Mercurial > repos > devteam > fastq_groomer

comparison fastq_groomer.xml @ 6:10d4df6a9d94 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
author iuc
date Sun, 23 Nov 2025 17:50:18 +0000
parents e9f8633db0a2
children
comparison
equal deleted inserted replaced
5:e9f8633db0a2 6:10d4df6a9d94
97 <tests> 97 <tests>
98 <!-- Test fix-id by default --> 98 <!-- Test fix-id by default -->
99 <test> 99 <test>
100 <param name="input_file" value="fastq_invalid-line3" ftype="fastq" /> 100 <param name="input_file" value="fastq_invalid-line3" ftype="fastq" />
101 <param name="input_type" value="sanger" /> 101 <param name="input_type" value="sanger" />
102 <param name="options_type_selector" value="basic" /> 102 <conditional name="options_type">
103 <param name="options_type_selector" value="basic" />
104 </conditional>
103 <output name="output_file" file="fastq_invalid-line3_fixed" /> 105 <output name="output_file" file="fastq_invalid-line3_fixed" />
104 </test> 106 </test>
105 <!-- Test fix-id by setting the option --> 107 <!-- Test fix-id by setting the option -->
106 <test> 108 <test>
107 <param name="input_file" value="fastq_invalid-line3" ftype="fastq" /> 109 <param name="input_file" value="fastq_invalid-line3" ftype="fastq" />
108 <param name="input_type" value="sanger" /> 110 <param name="input_type" value="sanger" />
109 <param name="options_type_selector" value="advanced" /> 111 <conditional name="options_type">
110 <param name="fix_id" value="--fix-id" /> 112 <param name="options_type_selector" value="advanced" />
113 <param name="fix_id" value="true" />
114 </conditional>
111 <output name="output_file" file="fastq_invalid-line3_fixed" /> 115 <output name="output_file" file="fastq_invalid-line3_fixed" />
112 </test> 116 </test>
113 <!-- Test fix-id / option not set; expect failure --> 117 <!-- Test fix-id / option not set; expect failure -->
114 <test expect_failure="true"> 118 <test expect_failure="true">
115 <param name="input_file" value="fastq_invalid-line3" ftype="fastq" /> 119 <param name="input_file" value="fastq_invalid-line3" ftype="fastq" />
116 <param name="input_type" value="sanger" /> 120 <param name="input_type" value="sanger" />
117 <param name="options_type_selector" value="advanced" /> 121 <conditional name="options_type">
118 <param name="fix_id" value="--no-fix-id" /> 122 <param name="options_type_selector" value="advanced" />
123 <param name="fix_id" value="false" />
124 </conditional>
119 </test> 125 </test>
120 <!-- These tests include test files adapted from supplemental material in Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 2009 Dec 16. --> 126 <!-- These tests include test files adapted from supplemental material in Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res. 2009 Dec 16. -->
121 <!-- Test basic options --> 127 <!-- Test basic options -->
122 <test> 128 <test>
123 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" /> 129 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" />
124 <param name="input_type" value="sanger" /> 130 <param name="input_type" value="sanger" />
125 <param name="options_type_selector" value="basic" /> 131 <conditional name="options_type">
132 <param name="options_type_selector" value="basic" />
133 </conditional>
126 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" /> 134 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
127 </test> 135 </test>
128 <test> 136 <test>
129 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" /> 137 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" />
130 <param name="input_type" value="cssanger" /> 138 <param name="input_type" value="cssanger" />
131 <param name="options_type_selector" value="basic" /> 139 <conditional name="options_type">
140 <param name="options_type_selector" value="basic" />
141 </conditional>
132 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" /> 142 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" />
133 </test> 143 </test>
134 <test> 144 <test>
135 <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" /> 145 <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" />
136 <param name="input_type" value="illumina" /> 146 <param name="input_type" value="illumina" />
137 <param name="options_type_selector" value="basic" /> 147 <conditional name="options_type">
148 <param name="options_type_selector" value="basic" />
149 </conditional>
138 <output name="output_file" file="illumina_full_range_as_sanger.fastqsanger" /> 150 <output name="output_file" file="illumina_full_range_as_sanger.fastqsanger" />
139 </test> 151 </test>
140 <test> 152 <test>
141 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" /> 153 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" />
142 <param name="input_type" value="solexa" /> 154 <param name="input_type" value="solexa" />
143 <param name="options_type_selector" value="basic" /> 155 <conditional name="options_type">
156 <param name="options_type_selector" value="basic" />
157 </conditional>
144 <output name="output_file" file="solexa_full_range_as_sanger.fastqsanger" /> 158 <output name="output_file" file="solexa_full_range_as_sanger.fastqsanger" />
145 </test> 159 </test>
146 <test> 160 <test>
147 <param name="input_file" value="sanger_full_range_as_illumina.fastqillumina" ftype="fastq" /> 161 <param name="input_file" value="sanger_full_range_as_illumina.fastqillumina" ftype="fastq" />
148 <param name="input_type" value="sanger" /> 162 <param name="input_type" value="sanger" />
149 <param name="options_type_selector" value="basic" /> 163 <conditional name="options_type">
164 <param name="options_type_selector" value="basic" />
165 </conditional>
150 <output name="output_file" file="sanger_full_range_as_illumina.fastqillumina" /> 166 <output name="output_file" file="sanger_full_range_as_illumina.fastqillumina" />
151 </test> 167 </test>
152 <!-- Test grooming from illumina --> 168 <!-- Test grooming from illumina -->
153 <test> 169 <test>
154 <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" /> 170 <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" />
155 <param name="input_type" value="illumina" /> 171 <param name="input_type" value="illumina" />
156 <param name="options_type_selector" value="advanced" /> 172 <conditional name="options_type">
157 <param name="output_type" value="illumina" /> 173 <param name="options_type_selector" value="advanced" />
158 <param name="force_quality_encoding" value="None" /> 174 <param name="output_type" value="illumina" />
159 <param name="summarize_input" value="summarize_input" /> 175 <param name="force_quality_encoding" value="None" />
176 <param name="summarize_input" value="summarize_input" />
177 </conditional>
160 <output name="output_file" file="illumina_full_range_original_illumina.fastqillumina" /> 178 <output name="output_file" file="illumina_full_range_original_illumina.fastqillumina" />
161 </test> 179 </test>
162 <test> 180 <test>
163 <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" /> 181 <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" />
164 <param name="input_type" value="illumina" /> 182 <param name="input_type" value="illumina" />
165 <param name="options_type_selector" value="advanced" /> 183 <conditional name="options_type">
166 <param name="output_type" value="sanger" /> 184 <param name="options_type_selector" value="advanced" />
167 <param name="force_quality_encoding" value="None" /> 185 <param name="output_type" value="sanger" />
168 <param name="summarize_input" value="summarize_input" /> 186 <param name="force_quality_encoding" value="None" />
187 <param name="summarize_input" value="summarize_input" />
188 </conditional>
169 <output name="output_file" file="illumina_full_range_as_sanger.fastqsanger" /> 189 <output name="output_file" file="illumina_full_range_as_sanger.fastqsanger" />
170 </test> 190 </test>
171 <test> 191 <test>
172 <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" /> 192 <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" />
173 <param name="input_type" value="illumina" /> 193 <param name="input_type" value="illumina" />
174 <param name="options_type_selector" value="advanced" /> 194 <conditional name="options_type">
175 <param name="output_type" value="solexa" /> 195 <param name="options_type_selector" value="advanced" />
176 <param name="force_quality_encoding" value="None" /> 196 <param name="output_type" value="solexa" />
177 <param name="summarize_input" value="summarize_input" /> 197 <param name="force_quality_encoding" value="None" />
198 <param name="summarize_input" value="summarize_input" />
199 </conditional>
178 <output name="output_file" file="illumina_full_range_as_solexa.fastqsolexa" /> 200 <output name="output_file" file="illumina_full_range_as_solexa.fastqsolexa" />
179 </test> 201 </test>
180 <test> 202 <test>
181 <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" /> 203 <param name="input_file" value="illumina_full_range_original_illumina.fastqillumina" ftype="fastq" />
182 <param name="input_type" value="illumina" /> 204 <param name="input_type" value="illumina" />
183 <param name="options_type_selector" value="advanced" /> 205 <conditional name="options_type">
184 <param name="output_type" value="cssanger" /> 206 <param name="options_type_selector" value="advanced" />
185 <param name="force_quality_encoding" value="None" /> 207 <param name="output_type" value="cssanger" />
186 <param name="summarize_input" value="summarize_input" /> 208 <param name="force_quality_encoding" value="None" />
209 <param name="summarize_input" value="summarize_input" />
210 </conditional>
187 <output name="output_file" file="illumina_full_range_as_cssanger.fastqcssanger" /> 211 <output name="output_file" file="illumina_full_range_as_cssanger.fastqcssanger" />
188 </test> 212 </test>
189 <!-- Test grooming from sanger --> 213 <!-- Test grooming from sanger -->
190 <test> 214 <test>
191 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" /> 215 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" />
192 <param name="input_type" value="sanger" /> 216 <param name="input_type" value="sanger" />
193 <param name="options_type_selector" value="advanced" /> 217 <conditional name="options_type">
194 <param name="output_type" value="sanger" /> 218 <param name="options_type_selector" value="advanced" />
195 <param name="force_quality_encoding" value="None" /> 219 <param name="output_type" value="sanger" />
196 <param name="summarize_input" value="summarize_input" /> 220 <param name="force_quality_encoding" value="None" />
221 <param name="summarize_input" value="summarize_input" />
222 </conditional>
197 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" /> 223 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
198 </test> 224 </test>
199 <test> 225 <test>
200 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" /> 226 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" />
201 <param name="input_type" value="sanger" /> 227 <param name="input_type" value="sanger" />
202 <param name="options_type_selector" value="advanced" /> 228 <conditional name="options_type">
203 <param name="output_type" value="illumina" /> 229 <param name="options_type_selector" value="advanced" />
204 <param name="force_quality_encoding" value="None" /> 230 <param name="output_type" value="illumina" />
205 <param name="summarize_input" value="summarize_input" /> 231 <param name="force_quality_encoding" value="None" />
232 <param name="summarize_input" value="summarize_input" />
233 </conditional>
206 <output name="output_file" file="sanger_full_range_as_illumina.fastqillumina" /> 234 <output name="output_file" file="sanger_full_range_as_illumina.fastqillumina" />
207 </test> 235 </test>
208 <test> 236 <test>
209 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" /> 237 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" />
210 <param name="input_type" value="sanger" /> 238 <param name="input_type" value="sanger" />
211 <param name="options_type_selector" value="advanced" /> 239 <conditional name="options_type">
212 <param name="output_type" value="solexa" /> 240 <param name="options_type_selector" value="advanced" />
213 <param name="force_quality_encoding" value="None" /> 241 <param name="output_type" value="solexa" />
214 <param name="summarize_input" value="summarize_input" /> 242 <param name="force_quality_encoding" value="None" />
243 <param name="summarize_input" value="summarize_input" />
244 </conditional>
215 <output name="output_file" file="sanger_full_range_as_solexa.fastqsolexa" /> 245 <output name="output_file" file="sanger_full_range_as_solexa.fastqsolexa" />
216 </test> 246 </test>
217 <test> 247 <test>
218 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" /> 248 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" />
219 <param name="input_type" value="sanger" /> 249 <param name="input_type" value="sanger" />
220 <param name="options_type_selector" value="advanced" /> 250 <conditional name="options_type">
221 <param name="output_type" value="cssanger" /> 251 <param name="options_type_selector" value="advanced" />
222 <param name="force_quality_encoding" value="None" /> 252 <param name="output_type" value="cssanger" />
223 <param name="summarize_input" value="summarize_input" /> 253 <param name="force_quality_encoding" value="None" />
254 <param name="summarize_input" value="summarize_input" />
255 </conditional>
224 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" /> 256 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" />
225 </test> 257 </test>
226 <!-- Test grooming from solexa --> 258 <!-- Test grooming from solexa -->
227 <test> 259 <test>
228 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" /> 260 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" />
229 <param name="input_type" value="solexa" /> 261 <param name="input_type" value="solexa" />
230 <param name="options_type_selector" value="advanced" /> 262 <conditional name="options_type">
231 <param name="output_type" value="solexa" /> 263 <param name="options_type_selector" value="advanced" />
232 <param name="force_quality_encoding" value="None" /> 264 <param name="output_type" value="solexa" />
233 <param name="summarize_input" value="summarize_input" /> 265 <param name="force_quality_encoding" value="None" />
266 <param name="summarize_input" value="summarize_input" />
267 </conditional>
234 <output name="output_file" file="solexa_full_range_original_solexa.fastqsolexa" /> 268 <output name="output_file" file="solexa_full_range_original_solexa.fastqsolexa" />
235 </test> 269 </test>
236 <test> 270 <test>
237 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" /> 271 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" />
238 <param name="input_type" value="solexa" /> 272 <param name="input_type" value="solexa" />
239 <param name="options_type_selector" value="advanced" /> 273 <conditional name="options_type">
240 <param name="output_type" value="illumina" /> 274 <param name="options_type_selector" value="advanced" />
241 <param name="force_quality_encoding" value="None" /> 275 <param name="output_type" value="illumina" />
242 <param name="summarize_input" value="summarize_input" /> 276 <param name="force_quality_encoding" value="None" />
277 <param name="summarize_input" value="summarize_input" />
278 </conditional>
243 <output name="output_file" file="solexa_full_range_as_illumina.fastqillumina" /> 279 <output name="output_file" file="solexa_full_range_as_illumina.fastqillumina" />
244 </test> 280 </test>
245 <test> 281 <test>
246 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" /> 282 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" />
247 <param name="input_type" value="solexa" /> 283 <param name="input_type" value="solexa" />
248 <param name="options_type_selector" value="advanced" /> 284 <conditional name="options_type">
249 <param name="output_type" value="sanger" /> 285 <param name="options_type_selector" value="advanced" />
250 <param name="force_quality_encoding" value="None" /> 286 <param name="output_type" value="sanger" />
251 <param name="summarize_input" value="summarize_input" /> 287 <param name="force_quality_encoding" value="None" />
288 <param name="summarize_input" value="summarize_input" />
289 </conditional>
252 <output name="output_file" file="solexa_full_range_as_sanger.fastqsanger" /> 290 <output name="output_file" file="solexa_full_range_as_sanger.fastqsanger" />
253 </test> 291 </test>
254 <test> 292 <test>
255 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" /> 293 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" />
256 <param name="input_type" value="solexa" /> 294 <param name="input_type" value="solexa" />
257 <param name="options_type_selector" value="advanced" /> 295 <conditional name="options_type">
258 <param name="output_type" value="cssanger" /> 296 <param name="options_type_selector" value="advanced" />
259 <param name="force_quality_encoding" value="None" /> 297 <param name="output_type" value="cssanger" />
260 <param name="summarize_input" value="summarize_input" /> 298 <param name="force_quality_encoding" value="None" />
299 <param name="summarize_input" value="summarize_input" />
300 </conditional>
261 <output name="output_file" file="solexa_full_range_as_cssanger.fastqcssanger" /> 301 <output name="output_file" file="solexa_full_range_as_cssanger.fastqcssanger" />
262 </test> 302 </test>
263 <!-- Test grooming from cssanger --> 303 <!-- Test grooming from cssanger -->
264 <test> 304 <test>
265 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" /> 305 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" />
266 <param name="input_type" value="cssanger" /> 306 <param name="input_type" value="cssanger" />
267 <param name="options_type_selector" value="advanced" /> 307 <conditional name="options_type">
268 <param name="output_type" value="cssanger" /> 308 <param name="options_type_selector" value="advanced" />
269 <param name="force_quality_encoding" value="None" /> 309 <param name="output_type" value="cssanger" />
270 <param name="summarize_input" value="summarize_input" /> 310 <param name="force_quality_encoding" value="None" />
311 <param name="summarize_input" value="summarize_input" />
312 </conditional>
271 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" /> 313 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" />
272 </test> 314 </test>
273 <test> 315 <test>
274 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" /> 316 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" />
275 <param name="input_type" value="cssanger" /> 317 <param name="input_type" value="cssanger" />
276 <param name="options_type_selector" value="advanced" /> 318 <conditional name="options_type">
277 <param name="output_type" value="sanger" /> 319 <param name="options_type_selector" value="advanced" />
278 <param name="force_quality_encoding" value="None" /> 320 <param name="output_type" value="sanger" />
279 <param name="summarize_input" value="summarize_input" /> 321 <param name="force_quality_encoding" value="None" />
322 <param name="summarize_input" value="summarize_input" />
323 </conditional>
280 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" /> 324 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
281 </test> 325 </test>
282 <test> 326 <test>
283 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" /> 327 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" />
284 <param name="input_type" value="cssanger" /> 328 <param name="input_type" value="cssanger" />
285 <param name="options_type_selector" value="advanced" /> 329 <conditional name="options_type">
286 <param name="output_type" value="illumina" /> 330 <param name="options_type_selector" value="advanced" />
287 <param name="force_quality_encoding" value="None" /> 331 <param name="output_type" value="illumina" />
288 <param name="summarize_input" value="summarize_input" /> 332 <param name="force_quality_encoding" value="None" />
333 <param name="summarize_input" value="summarize_input" />
334 </conditional>
289 <output name="output_file" file="sanger_full_range_as_illumina.fastqillumina" /> 335 <output name="output_file" file="sanger_full_range_as_illumina.fastqillumina" />
290 </test> 336 </test>
291 <test> 337 <test>
292 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" /> 338 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastq" />
293 <param name="input_type" value="cssanger" /> 339 <param name="input_type" value="cssanger" />
294 <param name="options_type_selector" value="advanced" /> 340 <conditional name="options_type">
295 <param name="output_type" value="solexa" /> 341 <param name="options_type_selector" value="advanced" />
296 <param name="force_quality_encoding" value="None" /> 342 <param name="output_type" value="solexa" />
297 <param name="summarize_input" value="summarize_input" /> 343 <param name="force_quality_encoding" value="None" />
344 <param name="summarize_input" value="summarize_input" />
345 </conditional>
298 <output name="output_file" file="sanger_full_range_as_solexa.fastqsolexa" /> 346 <output name="output_file" file="sanger_full_range_as_solexa.fastqsolexa" />
299 </test> 347 </test>
300 <test> 348 <test>
301 <param name="input_file" value="sanger_full_range_as_cssanger_adapter_base_with_quality_score.fastqcssanger_fake_score" ftype="fastq" /> 349 <param name="input_file" value="sanger_full_range_as_cssanger_adapter_base_with_quality_score.fastqcssanger_fake_score" ftype="fastq" />
302 <param name="input_type" value="cssanger" /> 350 <param name="input_type" value="cssanger" />
303 <param name="options_type_selector" value="advanced" /> 351 <conditional name="options_type">
304 <param name="output_type" value="cssanger" /> 352 <param name="options_type_selector" value="advanced" />
305 <param name="force_quality_encoding" value="None" /> 353 <param name="output_type" value="cssanger" />
306 <param name="summarize_input" value="summarize_input" /> 354 <param name="force_quality_encoding" value="None" />
355 <param name="summarize_input" value="summarize_input" />
356 </conditional>
307 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" /> 357 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" />
308 </test> 358 </test>
309 <!-- Test fastq with line wrapping --> 359 <!-- Test fastq with line wrapping -->
310 <test> 360 <test>
311 <param name="input_file" value="wrapping_original_sanger.fastqsanger" ftype="fastq" /> 361 <param name="input_file" value="wrapping_original_sanger.fastqsanger" ftype="fastq" />
312 <param name="input_type" value="sanger" /> 362 <param name="input_type" value="sanger" />
313 <param name="options_type_selector" value="advanced" /> 363 <conditional name="options_type">
314 <param name="output_type" value="sanger" /> 364 <param name="options_type_selector" value="advanced" />
315 <param name="force_quality_encoding" value="None" /> 365 <param name="output_type" value="sanger" />
316 <param name="summarize_input" value="summarize_input" /> 366 <param name="force_quality_encoding" value="None" />
367 <param name="summarize_input" value="summarize_input" />
368 </conditional>
317 <output name="output_file" file="wrapping_as_sanger.fastqsanger" /> 369 <output name="output_file" file="wrapping_as_sanger.fastqsanger" />
318 </test> 370 </test>
319 <test> 371 <test>
320 <param name="input_file" value="wrapping_original_sanger.fastqsanger" ftype="fastq" /> 372 <param name="input_file" value="wrapping_original_sanger.fastqsanger" ftype="fastq" />
321 <param name="input_type" value="sanger" /> 373 <param name="input_type" value="sanger" />
322 <param name="options_type_selector" value="advanced" /> 374 <conditional name="options_type">
323 <param name="output_type" value="illumina" /> 375 <param name="options_type_selector" value="advanced" />
324 <param name="force_quality_encoding" value="None" /> 376 <param name="output_type" value="illumina" />
325 <param name="summarize_input" value="summarize_input" /> 377 <param name="force_quality_encoding" value="None" />
378 <param name="summarize_input" value="summarize_input" />
379 </conditional>
326 <output name="output_file" file="wrapping_as_illumina.fastqillumina" /> 380 <output name="output_file" file="wrapping_as_illumina.fastqillumina" />
327 </test> 381 </test>
328 <test> 382 <test>
329 <param name="input_file" value="wrapping_original_sanger.fastqsanger" ftype="fastq" /> 383 <param name="input_file" value="wrapping_original_sanger.fastqsanger" ftype="fastq" />
330 <param name="input_type" value="sanger" /> 384 <param name="input_type" value="sanger" />
331 <param name="options_type_selector" value="advanced" /> 385 <conditional name="options_type">
332 <param name="output_type" value="solexa" /> 386 <param name="options_type_selector" value="advanced" />
333 <param name="force_quality_encoding" value="None" /> 387 <param name="output_type" value="solexa" />
334 <param name="summarize_input" value="summarize_input" /> 388 <param name="force_quality_encoding" value="None" />
389 <param name="summarize_input" value="summarize_input" />
390 </conditional>
335 <output name="output_file" file="wrapping_as_solexa.fastqsolexa" /> 391 <output name="output_file" file="wrapping_as_solexa.fastqsolexa" />
336 </test> 392 </test>
337 <!-- Test forcing quality score encoding --> 393 <!-- Test forcing quality score encoding -->
338 <!-- Sanger, range 0 - 93 --> 394 <!-- Sanger, range 0 - 93 -->
339 <test> 395 <test>
340 <param name="input_file" value="sanger_full_range_as_decimal_sanger.fastqsanger" ftype="fastq" /> 396 <param name="input_file" value="sanger_full_range_as_decimal_sanger.fastqsanger" ftype="fastq" />
341 <param name="input_type" value="sanger" /> 397 <param name="input_type" value="sanger" />
342 <param name="options_type_selector" value="advanced" /> 398 <conditional name="options_type">
343 <param name="output_type" value="sanger" /> 399 <param name="options_type_selector" value="advanced" />
344 <param name="force_quality_encoding" value="ascii" /> 400 <param name="output_type" value="sanger" />
345 <param name="summarize_input" value="summarize_input" /> 401 <param name="force_quality_encoding" value="ascii" />
402 <param name="summarize_input" value="summarize_input" />
403 </conditional>
346 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" /> 404 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
347 </test> 405 </test>
348 <test> 406 <test>
349 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" /> 407 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastq" />
350 <param name="input_type" value="sanger" /> 408 <param name="input_type" value="sanger" />
351 <param name="options_type_selector" value="advanced" /> 409 <conditional name="options_type">
352 <param name="output_type" value="sanger" /> 410 <param name="options_type_selector" value="advanced" />
353 <param name="force_quality_encoding" value="decimal" /> 411 <param name="output_type" value="sanger" />
354 <param name="summarize_input" value="summarize_input" /> 412 <param name="force_quality_encoding" value="decimal" />
413 <param name="summarize_input" value="summarize_input" />
414 </conditional>
355 <output name="output_file" file="sanger_full_range_as_decimal_sanger.fastqsanger" /> 415 <output name="output_file" file="sanger_full_range_as_decimal_sanger.fastqsanger" />
356 </test> 416 </test>
357 <test> 417 <test>
358 <param name="input_file" value="sanger_full_range_as_tab_decimal_sanger.fastqsanger" ftype="fastq" /> 418 <param name="input_file" value="sanger_full_range_as_tab_decimal_sanger.fastqsanger" ftype="fastq" />
359 <param name="input_type" value="sanger" /> 419 <param name="input_type" value="sanger" />
360 <param name="options_type_selector" value="advanced" /> 420 <conditional name="options_type">
361 <param name="output_type" value="sanger" /> 421 <param name="options_type_selector" value="advanced" />
362 <param name="force_quality_encoding" value="ascii" /> 422 <param name="output_type" value="sanger" />
363 <param name="summarize_input" value="summarize_input" /> 423 <param name="force_quality_encoding" value="ascii" />
424 <param name="summarize_input" value="summarize_input" />
425 </conditional>
364 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" /> 426 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" />
365 </test> 427 </test>
366 <!-- Solexa, range -5 - 62 --> 428 <!-- Solexa, range -5 - 62 -->
367 <test> 429 <test>
368 <param name="input_file" value="solexa_full_range_as_decimal_solexa.fastqsolexa" ftype="fastq" /> 430 <param name="input_file" value="solexa_full_range_as_decimal_solexa.fastqsolexa" ftype="fastq" />
369 <param name="input_type" value="solexa" /> 431 <param name="input_type" value="solexa" />
370 <param name="options_type_selector" value="advanced" /> 432 <conditional name="options_type">
371 <param name="output_type" value="solexa" /> 433 <param name="options_type_selector" value="advanced" />
372 <param name="force_quality_encoding" value="ascii" /> 434 <param name="output_type" value="solexa" />
373 <param name="summarize_input" value="summarize_input" /> 435 <param name="force_quality_encoding" value="ascii" />
436 <param name="summarize_input" value="summarize_input" />
437 </conditional>
374 <output name="output_file" file="solexa_full_range_original_solexa.fastqsolexa" /> 438 <output name="output_file" file="solexa_full_range_original_solexa.fastqsolexa" />
375 </test> 439 </test>
376 <test> 440 <test>
377 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" /> 441 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastq" />
378 <param name="input_type" value="solexa" /> 442 <param name="input_type" value="solexa" />
379 <param name="options_type_selector" value="advanced" /> 443 <conditional name="options_type">
380 <param name="output_type" value="solexa" /> 444 <param name="options_type_selector" value="advanced" />
381 <param name="force_quality_encoding" value="decimal" /> 445 <param name="output_type" value="solexa" />
382 <param name="summarize_input" value="summarize_input" /> 446 <param name="force_quality_encoding" value="decimal" />
447 <param name="summarize_input" value="summarize_input" />
448 </conditional>
383 <output name="output_file" file="solexa_full_range_as_decimal_solexa.fastqsolexa" /> 449 <output name="output_file" file="solexa_full_range_as_decimal_solexa.fastqsolexa" />
384 </test> 450 </test>
385 <!-- compressed formats --> 451 <!-- compressed formats -->
386 <test> 452 <test>
387 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger.gz" ftype="fastq.gz" /> 453 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger.gz" ftype="fastq.gz" />
388 <param name="input_type" value="sanger" /> 454 <param name="input_type" value="sanger" />
389 <param name="options_type_selector" value="basic" /> 455 <conditional name="options_type">
456 <param name="options_type_selector" value="basic" />
457 </conditional>
390 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" decompress="true" /> 458 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" decompress="true" />
391 </test> 459 </test>
392 <test> 460 <test>
393 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger.bz2" ftype="fastq.bz2" /> 461 <param name="input_file" value="sanger_full_range_as_cssanger.fastqcssanger.bz2" ftype="fastq.bz2" />
394 <param name="input_type" value="cssanger" /> 462 <param name="input_type" value="cssanger" />
395 <param name="options_type_selector" value="basic" /> 463 <conditional name="options_type">
464 <param name="options_type_selector" value="basic" />
465 </conditional>
396 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" decompress="true" /> 466 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" decompress="true" />
397 </test> 467 </test>
398 </tests> 468 </tests>
399 <help><![CDATA[ 469 <help><![CDATA[
400 **What it does** 470 **What it does**