio" label="Select the type of the top plot">
91 <option value="Counts">Counts</option> 94 <option value="Counts">Counts</option>
92 <option value="Coverage">Coverage</option> 95 <option value="Coverage">Coverage</option>
116 <param name="mergestrands" type="select" display="radio" label="Whether forward and reverse aligned reads should be merged or not in the histogram"> 119 <param name="mergestrands" type="select" display="radio" label="Whether forward and reverse aligned reads should be merged or not in the histogram">
117 <option value="nomerge">Do not merge</option> 120 <option value="nomerge">Do not merge</option>
118 <option value="merge">Merge forward and reverse reads</option> 121 <option value="merge">Merge forward and reverse reads</option>
119 </param> 122 </param>
120 </when> 123 </when>
124 <when value="cluster">
125 <param name="first_plot" type="hidden" value="Counts"/>
126 <param name="cluster" type="integer" label="Aggregation distance in nucleotides" value="1"
127 help="Sets the distance (in nt) below which reads are clustered to a single median position" />
128 </when>
121 </conditional> 129 </conditional>
122 <conditional name="ylimits_cond"> 130 <conditional name="ylimits_cond">
123 <param name="ylimits" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Do you wish to set an y axis limit to the plots?" 131 <param name="ylimits" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Do you wish to set an y axis limit to the plots?"
124 help="This limit won't be applied to size distribution plots"/> 132 help="This limit won't be applied to size distribution plots"/>
125 <when value="yes"> 133 <when value="yes">
138 </data> 146 </data>
139 <data format="pdf" name="output_pdf" label="small RNA maps" /> 147 <data format="pdf" name="output_pdf" label="small RNA maps" />
140 </outputs> 148 </outputs>
141 149
142 <tests> 150 <tests>
143 <test> 151 <test> <!-- 1 -->
144 <repeat name="series"> 152 <repeat name="series">
145 <param name="inputs" value="input1.bam" ftype="bam" /> 153 <param name="inputs" value="input1.bam" ftype="bam" />
146 <param name="normalization" value="1.0" /> 154 <param name="normalization" value="1.0" />
147 </repeat> 155 </repeat>
148 <repeat name="series"> 156 <repeat name="series">
149 <param name="inputs" value="input_new2.bam" ftype="bam" /> 157 <param name="inputs" value="input_new2.bam" ftype="bam" />
150 <param name="normalization" value="2.0" /> 158 <param name="normalization" value="2.0" />
151 </repeat> 159 </repeat>
152 <param name="minsize" value="0" /> 160 <param name="minsize" value="0" />
153 <param name="maxsize" value="10000" /> 161 <param name="maxsize" value="10000" />
154 <param name="cluster" value="0" />
155 <param name="plots_options_selector" value="one_plot" /> 162 <param name="plots_options_selector" value="one_plot" />
156 <param name="first_plot" value="Counts" /> 163 <param name="first_plot" value="Counts" />
157 <output file="input1_input2new_norm_1_2_counts.tab" name="output_tab" /> 164 <output file="input1_input2new_norm_1_2_counts.tab" name="output_tab" />
158 <output file="input1_input2new_norm_1_2_single_plot_counts.pdf" name="output_pdf" /> 165 <output file="input1_input2new_norm_1_2_single_plot_counts.pdf" name="output_pdf" />
159 </test> 166 </test>
160 <test> 167 <test> <!-- 2 -->
161 <repeat name="series"> 168 <repeat name="series">
162 <param name="inputs" value="input1.bam" ftype="bam" /> 169 <param name="inputs" value="input1.bam" ftype="bam" />
163 <param name="normalization" value="1.0" /> 170 <param name="normalization" value="1.0" />
164 </repeat> 171 </repeat>
165 <param name="minsize" value="0" /> 172 <param name="minsize" value="0" />
166 <param name="maxsize" value="10000" /> 173 <param name="maxsize" value="10000" />
167 <param name="cluster" value="0" />
168 <param name="ylimits" value="yes" /> 174 <param name="ylimits" value="yes" />
169 <param name="ymin" value="-5" /> 175 <param name="ymin" value="-5" />
170 <param name="ymax" value="5" /> 176 <param name="ymax" value="5" />
171 <param name="plots_options_selector" value="one_plot" /> 177 <param name="plots_options_selector" value="one_plot" />
172 <param name="first_plot" value="Counts" /> 178 <param name="first_plot" value="Counts" />
173 <output file="input1_counts_yminneg5_5.tab" name="output_tab" /> 179 <output file="input1_counts_yminneg5_5.tab" name="output_tab" />
174 <output file="input1_yminneg5_5_single_plot_counts.pdf" name="output_pdf" /> 180 <output file="input1_yminneg5_5_single_plot_counts.pdf" name="output_pdf" />
175 </test> 181 </test>
176 <test> 182 <test> <!-- 3 -->
177 <repeat name="series"> 183 <repeat name="series">
178 <param name="inputs" value="input1.bam" ftype="bam" /> 184 <param name="inputs" value="input1.bam" ftype="bam" />
179 <param name="normalization" value="1.0" /> 185 <param name="normalization" value="1.0" />
180 </repeat> 186 </repeat>
181 <param name="minsize" value="0" /> 187 <param name="minsize" value="0" />
182 <param name="maxsize" value="10000" /> 188 <param name="maxsize" value="10000" />
189 <param name="plots_options_selector" value="cluster" />
190 <param name="first_plot" value="Counts" />
183 <param name="cluster" value="5" /> 191 <param name="cluster" value="5" />
184 <param name="plots_options_selector" value="one_plot" /> 192 <output file="clustering.tab" name="output_tab" />
185 <param name="first_plot" value="Coverage" /> 193 <output file="clustering.pdf" name="output_pdf" />
186 <output file="input1_coverage_cluster5.tab" name="output_tab" /> 194 </test>
187 <output file="input1_cluster5_single_plot_coverage.pdf" name="output_pdf" /> 195 <test> <!-- 4 -->
188 </test>
189 <test>
190 <repeat name="series"> 196 <repeat name="series">
191 <param name="inputs" value="input1.bam" ftype="bam" /> 197 <param name="inputs" value="input1.bam" ftype="bam" />
192 <param name="normalization" value="1.0" /> 198 <param name="normalization" value="1.0" />
193 </repeat> 199 </repeat>
194 <param name="minsize" value="20" /> 200 <param name="minsize" value="20" />
195 <param name="maxsize" value="30" /> 201 <param name="maxsize" value="30" />
196 <param name="cluster" value="0" />
197 <param name="plots_options_selector" value="one_plot" /> 202 <param name="plots_options_selector" value="one_plot" />
198 <param name="first_plot" value="Size" /> 203 <param name="first_plot" value="Size" />
199 <output file="input1_min20_max30_size.tab" name="output_tab" /> 204 <output file="input1_min20_max30_size.tab" name="output_tab" />
200 <output file="input1_min20_max30_single_plot_size.pdf" name="output_pdf" /> 205 <output file="input1_min20_max30_single_plot_size.pdf" name="output_pdf" />
201 </test> 206 </test>
202 <test> 207 <test> <!-- 5 -->
203 <repeat name="series"> 208 <repeat name="series">
204 <param name="inputs" value="input1.bam" ftype="bam" /> 209 <param name="inputs" value="input1.bam" ftype="bam" />
205 <param name="normalization" value="1.0" /> 210 <param name="normalization" value="1.0" />
206 </repeat> 211 </repeat>
207 <param name="minsize" value="0" /> 212 <param name="minsize" value="0" />
208 <param name="maxsize" value="10000" /> 213 <param name="maxsize" value="10000" />
209 <param name="cluster" value="0" />
210 <param name="plots_options_selector" value="one_plot" /> 214 <param name="plots_options_selector" value="one_plot" />
211 <param name="first_plot" value="Mean" /> 215 <param name="first_plot" value="Mean" />
212 <output file="input1_mean.tab" name="output_tab" /> 216 <output file="input1_mean.tab" name="output_tab" />
213 <output file="input1__single_plot_mean.pdf" name="output_pdf" /> 217 <output file="input1__single_plot_mean.pdf" name="output_pdf" />
214 </test> 218 </test>
215 <test> 219 <test> <!-- 6 -->
216 <repeat name="series"> 220 <repeat name="series">
217 <param name="inputs" value="input1.bam" ftype="bam" /> 221 <param name="inputs" value="input1.bam" ftype="bam" />
218 <param name="normalization" value="1.0" /> 222 <param name="normalization" value="1.0" />
219 </repeat> 223 </repeat>
220 <param name="minsize" value="0" /> 224 <param name="minsize" value="0" />
221 <param name="maxsize" value="10000" /> 225 <param name="maxsize" value="10000" />
222 <param name="cluster" value="0" />
223 <param name="plots_options_selector" value="one_plot" /> 226 <param name="plots_options_selector" value="one_plot" />
224 <param name="first_plot" value="Median" /> 227 <param name="first_plot" value="Median" />
225 <output file="input1_median.tab" name="output_tab" /> 228 <output file="input1_median.tab" name="output_tab" />
226 <output file="input1_single_plot_median.pdf" name="output_pdf" /> 229 <output file="input1_single_plot_median.pdf" name="output_pdf" />
227 </test> 230 </test>
228 <test> 231 <test> <!-- 7 -->
229 <repeat name="series"> 232 <repeat name="series">
230 <param name="inputs" value="input1.bam" ftype="bam" /> 233 <param name="inputs" value="input1.bam" ftype="bam" />
231 <param name="normalization" value="1.0" /> 234 <param name="normalization" value="1.0" />
232 </repeat> 235 </repeat>
233 <repeat name="series"> 236 <repeat name="series">
234 <param name="inputs" value="input2.bam" ftype="bam" /> 237 <param name="inputs" value="input2.bam" ftype="bam" />
235 <param name="normalization" value="2.0" /> 238 <param name="normalization" value="2.0" />
236 </repeat> 239 </repeat>
237 <param name="minsize" value="0" /> 240 <param name="minsize" value="0" />
238 <param name="maxsize" value="10000" /> 241 <param name="maxsize" value="10000" />
239 <param name="cluster" value="0" />
240 <param name="plots_options_selector" value="one_plot" /> 242 <param name="plots_options_selector" value="one_plot" />
241 <param name="first_plot" value="Counts" /> 243 <param name="first_plot" value="Counts" />
242 <output file="input1_input2_norm_1_2_counts.tab" name="output_tab" /> 244 <output file="input1_input2_norm_1_2_counts.tab" name="output_tab" />
243 <output file="input1_input2_norm_1_2_single_plot_counts.pdf" name="output_pdf" /> 245 <output file="input1_input2_norm_1_2_single_plot_counts.pdf" name="output_pdf" />
244 </test> 246 </test>
245 <test> 247 <test> <!-- 8 -->
246 <repeat name="series"> 248 <repeat name="series">
247 <param name="inputs" value="input1.bam" ftype="bam" /> 249 <param name="inputs" value="input1.bam" ftype="bam" />
248 <param name="normalization" value="1.0" /> 250 <param name="normalization" value="1.0" />
249 </repeat> 251 </repeat>
250 <repeat name="series"> 252 <repeat name="series">
251 <param name="inputs" value="input2.bam" ftype="bam" /> 253 <param name="inputs" value="input2.bam" ftype="bam" />
252 <param name="normalization" value="1.0" /> 254 <param name="normalization" value="1.0" />
253 </repeat> 255 </repeat>
254 <param name="minsize" value="0" /> 256 <param name="minsize" value="0" />
255 <param name="maxsize" value="10000" /> 257 <param name="maxsize" value="10000" />
256 <param name="cluster" value="0" />
257 <param name="ylimits" value="yes" /> 258 <param name="ylimits" value="yes" />
258 <param name="ymin" value="-5" /> 259 <param name="ymin" value="-5" />
259 <param name="ymax" value="5" /> 260 <param name="ymax" value="5" />
260 <param name="plots_options_selector" value="two_plot" /> 261 <param name="plots_options_selector" value="two_plot" />
261 <param name="first_plot" value="Counts" /> 262 <param name="first_plot" value="Counts" />
262 <param name="extra_plot" value="Size" /> 263 <param name="extra_plot" value="Size" />
263 <output file="input1_input2_counts.tab" name="output_tab" /> 264 <output file="input1_input2_counts.tab" name="output_tab" />
264 <output file="input1_input2_size.tab" name="extra_output_tab" /> 265 <output file="input1_input2_size.tab" name="extra_output_tab" />
265 <output file="input1_input2_double_plot_counts_size_ylimneg5_5.pdf" name="output_pdf" /> 266 <output file="input1_input2_double_plot_counts_size_ylimneg5_5.pdf" name="output_pdf" />
266 </test> 267 </test>
267 <test> 268 <test> <!-- 9 -->
268 <repeat name="series"> 269 <repeat name="series">
269 <param name="inputs" value="input_single_chr.bam" ftype="bam" /> 270 <param name="inputs" value="input_single_chr.bam" ftype="bam" />
270 <param name="normalization" value="1.0" /> 271 <param name="normalization" value="1.0" />
271 </repeat> 272 </repeat>
272 <repeat name="series"> 273 <repeat name="series">
273 <param name="inputs" value="input_single_chr.bam" ftype="bam" /> 274 <param name="inputs" value="input_single_chr.bam" ftype="bam" />
274 <param name="normalization" value="1.0" /> 275 <param name="normalization" value="1.0" />
275 </repeat> 276 </repeat>
276 <repeat name="series"> 277 <repeat name="series">
277 <param name="inputs" value="input_single_chr.bam" ftype="bam" /> 278 <param name="inputs" value="input_single_chr.bam" ftype="bam" />
278 <param name="normalization" value="1.0" /> 279 <param name="normalization" value="1.0" />
279 </repeat> 280 </repeat>
280 <repeat name="series"> 281 <repeat name="series">
281 <param name="inputs" value="input_single_chr.bam" ftype="bam" /> 282 <param name="inputs" value="input_single_chr.bam" ftype="bam" />
282 <param name="normalization" value="1.0" /> 283 <param name="normalization" value="1.0" />
283 </repeat> 284 </repeat>
284 <repeat name="series"> 285 <repeat name="series">
285 <param name="inputs" value="input_single_chr.bam" ftype="bam" /> 286 <param name="inputs" value="input_single_chr.bam" ftype="bam" />
286 <param name="normalization" value="1.0" /> 287 <param name="normalization" value="1.0" />
287 </repeat> 288 </repeat>
288 <repeat name="series"> 289 <repeat name="series">
289 <param name="inputs" value="input_single_chr.bam" ftype="bam" /> 290 <param name="inputs" value="input_single_chr.bam" ftype="bam" />
290 <param name="normalization" value="1.0" /> 291 <param name="normalization" value="1.0" />
291 </repeat> 292 </repeat>
292 <param name="minsize" value="0" /> 293 <param name="minsize" value="0" />
293 <param name="maxsize" value="10000" /> 294 <param name="maxsize" value="10000" />
294 <param name="cluster" value="0" />
295 <param name="plots_options_selector" value="one_plot" /> 295 <param name="plots_options_selector" value="one_plot" />
296 <param name="first_plot" value="Coverage" /> 296 <param name="first_plot" value="Coverage" />
297 <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" />
298 <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" />
299 </test> 299 </test>
300 <test> 300 <test> <!-- 10 -->
301 <repeat name="series"> 301 <repeat name="series">
302 <param name="inputs" value="input1.bam" ftype="bam" /> 302 <param name="inputs" value="input1.bam" ftype="bam" />
303 <param name="normalization" value="1.0" /> 303 <param name="normalization" value="1.0" />
304 </repeat> 304 </repeat>
305 <repeat name="series"> 305 <repeat name="series">
306 <param name="inputs" value="input2.bam" ftype="bam" /> 306 <param name="inputs" value="input2.bam" ftype="bam" />
307 <param name="normalization" value="1.0" /> 307 <param name="normalization" value="1.0" />
308 </repeat> 308 </repeat>
309 <param name="minsize" value="0" /> 309 <param name="minsize" value="0" />
310 <param name="maxsize" value="10000" /> 310 <param name="maxsize" value="10000" />
311 <param name="cluster" value="0" />
312 <param name="plots_options_selector" value="global" /> 311 <param name="plots_options_selector" value="global" />
313 <param name="mergestrands" value="nomerge" /> 312 <param name="mergestrands" value="nomerge" />
314 <param name="first_plot" value="Size" /> 313 <param name="first_plot" value="Size" />
315 <output file="size.tab" name="output_tab" /> 314 <output file="size.tab" name="output_tab" />
316 <output file="global_nomerge.pdf" name="output_pdf" /> 315 <output file="global_nomerge.pdf" name="output_pdf" />
317 </test> 316 </test>
318 <test> 317 <test> <!-- 11 -->
319 <repeat name="series"> 318 <repeat name="series">
320 <param name="inputs" value="input1.bam" ftype="bam" /> 319 <param name="inputs" value="input1.bam" ftype="bam" />
321 <param name="normalization" value="1.0" /> 320 <param name="normalization" value="1.0" />
322 </repeat> 321 </repeat>
323 <repeat name="series"> 322 <repeat name="series">
324 <param name="inputs" value="input2.bam" ftype="bam" /> 323 <param name="inputs" value="input2.bam" ftype="bam" />
325 <param name="normalization" value="1.0" /> 324 <param name="normalization" value="1.0" />
326 </repeat> 325 </repeat>
327 <param name="minsize" value="0" /> 326 <param name="minsize" value="0" />
328 <param name="maxsize" value="10000" /> 327 <param name="maxsize" value="10000" />
329 <param name="cluster" value="0" />
330 <param name="plots_options_selector" value="global" /> 328 <param name="plots_options_selector" value="global" />
331 <param name="mergestrands" value="merge" /> 329 <param name="mergestrands" value="merge" />
332 <param name="first_plot" value="Size" /> 330 <param name="first_plot" value="Size" />
333 <output file="size.tab" name="output_tab" /> 331 <output file="size.tab" name="output_tab" />
334 <output file="global_merge.pdf" name="output_pdf" /> 332 <output file="global_merge.pdf" name="output_pdf" />