Mercurial > repos > artbio > small_rna_maps

comparison small_rna_maps.xml @ 8:1827b74f872b draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
author artbio
date Mon, 23 Oct 2017 08:29:39 -0400
parents a96e6a7df2b7
children 3ea75c573429
comparison
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7:a96e6a7df2b7 8:1827b74f872b
1 <tool id="small_rna_maps" name="small_rna_maps" version="2.2.0"> 1 <tool id="small_rna_maps" name="small_rna_maps" version="2.3.0">
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>
23 #end for 23 #end for
24 --sample_names 24 --sample_names
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
29 --maxsize $maxsize
28 #if str($plots_options.plots_options_selector ) == "two_plot": 30 #if str($plots_options.plots_options_selector ) == "two_plot":
29 --plot_methods '${plots_options.first_plot}' '${plots_options.extra_plot}' 31 --plot_methods '${plots_options.first_plot}' '${plots_options.extra_plot}'
30 --outputs '$output_tab' '$extra_output_tab' && 32 --outputs '$output_tab' '$extra_output_tab' &&
31 #elif str($plots_options.plots_options_selector ) == "global": 33 #elif str($plots_options.plots_options_selector ) == "global":
32 --plot_methods 'Size' 34 --plot_methods 'Size'
54 ]]></command> 56 ]]></command>
55 <inputs> 57 <inputs>
56 <param name="inputs" type="data" format="bam" label="Select multiple alignments to parse" multiple="True"/> 58 <param name="inputs" type="data" format="bam" label="Select multiple alignments to parse" multiple="True"/>
57 <param name="normalization" type="text" label="Enter size/normalization factors as a space-separated list. Leave blank for no normalization (default)" 59 <param name="normalization" type="text" label="Enter size/normalization factors as a space-separated list. Leave blank for no normalization (default)"
58 help="e.g. '1 0.75 1.23'. Values of the list map to the above selected files from bottom to top" /> 60 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 value="0" help="default value: 0" />
63 <param name="maxsize" type="integer" label="Maximal size of reads for inclusion in analysis"
64 value="10000" help="default value: 10000" />
59 <conditional name="plots_options"> 65 <conditional name="plots_options">
60 <param name="plots_options_selector" type="select" display="radio" label="Plot Options"> 66 <param name="plots_options_selector" type="select" display="radio" label="Plot Options">
61 <option value="one_plot">Just one plot per chromosome</option> 67 <option value="one_plot">Just one plot per chromosome</option>
62 <option value="two_plot" selected="True">Two plots per chromosome</option> 68 <option value="two_plot" selected="True">Two plots per chromosome</option>
63 <option value="global">Global read size distributions of aligned reads</option> 69 <option value="global">Global read size distributions of aligned reads</option>
106 </outputs> 112 </outputs>
107 113
108 <tests> 114 <tests>
109 <test> 115 <test>
110 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> 116 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
117 <param name="minsize" value="0" />
118 <param name="maxsize" value="10000" />
111 <param name="plots_options_selector" value="global" /> 119 <param name="plots_options_selector" value="global" />
112 <param name="mergestrands" value="nomerge" /> 120 <param name="mergestrands" value="nomerge" />
113 <param name="first_plot" value="Size" /> 121 <param name="first_plot" value="Size" />
114 <param name="normalization" value="1 1" /> 122 <param name="normalization" value="1 1" />
115 <output file="size.tab" name="output_tab" /> 123 <output file="size.tab" name="output_tab" />
116 <output file="global_nomerge.pdf" name="output_pdf" /> 124 <output file="global_nomerge.pdf" name="output_pdf" />
117 </test> 125 </test>
118 <test> 126 <test>
119 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> 127 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
128 <param name="minsize" value="0" />
129 <param name="maxsize" value="10000" />
120 <param name="plots_options_selector" value="global" /> 130 <param name="plots_options_selector" value="global" />
121 <param name="mergestrands" value="merge" /> 131 <param name="mergestrands" value="merge" />
122 <param name="first_plot" value="Size" /> 132 <param name="first_plot" value="Size" />
123 <param name="normalization" value="1 1" /> 133 <param name="normalization" value="1 1" />
124 <output file="size.tab" name="output_tab" /> 134 <output file="size.tab" name="output_tab" />
125 <output file="global_merge.pdf" name="output_pdf" /> 135 <output file="global_merge.pdf" name="output_pdf" />
126 </test> 136 </test>
127 <test> 137 <test>
128 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> 138 <param name="inputs" value="input1.bam" ftype="bam"/>
139 <param name="minsize" value="20" />
140 <param name="maxsize" value="30" />
141 <param name="plots_options_selector" value="global" />
142 <param name="mergestrands" value="merge" />
143 <param name="first_plot" value="Size" />
144 <param name="normalization" value="1 1" />
145 <output file="size20-30.tab" name="output_tab" />
146 <output file="global_merge_20-30.pdf" name="output_pdf" />
147 </test>
148 <test>
149 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
150 <param name="minsize" value="0" />
151 <param name="maxsize" value="10000" />
129 <param name="plots_options_selector" value="two_plot" /> 152 <param name="plots_options_selector" value="two_plot" />
130 <param name="first_plot" value="Counts" /> 153 <param name="first_plot" value="Counts" />
131 <param name="extra_plot" value="Mean" /> 154 <param name="extra_plot" value="Mean" />
132 <param name="normalization" value="1 1" /> 155 <param name="normalization" value="1 1" />
133 <output file="count.tab" name="output_tab" /> 156 <output file="count.tab" name="output_tab" />
134 <output file="mean.tab" name="extra_output_tab" /> 157 <output file="mean.tab" name="extra_output_tab" />
135 <output file="count-mean.pdf" name="output_pdf" /> 158 <output file="count-mean.pdf" name="output_pdf" />
136 </test> 159 </test>
137 <test> 160 <test>
161 <param name="inputs" value="input2.bam,input1.bam" ftype="bam"/>
162 <param name="minsize" value="20" />
163 <param name="maxsize" value="30" />
164 <param name="plots_options_selector" value="two_plot" />
165 <param name="first_plot" value="Counts" />
166 <param name="extra_plot" value="Mean" />
167 <param name="normalization" value="1 1" />
168 <output file="count20-30.tab" name="output_tab" />
169 <output file="mean20-30.tab" name="extra_output_tab" />
170 <output file="count-mean-20-30.pdf" name="output_pdf" />
171 </test>
172 <test>
138 <param name="inputs" value="input1.bam,input1.bam" ftype="bam"/> 173 <param name="inputs" value="input1.bam,input1.bam" ftype="bam"/>
174 <param name="minsize" value="0" />
175 <param name="maxsize" value="10000" />
139 <param name="plots_options_selector" value="two_plot" /> 176 <param name="plots_options_selector" value="two_plot" />
140 <param name="first_plot" value="Counts" /> 177 <param name="first_plot" value="Counts" />
141 <param name="extra_plot" value="Mean" /> 178 <param name="extra_plot" value="Mean" />
142 <param name="normalization" value="1 1" /> 179 <param name="normalization" value="1 1" />
143 <output file="doubled_count.tab" name="output_tab" /> 180 <output file="doubled_count.tab" name="output_tab" />
144 <output file="doubled_mean.tab" name="extra_output_tab" /> 181 <output file="doubled_mean.tab" name="extra_output_tab" />
145 <output file="doubled_count-mean.pdf" name="output_pdf" /> 182 <output file="doubled_count-mean.pdf" name="output_pdf" />
146 </test> 183 </test>
147 <test> 184 <test>
148 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> 185 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
186 <param name="minsize" value="0" />
187 <param name="maxsize" value="10000" />
149 <param name="plots_options_selector" value="two_plot" /> 188 <param name="plots_options_selector" value="two_plot" />
150 <param name="first_plot" value="Counts" /> 189 <param name="first_plot" value="Counts" />
151 <param name="extra_plot" value="Median" /> 190 <param name="extra_plot" value="Median" />
152 <param name="normalization" value="1 1" /> 191 <param name="normalization" value="1 1" />
153 <output file="count.tab" name="output_tab" /> 192 <output file="count.tab" name="output_tab" />
154 <output file="median.tab" name="extra_output_tab" /> 193 <output file="median.tab" name="extra_output_tab" />
155 <output file="count-median.pdf" name="output_pdf" /> 194 <output file="count-median.pdf" name="output_pdf" />
156 </test> 195 </test>
157 <test> 196 <test>
158 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> 197 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
198 <param name="minsize" value="0" />
199 <param name="maxsize" value="10000" />
159 <param name="plots_options_selector" value="two_plot" /> 200 <param name="plots_options_selector" value="two_plot" />
160 <param name="first_plot" value="Counts" /> 201 <param name="first_plot" value="Counts" />
161 <param name="extra_plot" value="Coverage" /> 202 <param name="extra_plot" value="Coverage" />
162 <param name="normalization" value="1 1" /> 203 <param name="normalization" value="1 1" />
163 <output file="count.tab" name="output_tab" /> 204 <output file="count.tab" name="output_tab" />
164 <output file="coverage.tab" name="extra_output_tab" /> 205 <output file="coverage.tab" name="extra_output_tab" />
165 <output file="count-coverage.pdf" name="output_pdf" /> 206 <output file="count-coverage.pdf" name="output_pdf" />
166 </test> 207 </test>
167 <test> 208 <test>
168 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> 209 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
210 <param name="minsize" value="0" />
211 <param name="maxsize" value="10000" />
169 <param name="plots_options_selector" value="two_plot" /> 212 <param name="plots_options_selector" value="two_plot" />
170 <param name="first_plot" value="Counts" /> 213 <param name="first_plot" value="Counts" />
171 <param name="extra_plot" value="Size" /> 214 <param name="extra_plot" value="Size" />
172 <param name="normalization" value="1 1" /> 215 <param name="normalization" value="1 1" />
173 <output file="count.tab" name="output_tab" /> 216 <output file="count.tab" name="output_tab" />
174 <output file="size.tab" name="extra_output_tab" /> 217 <output file="size.tab" name="extra_output_tab" />
175 <output file="count-size.pdf" name="output_pdf" /> 218 <output file="count-size.pdf" name="output_pdf" />
176 </test> 219 </test>
177 <test> 220 <test>
178 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> 221 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
222 <param name="minsize" value="0" />
223 <param name="maxsize" value="10000" />
179 <param name="plots_options_selector" value="two_plot" /> 224 <param name="plots_options_selector" value="two_plot" />
180 <param name="first_plot" value="Size" /> 225 <param name="first_plot" value="Size" />
181 <param name="extra_plot" value="Counts" /> 226 <param name="extra_plot" value="Counts" />
182 <param name="normalization" value="1 1" /> 227 <param name="normalization" value="1 1" />
183 <output file="size.tab" name="output_tab" /> 228 <output file="size.tab" name="output_tab" />
184 <output file="count.tab" name="extra_output_tab" /> 229 <output file="count.tab" name="extra_output_tab" />
185 <output file="size-count.pdf" name="output_pdf" /> 230 <output file="size-count.pdf" name="output_pdf" />
186 </test> 231 </test>
187 <test> 232 <test>
188 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> 233 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
234 <param name="minsize" value="0" />
235 <param name="maxsize" value="10000" />
189 <param name="plots_options_selector" value="two_plot" /> 236 <param name="plots_options_selector" value="two_plot" />
190 <param name="first_plot" value="Size" /> 237 <param name="first_plot" value="Size" />
191 <param name="extra_plot" value="Counts" /> 238 <param name="extra_plot" value="Counts" />
192 <param name="normalization" value="1 0.75" /> 239 <param name="normalization" value="1 0.75" />
193 <output file="size.tab" name="output_tab" /> 240 <output file="size.tab" name="output_tab" />
194 <output file="count.tab" name="extra_output_tab" /> 241 <output file="count.tab" name="extra_output_tab" />
195 <output file="size-count_normed.pdf" name="output_pdf" /> 242 <output file="size-count_normed.pdf" name="output_pdf" />
196 </test> 243 </test>
197 <test> 244 <test>
198 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> 245 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
246 <param name="minsize" value="0" />
247 <param name="maxsize" value="10000" />
199 <param name="plots_options_selector" value="one_plot" /> 248 <param name="plots_options_selector" value="one_plot" />
200 <param name="normalization" value="1 1" /> 249 <param name="normalization" value="1 1" />
201 <param name="first_plot" value="Counts" /> 250 <param name="first_plot" value="Counts" />
202 <output file="count.tab" name="output_tab" /> 251 <output file="count.tab" name="output_tab" />
203 <output file="count.pdf" name="output_pdf" /> 252 <output file="count.pdf" name="output_pdf" />
204 </test> 253 </test>
205 <test> 254 <test>
206 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> 255 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
256 <param name="minsize" value="0" />
257 <param name="maxsize" value="10000" />
207 <param name="plots_options_selector" value="one_plot" /> 258 <param name="plots_options_selector" value="one_plot" />
208 <param name="first_plot" value="Size" /> 259 <param name="first_plot" value="Size" />
209 <param name="normalization" value="1 1" /> 260 <param name="normalization" value="1 1" />
210 <output file="size.tab" name="output_tab" /> 261 <output file="size.tab" name="output_tab" />
211 <output file="size.pdf" name="output_pdf" /> 262 <output file="size.pdf" name="output_pdf" />
212 </test> 263 </test>
213 <test> 264 <test>
214 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> 265 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
266 <param name="minsize" value="0" />
267 <param name="maxsize" value="10000" />
215 <param name="plots_options_selector" value="one_plot" /> 268 <param name="plots_options_selector" value="one_plot" />
216 <param name="first_plot" value="Coverage" /> 269 <param name="first_plot" value="Coverage" />
217 <param name="normalization" value="1 1" /> 270 <param name="normalization" value="1 1" />
218 <output file="coverage.tab" name="output_tab" /> 271 <output file="coverage.tab" name="output_tab" />
219 <output file="coverage.pdf" name="output_pdf" /> 272 <output file="coverage.pdf" name="output_pdf" />
220 </test> 273 </test>
221 <test> 274 <test>
222 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/> 275 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
276 <param name="minsize" value="0" />
277 <param name="maxsize" value="10000" />
223 <param name="plots_options_selector" value="one_plot" /> 278 <param name="plots_options_selector" value="one_plot" />
224 <param name="first_plot" value="Coverage" /> 279 <param name="first_plot" value="Coverage" />
225 <param name="normalization" value="1 0.2" /> 280 <param name="normalization" value="1 0.2" />
226 <output file="coverage.tab" name="output_tab" /> 281 <output file="coverage.tab" name="output_tab" />
227 <output file="coverage_normed.pdf" name="output_pdf" /> 282 <output file="coverage_normed.pdf" name="output_pdf" />