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comparison fastq_filter.xml @ 6:ff7d49ec777f 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_filter commit a5766d27dcddd1891766476a913d0eae1ec7a3c9
author iuc
date Sun, 23 Nov 2025 17:50:05 +0000
parents 144275714590
children
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5:144275714590 6:ff7d49ec777f
107 <param name="max_size" value="0"/> 107 <param name="max_size" value="0"/>
108 <param name="min_quality" value="0"/> 108 <param name="min_quality" value="0"/>
109 <param name="max_quality" value="0"/> 109 <param name="max_quality" value="0"/>
110 <param name="max_num_deviants" value="0"/> 110 <param name="max_num_deviants" value="0"/>
111 <param name="paired_end" value="false"/> 111 <param name="paired_end" value="false"/>
112 <param name="base_offset_type" value="offsets_absolute"/> 112 <repeat name="fastq_filters">
113 <param name="left_column_offset" value="0"/> 113 <conditional name="offset_type">
114 <param name="right_column_offset" value="0"/> 114 <param name="base_offset_type" value="offsets_absolute"/>
115 <param name="score_operation" value="min"/> 115 <param name="left_column_offset" value="0"/>
116 <param name="score_comparison" value="&gt;="/> 116 <param name="right_column_offset" value="0"/>
117 <param name="score" value="0"/> 117 </conditional>
118 <param name="score_operation" value="min"/>
119 <param name="score_comparison" value="&gt;="/>
120 <param name="score" value="0"/>
121 </repeat>
118 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> 122 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
119 </test> 123 </test>
120 <!-- Do nothing filter compressed --> 124 <!-- Do nothing filter compressed -->
121 <test> 125 <test>
122 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger.gz" ftype="fastqsanger.gz"/> 126 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger.gz" ftype="fastqsanger.gz"/>
124 <param name="max_size" value="0"/> 128 <param name="max_size" value="0"/>
125 <param name="min_quality" value="0"/> 129 <param name="min_quality" value="0"/>
126 <param name="max_quality" value="0"/> 130 <param name="max_quality" value="0"/>
127 <param name="max_num_deviants" value="0"/> 131 <param name="max_num_deviants" value="0"/>
128 <param name="paired_end" value="false"/> 132 <param name="paired_end" value="false"/>
129 <param name="base_offset_type" value="offsets_absolute"/> 133 <repeat name="fastq_filters">
130 <param name="left_column_offset" value="0"/> 134 <conditional name="offset_type">
131 <param name="right_column_offset" value="0"/> 135 <param name="base_offset_type" value="offsets_absolute"/>
132 <param name="score_operation" value="min"/> 136 <param name="left_column_offset" value="0"/>
133 <param name="score_comparison" value="&gt;="/> 137 <param name="right_column_offset" value="0"/>
134 <param name="score" value="0"/> 138 </conditional>
139 <param name="score_operation" value="min"/>
140 <param name="score_comparison" value="&gt;="/>
141 <param name="score" value="0"/>
142 </repeat>
135 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger.gz" ftype="fastqsanger.gz" decompress="true"/> 143 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger.gz" ftype="fastqsanger.gz" decompress="true"/>
136 </test> 144 </test>
137 <!-- crippled input types prevent this test <test> 145 <!-- crippled input types prevent this test <test>
138 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastqsolexa"/> 146 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastqsolexa"/>
139 <param name="min_size" value="0"/> 147 <param name="min_size" value="0"/>
157 <param name="max_size" value="0"/> 165 <param name="max_size" value="0"/>
158 <param name="min_quality" value="0"/> 166 <param name="min_quality" value="0"/>
159 <param name="max_quality" value="0"/> 167 <param name="max_quality" value="0"/>
160 <param name="max_num_deviants" value="0"/> 168 <param name="max_num_deviants" value="0"/>
161 <param name="paired_end" value="false"/> 169 <param name="paired_end" value="false"/>
162 <param name="base_offset_type" value="offsets_absolute"/> 170 <repeat name="fastq_filters">
163 <param name="left_column_offset" value="0"/> 171 <conditional name="offset_type">
164 <param name="right_column_offset" value="0"/> 172 <param name="base_offset_type" value="offsets_absolute"/>
165 <param name="score_operation" value="min"/> 173 <param name="left_column_offset" value="0"/>
166 <param name="score_comparison" value="&gt;="/> 174 <param name="right_column_offset" value="0"/>
167 <param name="score" value="0"/> 175 </conditional>
176 <param name="score_operation" value="min"/>
177 <param name="score_comparison" value="&gt;="/>
178 <param name="score" value="0"/>
179 </repeat>
168 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastqcssanger" /> 180 <output name="output_file" file="sanger_full_range_as_cssanger.fastqcssanger" ftype="fastqcssanger" />
169 </test> 181 </test>
170 <!-- Remove all Filter --> 182 <!-- Remove all Filter -->
171 <test> 183 <test>
172 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger"/> 184 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger"/>
174 <param name="max_size" value="0"/> 186 <param name="max_size" value="0"/>
175 <param name="min_quality" value="1"/> 187 <param name="min_quality" value="1"/>
176 <param name="max_quality" value="0"/> 188 <param name="max_quality" value="0"/>
177 <param name="max_num_deviants" value="0"/> 189 <param name="max_num_deviants" value="0"/>
178 <param name="paired_end" value="false"/> 190 <param name="paired_end" value="false"/>
179 <param name="base_offset_type" value="offsets_absolute"/> 191 <repeat name="fastq_filters">
180 <param name="left_column_offset" value="0"/> 192 <conditional name="offset_type">
181 <param name="right_column_offset" value="0"/> 193 <param name="base_offset_type" value="offsets_absolute"/>
182 <param name="score_operation" value="min"/> 194 <param name="left_column_offset" value="0"/>
183 <param name="score_comparison" value="&gt;="/> 195 <param name="right_column_offset" value="0"/>
184 <param name="score" value="0"/> 196 </conditional>
197 <param name="score_operation" value="min"/>
198 <param name="score_comparison" value="&gt;="/>
199 <param name="score" value="0"/>
200 </repeat>
185 <output name="output_file" file="empty_file.dat" ftype="fastqsanger" /> 201 <output name="output_file" file="empty_file.dat" ftype="fastqsanger" />
186 </test> 202 </test>
187 <!-- crippled input types prevent this test <test> 203 <!-- crippled input types prevent this test <test>
188 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastqsolexa"/> 204 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastqsolexa"/>
189 <param name="min_size" value="0"/> 205 <param name="min_size" value="0"/>
207 <param name="max_size" value="0"/> 223 <param name="max_size" value="0"/>
208 <param name="min_quality" value="1"/> 224 <param name="min_quality" value="1"/>
209 <param name="max_quality" value="0"/> 225 <param name="max_quality" value="0"/>
210 <param name="max_num_deviants" value="1"/> 226 <param name="max_num_deviants" value="1"/>
211 <param name="paired_end" value="false"/> 227 <param name="paired_end" value="false"/>
212 <param name="base_offset_type" value="offsets_absolute"/> 228 <repeat name="fastq_filters">
213 <param name="left_column_offset" value="0"/> 229 <conditional name="offset_type">
214 <param name="right_column_offset" value="0"/> 230 <param name="base_offset_type" value="offsets_absolute"/>
215 <param name="score_operation" value="min"/> 231 <param name="left_column_offset" value="0"/>
216 <param name="score_comparison" value="&gt;="/> 232 <param name="right_column_offset" value="0"/>
217 <param name="score" value="0"/> 233 </conditional>
234 <param name="score_operation" value="min"/>
235 <param name="score_comparison" value="&gt;="/>
236 <param name="score" value="0"/>
237 </repeat>
218 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> 238 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
219 </test> 239 </test>
220 <!-- crippled input types prevent this test<test> 240 <!-- crippled input types prevent this test<test>
221 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastqsolexa"/> 241 <param name="input_file" value="solexa_full_range_original_solexa.fastqsolexa" ftype="fastqsolexa"/>
222 <param name="min_size" value="0"/> 242 <param name="min_size" value="0"/>
240 <param name="max_size" value="0"/> 260 <param name="max_size" value="0"/>
241 <param name="min_quality" value="0"/> 261 <param name="min_quality" value="0"/>
242 <param name="max_quality" value="0"/> 262 <param name="max_quality" value="0"/>
243 <param name="max_num_deviants" value="0"/> 263 <param name="max_num_deviants" value="0"/>
244 <param name="paired_end" value="false"/> 264 <param name="paired_end" value="false"/>
245 <param name="base_offset_type" value="offsets_absolute"/> 265 <repeat name="fastq_filters">
246 <param name="left_column_offset" value="1"/> 266 <conditional name="offset_type">
247 <param name="right_column_offset" value="1"/> 267 <param name="base_offset_type" value="offsets_absolute"/>
248 <param name="score_operation" value="min"/> 268 <param name="left_column_offset" value="1"/>
249 <param name="score_comparison" value="&gt;="/> 269 <param name="right_column_offset" value="1"/>
250 <param name="score" value="1"/> 270 </conditional>
251 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> 271 <param name="score_operation" value="min"/>
252 </test> 272 <param name="score_comparison" value="&gt;="/>
253 <test> 273 <param name="score" value="1"/>
254 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger"/> 274 </repeat>
255 <param name="min_size" value="0"/> 275 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
256 <param name="max_size" value="0"/> 276 </test>
257 <param name="min_quality" value="0"/> 277 <test>
258 <param name="max_quality" value="0"/> 278 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger"/>
259 <param name="max_num_deviants" value="0"/> 279 <param name="min_size" value="0"/>
260 <param name="paired_end" value="false"/> 280 <param name="max_size" value="0"/>
261 <param name="base_offset_type" value="offsets_absolute"/> 281 <param name="min_quality" value="0"/>
262 <param name="left_column_offset" value="1"/> 282 <param name="max_quality" value="0"/>
263 <param name="right_column_offset" value="1"/> 283 <param name="max_num_deviants" value="0"/>
264 <param name="score_operation" value="max"/> 284 <param name="paired_end" value="false"/>
265 <param name="score_comparison" value="&lt;="/> 285 <repeat name="fastq_filters">
266 <param name="score" value="92"/> 286 <conditional name="offset_type">
287 <param name="base_offset_type" value="offsets_absolute"/>
288 <param name="left_column_offset" value="1"/>
289 <param name="right_column_offset" value="1"/>
290 </conditional>
291 <param name="score_operation" value="max"/>
292 <param name="score_comparison" value="&lt;="/>
293 <param name="score" value="92"/>
294 </repeat>
267 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> 295 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
268 </test> 296 </test>
269 <!-- percent based offsets --> 297 <!-- percent based offsets -->
270 <test> 298 <test>
271 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger"/> 299 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger"/>
273 <param name="max_size" value="0"/> 301 <param name="max_size" value="0"/>
274 <param name="min_quality" value="0"/> 302 <param name="min_quality" value="0"/>
275 <param name="max_quality" value="0"/> 303 <param name="max_quality" value="0"/>
276 <param name="max_num_deviants" value="0"/> 304 <param name="max_num_deviants" value="0"/>
277 <param name="paired_end" value="false"/> 305 <param name="paired_end" value="false"/>
278 <param name="base_offset_type" value="offsets_percent"/> 306 <repeat name="fastq_filters">
279 <param name="left_column_offset" value="1.075"/> 307 <conditional name="offset_type">
280 <param name="right_column_offset" value="1.075"/> 308 <param name="base_offset_type" value="offsets_percent"/>
281 <param name="score_operation" value="min"/> 309 <param name="left_column_offset" value="1.075"/>
282 <param name="score_comparison" value="&gt;="/> 310 <param name="right_column_offset" value="1.075"/>
283 <param name="score" value="1"/> 311 </conditional>
312 <param name="score_operation" value="min"/>
313 <param name="score_comparison" value="&gt;="/>
314 <param name="score" value="1"/>
315 </repeat>
284 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> 316 <output name="output_file" file="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
285 </test> 317 </test>
286 <test> 318 <test>
287 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger"/> 319 <param name="input_file" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger"/>
288 <param name="min_size" value="0"/> 320 <param name="min_size" value="0"/>
289 <param name="max_size" value="0"/> 321 <param name="max_size" value="0"/>
290 <param name="min_quality" value="0"/> 322 <param name="min_quality" value="0"/>
291 <param name="max_quality" value="0"/> 323 <param name="max_quality" value="0"/>
292 <param name="max_num_deviants" value="0"/> 324 <param name="max_num_deviants" value="0"/>
293 <param name="paired_end" value="true"/> 325 <param name="paired_end" value="true"/>
294 <param name="base_offset_type" value="offsets_percent"/> 326 <repeat name="fastq_filters">
295 <param name="left_column_offset" value="1"/> 327 <conditional name="offset_type">
296 <param name="right_column_offset" value="1"/> 328 <param name="base_offset_type" value="offsets_percent"/>
297 <param name="score_operation" value="min"/> 329 <param name="left_column_offset" value="1"/>
298 <param name="score_comparison" value="&gt;="/> 330 <param name="right_column_offset" value="1"/>
299 <param name="score" value="1"/> 331 </conditional>
332 <param name="score_operation" value="min"/>
333 <param name="score_comparison" value="&gt;="/>
334 <param name="score" value="1"/>
335 </repeat>
300 <output name="output_file" file="empty_file.dat" ftype="fastqsanger" /> 336 <output name="output_file" file="empty_file.dat" ftype="fastqsanger" />
301 </test> 337 </test>
302 </tests> 338 </tests>
303 <help><![CDATA[ 339 <help><![CDATA[
304 This tool allows you to build complex filters to be applied to each read in a FASTQ file. 340 This tool allows you to build complex filters to be applied to each read in a FASTQ file.