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comparison small_rna_maps.xml @ 9:3ea75c573429 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5
author artbio
date Tue, 07 Nov 2017 12:31:28 -0500
parents 1827b74f872b
children c3fb2a864526
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8:1827b74f872b 9:3ea75c573429
1 <tool id="small_rna_maps" name="small_rna_maps" version="2.3.0"> 1 <tool id="small_rna_maps" name="small_rna_maps" version="2.4.0">
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>
25 #for $sample in $inputs 25 #for $sample in $inputs
26 '$sample.name' 26 '$sample.name'
27 #end for 27 #end for
28 --minsize $minsize 28 --minsize $minsize
29 --maxsize $maxsize 29 --maxsize $maxsize
30 --cluster $cluster
30 #if str($plots_options.plots_options_selector ) == "two_plot": 31 #if str($plots_options.plots_options_selector ) == "two_plot":
31 --plot_methods '${plots_options.first_plot}' '${plots_options.extra_plot}' 32 --plot_methods '${plots_options.first_plot}' '${plots_options.extra_plot}'
32 --outputs '$output_tab' '$extra_output_tab' && 33 --outputs '$output_tab' '$extra_output_tab' &&
33 #elif str($plots_options.plots_options_selector ) == "global": 34 #elif str($plots_options.plots_options_selector ) == "global":
34 --plot_methods 'Size' 35 --plot_methods 'Size'
60 help="e.g. '1 0.75 1.23'. Values of the list map to the above selected files from bottom to top" /> 61 help="e.g. '1 0.75 1.23'. Values of the list map to the above selected files from bottom to top" />
61 <param name="minsize" type="integer" label="Minimal size of reads for inclusion in analysis" 62 <param name="minsize" type="integer" label="Minimal size of reads for inclusion in analysis"
62 value="0" help="default value: 0" /> 63 value="0" help="default value: 0" />
63 <param name="maxsize" type="integer" label="Maximal size of reads for inclusion in analysis" 64 <param name="maxsize" type="integer" label="Maximal size of reads for inclusion in analysis"
64 value="10000" help="default value: 10000" /> 65 value="10000" help="default value: 10000" />
66 <param name="cluster" type="integer" label="aggregation distance in nucleotides"
67 value="0" help="if not 0, sets the distance (in nt) below which data are clustered to a single median position" />
65 <conditional name="plots_options"> 68 <conditional name="plots_options">
66 <param name="plots_options_selector" type="select" display="radio" label="Plot Options"> 69 <param name="plots_options_selector" type="select" display="radio" label="Plot Options">
67 <option value="one_plot">Just one plot per chromosome</option> 70 <option value="one_plot">Just one plot per chromosome</option>
68 <option value="two_plot" selected="True">Two plots per chromosome</option> 71 <option value="two_plot" selected="True">Two plots per chromosome</option>
69 <option value="global">Global read size distributions of aligned reads</option> 72 <option value="global">Global read size distributions of aligned reads</option>
113 116
114 <tests> 117 <tests>
115 <test> 118 <test>
116 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> 119 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
117 <param name="minsize" value="0" /> 120 <param name="minsize" value="0" />
118 <param name="maxsize" value="10000" /> 121 <param name="cluster" value="5" />
122 <param name="maxsize" value="10000" />
123 <param name="plots_options_selector" value="one_plot" />
124 <param name="normalization" value="1 1" />
125 <param name="first_plot" value="Counts" />
126 <output file="count_cluster_5.tab" name="output_tab" />
127 <output file="count_cluster_5.pdf" name="output_pdf" />
128 </test>
129 <test>
130 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
131 <param name="minsize" value="0" />
132 <param name="maxsize" value="10000" />
133 <param name="cluster" value="0" />
119 <param name="plots_options_selector" value="global" /> 134 <param name="plots_options_selector" value="global" />
120 <param name="mergestrands" value="nomerge" /> 135 <param name="mergestrands" value="nomerge" />
121 <param name="first_plot" value="Size" /> 136 <param name="first_plot" value="Size" />
122 <param name="normalization" value="1 1" /> 137 <param name="normalization" value="1 1" />
123 <output file="size.tab" name="output_tab" /> 138 <output file="size.tab" name="output_tab" />
125 </test> 140 </test>
126 <test> 141 <test>
127 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> 142 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
128 <param name="minsize" value="0" /> 143 <param name="minsize" value="0" />
129 <param name="maxsize" value="10000" /> 144 <param name="maxsize" value="10000" />
145 <param name="cluster" value="0" />
130 <param name="plots_options_selector" value="global" /> 146 <param name="plots_options_selector" value="global" />
131 <param name="mergestrands" value="merge" /> 147 <param name="mergestrands" value="merge" />
132 <param name="first_plot" value="Size" /> 148 <param name="first_plot" value="Size" />
133 <param name="normalization" value="1 1" /> 149 <param name="normalization" value="1 1" />
134 <output file="size.tab" name="output_tab" /> 150 <output file="size.tab" name="output_tab" />
136 </test> 152 </test>
137 <test> 153 <test>
138 <param name="inputs" value="input1.bam" ftype="bam"/> 154 <param name="inputs" value="input1.bam" ftype="bam"/>
139 <param name="minsize" value="20" /> 155 <param name="minsize" value="20" />
140 <param name="maxsize" value="30" /> 156 <param name="maxsize" value="30" />
157 <param name="cluster" value="0" />
141 <param name="plots_options_selector" value="global" /> 158 <param name="plots_options_selector" value="global" />
142 <param name="mergestrands" value="merge" /> 159 <param name="mergestrands" value="merge" />
143 <param name="first_plot" value="Size" /> 160 <param name="first_plot" value="Size" />
144 <param name="normalization" value="1 1" /> 161 <param name="normalization" value="1 1" />
145 <output file="size20-30.tab" name="output_tab" /> 162 <output file="size20-30.tab" name="output_tab" />
147 </test> 164 </test>
148 <test> 165 <test>
149 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> 166 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
150 <param name="minsize" value="0" /> 167 <param name="minsize" value="0" />
151 <param name="maxsize" value="10000" /> 168 <param name="maxsize" value="10000" />
169 <param name="cluster" value="0" />
152 <param name="plots_options_selector" value="two_plot" /> 170 <param name="plots_options_selector" value="two_plot" />
153 <param name="first_plot" value="Counts" /> 171 <param name="first_plot" value="Counts" />
154 <param name="extra_plot" value="Mean" /> 172 <param name="extra_plot" value="Mean" />
155 <param name="normalization" value="1 1" /> 173 <param name="normalization" value="1 1" />
156 <output file="count.tab" name="output_tab" /> 174 <output file="count.tab" name="output_tab" />
159 </test> 177 </test>
160 <test> 178 <test>
161 <param name="inputs" value="input2.bam,input1.bam" ftype="bam"/> 179 <param name="inputs" value="input2.bam,input1.bam" ftype="bam"/>
162 <param name="minsize" value="20" /> 180 <param name="minsize" value="20" />
163 <param name="maxsize" value="30" /> 181 <param name="maxsize" value="30" />
182 <param name="cluster" value="0" />
164 <param name="plots_options_selector" value="two_plot" /> 183 <param name="plots_options_selector" value="two_plot" />
165 <param name="first_plot" value="Counts" /> 184 <param name="first_plot" value="Counts" />
166 <param name="extra_plot" value="Mean" /> 185 <param name="extra_plot" value="Mean" />
167 <param name="normalization" value="1 1" /> 186 <param name="normalization" value="1 1" />
168 <output file="count20-30.tab" name="output_tab" /> 187 <output file="count20-30.tab" name="output_tab" />
171 </test> 190 </test>
172 <test> 191 <test>
173 <param name="inputs" value="input1.bam,input1.bam" ftype="bam"/> 192 <param name="inputs" value="input1.bam,input1.bam" ftype="bam"/>
174 <param name="minsize" value="0" /> 193 <param name="minsize" value="0" />
175 <param name="maxsize" value="10000" /> 194 <param name="maxsize" value="10000" />
195 <param name="cluster" value="0" />
176 <param name="plots_options_selector" value="two_plot" /> 196 <param name="plots_options_selector" value="two_plot" />
177 <param name="first_plot" value="Counts" /> 197 <param name="first_plot" value="Counts" />
178 <param name="extra_plot" value="Mean" /> 198 <param name="extra_plot" value="Mean" />
179 <param name="normalization" value="1 1" /> 199 <param name="normalization" value="1 1" />
180 <output file="doubled_count.tab" name="output_tab" /> 200 <output file="doubled_count.tab" name="output_tab" />
183 </test> 203 </test>
184 <test> 204 <test>
185 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> 205 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
186 <param name="minsize" value="0" /> 206 <param name="minsize" value="0" />
187 <param name="maxsize" value="10000" /> 207 <param name="maxsize" value="10000" />
208 <param name="cluster" value="0" />
188 <param name="plots_options_selector" value="two_plot" /> 209 <param name="plots_options_selector" value="two_plot" />
189 <param name="first_plot" value="Counts" /> 210 <param name="first_plot" value="Counts" />
190 <param name="extra_plot" value="Median" /> 211 <param name="extra_plot" value="Median" />
191 <param name="normalization" value="1 1" /> 212 <param name="normalization" value="1 1" />
192 <output file="count.tab" name="output_tab" /> 213 <output file="count.tab" name="output_tab" />
195 </test> 216 </test>
196 <test> 217 <test>
197 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> 218 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
198 <param name="minsize" value="0" /> 219 <param name="minsize" value="0" />
199 <param name="maxsize" value="10000" /> 220 <param name="maxsize" value="10000" />
221 <param name="cluster" value="0" />
200 <param name="plots_options_selector" value="two_plot" /> 222 <param name="plots_options_selector" value="two_plot" />
201 <param name="first_plot" value="Counts" /> 223 <param name="first_plot" value="Counts" />
202 <param name="extra_plot" value="Coverage" /> 224 <param name="extra_plot" value="Coverage" />
203 <param name="normalization" value="1 1" /> 225 <param name="normalization" value="1 1" />
204 <output file="count.tab" name="output_tab" /> 226 <output file="count.tab" name="output_tab" />
207 </test> 229 </test>
208 <test> 230 <test>
209 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> 231 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
210 <param name="minsize" value="0" /> 232 <param name="minsize" value="0" />
211 <param name="maxsize" value="10000" /> 233 <param name="maxsize" value="10000" />
234 <param name="cluster" value="0" />
212 <param name="plots_options_selector" value="two_plot" /> 235 <param name="plots_options_selector" value="two_plot" />
213 <param name="first_plot" value="Counts" /> 236 <param name="first_plot" value="Counts" />
214 <param name="extra_plot" value="Size" /> 237 <param name="extra_plot" value="Size" />
215 <param name="normalization" value="1 1" /> 238 <param name="normalization" value="1 1" />
216 <output file="count.tab" name="output_tab" /> 239 <output file="count.tab" name="output_tab" />
219 </test> 242 </test>
220 <test> 243 <test>
221 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> 244 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
222 <param name="minsize" value="0" /> 245 <param name="minsize" value="0" />
223 <param name="maxsize" value="10000" /> 246 <param name="maxsize" value="10000" />
247 <param name="cluster" value="0" />
224 <param name="plots_options_selector" value="two_plot" /> 248 <param name="plots_options_selector" value="two_plot" />
225 <param name="first_plot" value="Size" /> 249 <param name="first_plot" value="Size" />
226 <param name="extra_plot" value="Counts" /> 250 <param name="extra_plot" value="Counts" />
227 <param name="normalization" value="1 1" /> 251 <param name="normalization" value="1 1" />
228 <output file="size.tab" name="output_tab" /> 252 <output file="size.tab" name="output_tab" />
231 </test> 255 </test>
232 <test> 256 <test>
233 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> 257 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
234 <param name="minsize" value="0" /> 258 <param name="minsize" value="0" />
235 <param name="maxsize" value="10000" /> 259 <param name="maxsize" value="10000" />
260 <param name="cluster" value="0" />
236 <param name="plots_options_selector" value="two_plot" /> 261 <param name="plots_options_selector" value="two_plot" />
237 <param name="first_plot" value="Size" /> 262 <param name="first_plot" value="Size" />
238 <param name="extra_plot" value="Counts" /> 263 <param name="extra_plot" value="Counts" />
239 <param name="normalization" value="1 0.75" /> 264 <param name="normalization" value="1 0.75" />
240 <output file="size.tab" name="output_tab" /> 265 <output file="size.tab" name="output_tab" />
242 <output file="size-count_normed.pdf" name="output_pdf" /> 267 <output file="size-count_normed.pdf" name="output_pdf" />
243 </test> 268 </test>
244 <test> 269 <test>
245 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> 270 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
246 <param name="minsize" value="0" /> 271 <param name="minsize" value="0" />
272 <param name="cluster" value="0" />
247 <param name="maxsize" value="10000" /> 273 <param name="maxsize" value="10000" />
248 <param name="plots_options_selector" value="one_plot" /> 274 <param name="plots_options_selector" value="one_plot" />
249 <param name="normalization" value="1 1" /> 275 <param name="normalization" value="1 1" />
250 <param name="first_plot" value="Counts" /> 276 <param name="first_plot" value="Counts" />
251 <output file="count.tab" name="output_tab" /> 277 <output file="count.tab" name="output_tab" />
253 </test> 279 </test>
254 <test> 280 <test>
255 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> 281 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
256 <param name="minsize" value="0" /> 282 <param name="minsize" value="0" />
257 <param name="maxsize" value="10000" /> 283 <param name="maxsize" value="10000" />
284 <param name="cluster" value="0" />
258 <param name="plots_options_selector" value="one_plot" /> 285 <param name="plots_options_selector" value="one_plot" />
259 <param name="first_plot" value="Size" /> 286 <param name="first_plot" value="Size" />
260 <param name="normalization" value="1 1" /> 287 <param name="normalization" value="1 1" />
261 <output file="size.tab" name="output_tab" /> 288 <output file="size.tab" name="output_tab" />
262 <output file="size.pdf" name="output_pdf" /> 289 <output file="size.pdf" name="output_pdf" />
263 </test> 290 </test>
264 <test> 291 <test>
265 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> 292 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
266 <param name="minsize" value="0" /> 293 <param name="minsize" value="0" />
267 <param name="maxsize" value="10000" /> 294 <param name="maxsize" value="10000" />
295 <param name="cluster" value="0" />
268 <param name="plots_options_selector" value="one_plot" /> 296 <param name="plots_options_selector" value="one_plot" />
269 <param name="first_plot" value="Coverage" /> 297 <param name="first_plot" value="Coverage" />
270 <param name="normalization" value="1 1" /> 298 <param name="normalization" value="1 1" />
271 <output file="coverage.tab" name="output_tab" /> 299 <output file="coverage.tab" name="output_tab" />
272 <output file="coverage.pdf" name="output_pdf" /> 300 <output file="coverage.pdf" name="output_pdf" />
273 </test> 301 </test>
274 <test> 302 <test>
275 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> 303 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
276 <param name="minsize" value="0" /> 304 <param name="minsize" value="0" />
277 <param name="maxsize" value="10000" /> 305 <param name="maxsize" value="10000" />
306 <param name="cluster" value="0" />
278 <param name="plots_options_selector" value="one_plot" /> 307 <param name="plots_options_selector" value="one_plot" />
279 <param name="first_plot" value="Coverage" /> 308 <param name="first_plot" value="Coverage" />
280 <param name="normalization" value="1 0.2" /> 309 <param name="normalization" value="1 0.2" />
281 <output file="coverage.tab" name="output_tab" /> 310 <output file="coverage.tab" name="output_tab" />
282 <output file="coverage_normed.pdf" name="output_pdf" /> 311 <output file="coverage_normed.pdf" name="output_pdf" />