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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit ade7dfd3c1f1c5369e338013c5ca2ec7115cafe6-dirty
author bebatut
date Wed, 27 Jan 2016 03:55:09 -0500
parents 10ac5c567b73
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3:10ac5c567b73 4:acaf871de2ea
23 ]]> 23 ]]>
24 </version_command> 24 </version_command>
25 25
26 <command> 26 <command>
27 <![CDATA[ 27 <![CDATA[
28 perl \${PRINSEQ_DIR}/prinseq-lite.pl 28 perl \${PRINSEQ_DIR}/prinseq-lite.pl
29 -fastq $sequence_to_control_file 29 #if $seq_type.seq_type_opt == 'single':
30 -fastq "$seq_type.input_singles"
31 #if $seq_type.input_singles.ext == 'fastqillumina':
32 -phred64
33 #end if
34 #else:
35 -fastq "$seq_type.input_mate1"
36 -fastq2 "$seq_type.input_mate2"
37 #if $seq_type.input_mate1.ext != $seq_type.input_mate2.ext:
38 #import sys
39 #silent sys.stderr.write( 'Both pairs from your paired-end library need to be from the same filetype.' )
40 #end if
41 #if $seq_type.input_mate1.ext == 'fastqillumina':
42 -phred64
43 #end if
44 #end if
45
30 -out_good good_sequences 46 -out_good good_sequences
31 -out_bad rejected_sequences 47 -out_bad rejected_sequences
32 48
33 #if $filter_treatments.apply_filter_treatments : 49 #if $filter_treatments.apply_filter_treatments :
34 #set length_filter_treatments=$filter_treatments.length_filter_treatments 50 #set length_filter_treatments=$filter_treatments.length_filter_treatments
35 #if $length_filter_treatments.apply_length_filter_treatments : 51 #if $length_filter_treatments.apply_length_filter_treatments :
36 #set min_length_filter_treatments=$length_filter_treatments.min_length_filter_treatments 52 #set min_length_filter_treatments=$length_filter_treatments.min_length_filter_treatments
37 #if $min_length_filter_treatments.apply_min_length_filter_treatments : 53 #if $min_length_filter_treatments.apply_min_length_filter_treatments :
38 -min_len $min_length_filter_treatments.min_length_filter_treatment_value 54 -min_len $min_length_filter_treatments.min_length_filter_treatment_value
39 #end if 55 #end if
56
40 #set max_length_filter_treatments=$length_filter_treatments.max_length_filter_treatments 57 #set max_length_filter_treatments=$length_filter_treatments.max_length_filter_treatments
41 #if $max_length_filter_treatments.apply_max_length_filter_treatments : 58 #if $max_length_filter_treatments.apply_max_length_filter_treatments :
42 -max_len $max_length_filter_treatments.max_length_filter_treatment_value 59 -max_len $max_length_filter_treatments.max_length_filter_treatment_value
43 #end if 60 #end if
44 #end if 61 #end if
47 #if $quality_filter_treatments.apply_quality_filter_treatments: 64 #if $quality_filter_treatments.apply_quality_filter_treatments:
48 #set min_quality_filter_treatments=$quality_filter_treatments.min_quality_filter_treatments 65 #set min_quality_filter_treatments=$quality_filter_treatments.min_quality_filter_treatments
49 #if $min_quality_filter_treatments.apply_min_quality_filter_treatments : 66 #if $min_quality_filter_treatments.apply_min_quality_filter_treatments :
50 -min_qual_score $min_quality_filter_treatments.min_quality_filter_treatment_value 67 -min_qual_score $min_quality_filter_treatments.min_quality_filter_treatment_value
51 #end if 68 #end if
69
52 #set max_quality_filter_treatments=$quality_filter_treatments.max_quality_filter_treatments 70 #set max_quality_filter_treatments=$quality_filter_treatments.max_quality_filter_treatments
53 #if $max_quality_filter_treatments.apply_max_quality_filter_treatments : 71 #if $max_quality_filter_treatments.apply_max_quality_filter_treatments :
54 -max_qual_score $max_quality_filter_treatments.max_quality_filter_treatment_value 72 -max_qual_score $max_quality_filter_treatments.max_quality_filter_treatment_value
55 #end if 73 #end if
74
56 #set mean_quality_filter_treatments=$quality_filter_treatments.mean_quality_filter_treatments 75 #set mean_quality_filter_treatments=$quality_filter_treatments.mean_quality_filter_treatments
57 #if $mean_quality_filter_treatments.apply_mean_quality_filter_treatments: 76 #if $mean_quality_filter_treatments.apply_mean_quality_filter_treatments:
58 #set min_mean_quality_filter_treatments=$mean_quality_filter_treatments.min_mean_quality_filter_treatments 77 #set min_mean_quality_filter_treatments=$mean_quality_filter_treatments.min_mean_quality_filter_treatments
59 #if $min_mean_quality_filter_treatments.apply_min_mean_quality_filter_treatments: 78 #if $min_mean_quality_filter_treatments.apply_min_mean_quality_filter_treatments:
60 -min_qual_mean $min_mean_quality_filter_treatments.min_mean_quality_filter_treatment_value 79 -min_qual_mean $min_mean_quality_filter_treatments.min_mean_quality_filter_treatment_value
61 #end if 80 #end if
81
62 #set max_mean_quality_filter_treatments=$mean_quality_filter_treatments.max_mean_quality_filter_treatments 82 #set max_mean_quality_filter_treatments=$mean_quality_filter_treatments.max_mean_quality_filter_treatments
63 #if $max_mean_quality_filter_treatments.apply_max_mean_quality_filter_treatments: 83 #if $max_mean_quality_filter_treatments.apply_max_mean_quality_filter_treatments:
64 -max_qual_mean $max_mean_quality_filter_treatments.max_mean_quality_filter_treatment_value 84 -max_qual_mean $max_mean_quality_filter_treatments.max_mean_quality_filter_treatment_value
65 #end if 85 #end if
66 #end if 86 #end if
72 #if $GC_perc_content_filter_treatments.apply_GC_perc_content_filter_treatments : 92 #if $GC_perc_content_filter_treatments.apply_GC_perc_content_filter_treatments :
73 #set min_GC_perc_content_filter_treatments=$GC_perc_content_filter_treatments.min_GC_perc_content_filter_treatments 93 #set min_GC_perc_content_filter_treatments=$GC_perc_content_filter_treatments.min_GC_perc_content_filter_treatments
74 #if $min_GC_perc_content_filter_treatments.apply_min_GC_perc_content_filter_treatments : 94 #if $min_GC_perc_content_filter_treatments.apply_min_GC_perc_content_filter_treatments :
75 -min_gc $min_GC_perc_content_filter_treatments.min_GC_perc_content_filter_treatment_value 95 -min_gc $min_GC_perc_content_filter_treatments.min_GC_perc_content_filter_treatment_value
76 #end if 96 #end if
77 set max_GC_perc_content_filter_treatments=$GC_perc_content_filter_treatments.max_GC_perc_content_filter_treatments 97
98 #set max_GC_perc_content_filter_treatments=$GC_perc_content_filter_treatments.max_GC_perc_content_filter_treatments
78 #if $max_GC_perc_content_filter_treatments.apply_max_GC_perc_content_filter_treatments : 99 #if $max_GC_perc_content_filter_treatments.apply_max_GC_perc_content_filter_treatments :
79 -max_gc $max_GC_perc_content_filter_treatments.max_GC_perc_content_filter_treatment_value 100 -max_gc $max_GC_perc_content_filter_treatments.max_GC_perc_content_filter_treatment_value
80 #end if 101 #end if
81 #end if 102 #end if
103
82 #set N_number_content_filter_treatments=$base_content_filter_treatments.N_number_content_filter_treatments 104 #set N_number_content_filter_treatments=$base_content_filter_treatments.N_number_content_filter_treatments
83 #if $N_number_content_filter_treatments.apply_N_number_content_filter_treatments : 105 #if $N_number_content_filter_treatments.apply_N_number_content_filter_treatments :
84 -ns_max_n $N_number_content_filter_treatments.N_number_content_filter_treatment_value 106 -ns_max_n $N_number_content_filter_treatments.N_number_content_filter_treatment_value
85 #end if 107 #end if
108
86 #set N_percentage_content_filter_treatments=$base_content_filter_treatments.N_percentage_content_filter_treatments 109 #set N_percentage_content_filter_treatments=$base_content_filter_treatments.N_percentage_content_filter_treatments
87 #if $N_percentage_content_filter_treatments.apply_N_percentage_content_filter_treatments : 110 #if $N_percentage_content_filter_treatments.apply_N_percentage_content_filter_treatments :
88 -ns_max_p $N_percentage_content_filter_treatments.N_percentage_content_filter_treatment_value 111 -ns_max_p $N_percentage_content_filter_treatments.N_percentage_content_filter_treatment_value
89 #end if 112 #end if
90 #if $base_content_filter_treatments.apply_other_base_content_filter_treatments : 113
91 -noniupac 114 $base_content_filter_treatments.apply_other_base_content_filter_treatments
92 #end if
93 #end if 115 #end if
94 116
95 #set complexity_filter_treatments=$filter_treatments.complexity_filter_treatments 117 #set complexity_filter_treatments=$filter_treatments.complexity_filter_treatments
96 #if $complexity_filter_treatments.apply_complexity_filter_treatments : 118 #if $complexity_filter_treatments.apply_complexity_filter_treatments :
97 -lc_method $complexity_filter_treatments.method_complexity_filter_treatments 119 -lc_method $complexity_filter_treatments.method_complexity_filter_treatments
112 #if $nb_position_trimming_treatments.apply_nb_position_trimming_treatments : 134 #if $nb_position_trimming_treatments.apply_nb_position_trimming_treatments :
113 #set left_position_trimming_treatments=$nb_position_trimming_treatments.left_position_trimming_treatments 135 #set left_position_trimming_treatments=$nb_position_trimming_treatments.left_position_trimming_treatments
114 #if $left_position_trimming_treatments.apply_left_position_trimming_treatments : 136 #if $left_position_trimming_treatments.apply_left_position_trimming_treatments :
115 -trim_left $left_position_trimming_treatments.left_position_trimming_treatment_value 137 -trim_left $left_position_trimming_treatments.left_position_trimming_treatment_value
116 #end if 138 #end if
139
117 #set right_position_trimming_treatments=$nb_position_trimming_treatments.right_position_trimming_treatments 140 #set right_position_trimming_treatments=$nb_position_trimming_treatments.right_position_trimming_treatments
118 #if $right_position_trimming_treatments.apply_right_position_trimming_treatments : 141 #if $right_position_trimming_treatments.apply_right_position_trimming_treatments :
119 -trim_right $right_position_trimming_treatments.right_position_trimming_treatment_value 142 -trim_right $right_position_trimming_treatments.right_position_trimming_treatment_value
120 #end if 143 #end if
121 #end if 144 #end if
145
122 #set percentage_position_trimming_treatments=$position_trimming_treatments.percentage_position_trimming_treatments 146 #set percentage_position_trimming_treatments=$position_trimming_treatments.percentage_position_trimming_treatments
123 #if $percentage_position_trimming_treatments.apply_percentage_position_trimming_treatments : 147 #if $percentage_position_trimming_treatments.apply_percentage_position_trimming_treatments :
124 #set left_percentage_position_trimming_treatments=$percentage_position_trimming_treatments.left_percentage_position_trimming_treatments 148 #set left_percentage_position_trimming_treatments=$percentage_position_trimming_treatments.left_percentage_position_trimming_treatments
125 #if $left_percentage_position_trimming_treatments.apply_left_percentage_position_trimming_treatments : 149 #if $left_percentage_position_trimming_treatments.apply_left_percentage_position_trimming_treatments :
126 -trim_left_p $left_percentage_position_trimming_treatments.left_percentage_position_trimming_treatment_value 150 -trim_left_p $left_percentage_position_trimming_treatments.left_percentage_position_trimming_treatment_value
127 #end if 151 #end if
152
128 #set right_percentage_position_trimming_treatments=$percentage_position_trimming_treatments.right_percentage_position_trimming_treatments 153 #set right_percentage_position_trimming_treatments=$percentage_position_trimming_treatments.right_percentage_position_trimming_treatments
129 #if $right_percentage_position_trimming_treatments.apply_right_percentage_position_trimming_treatments : 154 #if $right_percentage_position_trimming_treatments.apply_right_percentage_position_trimming_treatments :
130 -trim_right_p $right_percentage_position_trimming_treatments.right_percentage_position_trimming_treatment_value 155 -trim_right_p $right_percentage_position_trimming_treatments.right_percentage_position_trimming_treatment_value
131 #end if 156 #end if
132 #end if 157 #end if
138 #if $a_t_tail_trimming_treatments.apply_a_t_tail_trimming_treatments : 163 #if $a_t_tail_trimming_treatments.apply_a_t_tail_trimming_treatments :
139 #set left_a_t_tail_trimming_treatments=$a_t_tail_trimming_treatments.left_a_t_tail_trimming_treatments 164 #set left_a_t_tail_trimming_treatments=$a_t_tail_trimming_treatments.left_a_t_tail_trimming_treatments
140 #if $left_a_t_tail_trimming_treatments.apply_left_a_t_tail_trimming_treatments : 165 #if $left_a_t_tail_trimming_treatments.apply_left_a_t_tail_trimming_treatments :
141 -trim_tail_left $left_a_t_tail_trimming_treatments.left_a_t_tail_trimming_treatment_value 166 -trim_tail_left $left_a_t_tail_trimming_treatments.left_a_t_tail_trimming_treatment_value
142 #end if 167 #end if
168
143 #set right_a_t_tail_trimming_treatments=$a_t_tail_trimming_treatments.right_a_t_tail_trimming_treatments 169 #set right_a_t_tail_trimming_treatments=$a_t_tail_trimming_treatments.right_a_t_tail_trimming_treatments
144 #if right_a_t_tail_trimming_treatments.apply_right_a_t_tail_trimming_treatments : 170 #if $right_a_t_tail_trimming_treatments.apply_right_a_t_tail_trimming_treatments :
145 -trim_tail_right $right_a_t_tail_trimming_treatments.right_a_t_tail_trimming_treatment_value 171 -trim_tail_right $right_a_t_tail_trimming_treatments.right_a_t_tail_trimming_treatment_value
146 #end if 172 #end if
147 #end if 173 #end if
174
148 #set ns_tail_trimming_treatments=$tail_trimming_treatments.ns_tail_trimming_treatments 175 #set ns_tail_trimming_treatments=$tail_trimming_treatments.ns_tail_trimming_treatments
149 #if $ns_tail_trimming_treatments.apply_ns_tail_trimming_treatments : 176 #if $ns_tail_trimming_treatments.apply_ns_tail_trimming_treatments :
150 #set left_ns_tail_trimming_treatments=$ns_tail_trimming_treatments.left_ns_tail_trimming_treatments 177 #set left_ns_tail_trimming_treatments=$ns_tail_trimming_treatments.left_ns_tail_trimming_treatments
151 #if $left_ns_tail_trimming_treatments.apply_left_ns_tail_trimming_treatments : 178 #if $left_ns_tail_trimming_treatments.apply_left_ns_tail_trimming_treatments :
152 -trim_ns_left $left_ns_tail_trimming_treatments.left_ns_tail_trimming_treatment_value 179 -trim_ns_left $left_ns_tail_trimming_treatments.left_ns_tail_trimming_treatment_value
153 #end if 180 #end if
181
154 #set right_ns_tail_trimming_treatments=$ns_tail_trimming_treatments.right_ns_tail_trimming_treatments 182 #set right_ns_tail_trimming_treatments=$ns_tail_trimming_treatments.right_ns_tail_trimming_treatments
155 #if $right_ns_tail_trimming_treatments.apply_right_ns_tail_trimming_treatments : 183 #if $right_ns_tail_trimming_treatments.apply_right_ns_tail_trimming_treatments :
156 -trim_ns_right $right_ns_tail_trimming_treatments.right_ns_tail_trimming_treatment_value 184 -trim_ns_right $right_ns_tail_trimming_treatments.right_ns_tail_trimming_treatment_value
157 #end if 185 #end if
158 #end if 186 #end if
162 #if $quality_trimming_treatments.apply_quality_trimming_treatments : 190 #if $quality_trimming_treatments.apply_quality_trimming_treatments :
163 #set left_quality_trimming_treatments=$quality_trimming_treatments.left_quality_trimming_treatments 191 #set left_quality_trimming_treatments=$quality_trimming_treatments.left_quality_trimming_treatments
164 #if $left_quality_trimming_treatments.apply_left_quality_trimming_treatments : 192 #if $left_quality_trimming_treatments.apply_left_quality_trimming_treatments :
165 -trim_qual_left $left_quality_trimming_treatments.left_quality_trimming_treatment_value 193 -trim_qual_left $left_quality_trimming_treatments.left_quality_trimming_treatment_value
166 #end if 194 #end if
195
167 #set right_quality_trimming_treatments=$quality_trimming_treatments.right_quality_trimming_treatments 196 #set right_quality_trimming_treatments=$quality_trimming_treatments.right_quality_trimming_treatments
168 #if $right_quality_trimming_treatments.apply_right_quality_trimming_treatments : 197 #if $right_quality_trimming_treatments.apply_right_quality_trimming_treatments :
169 -trim_qual_right $right_quality_trimming_treatments.right_quality_trimming_treatment_value 198 -trim_qual_right $right_quality_trimming_treatments.right_quality_trimming_treatment_value
170 #end if 199 #end if
200
171 -trim_qual_type $quality_trimming_treatments.type_quality_trimming_treatments 201 -trim_qual_type $quality_trimming_treatments.type_quality_trimming_treatments
172 -trim_qual_rule $quality_trimming_treatments.rule_quality_trimming_treatments 202 -trim_qual_rule $quality_trimming_treatments.rule_quality_trimming_treatments
173 -trim_qual_window $quality_trimming_treatments.window_quality_trimming_treatments 203 -trim_qual_window $quality_trimming_treatments.window_quality_trimming_treatments
174 -trim_qual_step $quality_trimming_treatments.step_quality_trimming_treatments 204 -trim_qual_step $quality_trimming_treatments.step_quality_trimming_treatments
175 #end if 205 #end if
176 206
177 #end if 207 #end if
178 ]]> 208
209 -graph_stats "$graph_stats"
210 -graph_data stats.gd
211 ;
212
213 # perl \${PRINSEQ_DIR}/prinseq-graphs-noPCA.pl -i stats.gd -html_all -o stats_html
214
215
216 ]]>
179 </command> 217 </command>
180 218
181 <inputs> 219 <inputs>
182 <param name="sequence_to_control_file" type="data" format="fastq" label="Input 220 <conditional name="seq_type">
183 sequence file" help="The file must be in fastq format for quality 221 <param name="seq_type_opt" type="select" label="Is this library paired- or single-end?">
184 scores"/> 222 <option value="single">Single-end</option>
223 <option value="paired">Paired-end</option>
224 </param>
225 <when value="single">
226 <param name="input_singles" type="data" format="fastqsanger,fastqillumina,fastq" label="FASTQ file" help="FASTQ files." />
227 </when>
228 <when value="paired">
229 <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq" label="FASTQ file" help="FASTQ files." />
230 <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq" label="FASTQ file" help="FASTQ files." />
231 </when>
232 </conditional>
185 233
186 <conditional name="filter_treatments"> 234 <conditional name="filter_treatments">
187 <param name='apply_filter_treatments' type='boolean' checked="true" 235 <param name='apply_filter_treatments' type='boolean' checked="true"
188 label="Apply filter treatments?" help=""/> 236 truevalue="true" falsevalue="false" label="Apply filter treatments?"
237 help=""/>
189 <when value="true"> 238 <when value="true">
190 <conditional name="length_filter_treatments"> 239 <conditional name="length_filter_treatments">
191 <param name='apply_length_filter_treatments' type='boolean' 240 <param name='apply_length_filter_treatments' type='boolean'
192 checked="true" label="Filter sequence based on their 241 checked="true" truevalue="true" falsevalue="false"
193 length?" help="By default, sequences smaller than 60 bp 242 label="Filter sequence based on their length?" help="By
243 default, sequences smaller than 60 bp
194 are removed. No top threshold is defined"/> 244 are removed. No top threshold is defined"/>
195 <when value="true"> 245 <when value="true">
196 <conditional name="min_length_filter_treatments"> 246 <conditional name="min_length_filter_treatments">
197 <param name='apply_min_length_filter_treatments' 247 <param name='apply_min_length_filter_treatments'
198 type='boolean' checked="true" label="Filter too 248 type='boolean' checked="true" truevalue="true"
249 falsevalue="false" label="Filter too
199 small sequences?" help="By default, sequences 250 small sequences?" help="By default, sequences
200 smaller than 60 bp are removed."/> 251 smaller than 60 bp are removed."/>
201 <when value="true"> 252 <when value="true">
202 <param name="min_length_filter_treatment_value" type="integer" min="0" 253 <param name="min_length_filter_treatment_value" type="integer" min="0"
203 max="3000" value="60" label="Minimum length t 254 max="3000" value="60" label="Minimum length t
204 hreshold to conserve sequences" help=""/> 255 hreshold to conserve sequences" help="(-min_len)"/>
205 </when> 256 </when>
257 <when value="false" />
206 </conditional> 258 </conditional>
207 <conditional name="max_length_filter_treatments"> 259 <conditional name="max_length_filter_treatments">
208 <param name='apply_max_length_filter_treatments' 260 <param name='apply_max_length_filter_treatments'
209 type='boolean' checked="false" label="Filter too 261 type='boolean' truevalue="true" falsevalue="false"
262 checked="false" label="Filter too
210 big sequences?" help="By default, no treatment 263 big sequences?" help="By default, no treatment
211 based on a maximal length is made"/> 264 based on a maximal length is made"/>
212 <when value="true"> 265 <when value="true">
213 <param name="max_length_filter_treatment_value" type="integer" min="0" 266 <param name="max_length_filter_treatment_value" type="integer" min="0"
214 max="3000" value="1000" label="Maximal length 267 max="3000" value="1000" label="Maximal length
215 threshold to conserve sequences" help=""/> 268 threshold to conserve sequences" help="(-max_len)"/>
216 </when> 269 </when>
270 <when value="false" />
217 </conditional> 271 </conditional>
218 </when> 272 </when>
273 <when value="false" />
219 </conditional> 274 </conditional>
220 <conditional name="quality_filter_treatments"> 275 <conditional name="quality_filter_treatments">
221 <param name='apply_quality_filter_treatments' type='boolean' 276 <param name='apply_quality_filter_treatments' type='boolean'
222 checked="true" label="Filter sequences based on quality 277 checked="true" truevalue="true" falsevalue="false"
278 label="Filter sequences based on quality
223 score?" help="By default, sequences with a mean score 279 score?" help="By default, sequences with a mean score
224 below 15 are removed."/> 280 below 15 are removed."/>
225 <when value="true"> 281 <when value="true">
226 <conditional name="min_quality_filter_treatments"> 282 <conditional name="min_quality_filter_treatments">
227 <param name='apply_min_quality_filter_treatments' 283 <param name='apply_min_quality_filter_treatments'
228 type='boolean' checked="false" label="Filter sequences 284 type='boolean' checked="false" truevalue="true"
285 falsevalue="false" label="Filter sequences
229 based on their minimum score?" help="By default, 286 based on their minimum score?" help="By default,
230 no treatment based on a minimum score is made"/> 287 no treatment based on a minimum score is made"/>
231 <when value="true"> 288 <when value="true">
232 <param name="min_quality_filter_treatment_value" type="integer" min="0" 289 <param name="min_quality_filter_treatment_value" type="integer" min="0"
233 max="40" value="2" label="Minimum score threshold 290 max="40" value="2" label="Minimum score threshold
234 to conserve sequences" help=""/> 291 to conserve sequences" help="(-min_qual_score)"/>
235 </when> 292 </when>
293 <when value="false" />
236 </conditional> 294 </conditional>
237 <conditional name="max_quality_filter_treatments"> 295 <conditional name="max_quality_filter_treatments">
238 <param name='apply_max_quality_filter_treatments' 296 <param name='apply_max_quality_filter_treatments'
239 type='boolean' checked="false" label="Filter sequences 297 type='boolean' checked="false" truevalue="true"
298 falsevalue="false" label="Filter sequences
240 based on their maximum score?" help="By default, 299 based on their maximum score?" help="By default,
241 no treatment based on a maximum score is made"/> 300 no treatment based on a maximum score is made"/>
242 <when value="true"> 301 <when value="true">
243 <param name="max_quality_filter_treatment_value" type="integer" min="0" 302 <param name="max_quality_filter_treatment_value" type="integer" min="0"
244 max="40" value="38" label="Maximum score 303 max="40" value="38" label="Maximum score
245 threshold to conserve sequences" help=""/> 304 threshold to conserve sequences" help="(-max_qual_score)"/>
246 </when> 305 </when>
306 <when value="false" />
247 </conditional> 307 </conditional>
248 <conditional name="mean_quality_filter_treatments"> 308 <conditional name="mean_quality_filter_treatments">
249 <param name='apply_mean_quality_filter_treatments' 309 <param name='apply_mean_quality_filter_treatments'
250 type='boolean' checked="true" label="Filter sequences 310 type='boolean' checked="true" truevalue="true"
311 falsevalue="false" label="Filter sequences
251 based on their mean score?" help="By default, 312 based on their mean score?" help="By default,
252 sequences with a mean score below 15 are removed."/> 313 sequences with a mean score below 15 are removed."/>
253 <when value="true"> 314 <when value="true">
254 <conditional name="min_mean_quality_filter_treatments"> 315 <conditional name="min_mean_quality_filter_treatments">
255 <param name='apply_min_mean_quality_filter_treatments' 316 <param name='apply_min_mean_quality_filter_treatments'
256 type='boolean' checked="true" label="Filter 317 type='boolean' checked="true" truevalue="true"
318 falsevalue="false" label="Filter
257 sequences with too small mean score?" 319 sequences with too small mean score?"
258 help="By default, sequences with a mean 320 help="By default, sequences with a mean
259 score below 15 are removed."/> 321 score below 15 are removed."/>
260 <when value="true"> 322 <when value="true">
261 <param name="min_mean_quality_filter_treatment_value" 323 <param name="min_mean_quality_filter_treatment_value"
262 type="integer" min="0" 324 type="integer" min="0"
263 max="40" value="15" label="Minimum mean 325 max="40" value="15" label="Minimum mean
264 score threshold to conserve sequences" 326 score threshold to conserve sequences"
265 help=""/> 327 help="(-min_qual_mean)"/>
266 </when> 328 </when>
329 <when value="false" />
267 </conditional> 330 </conditional>
268 <conditional name="max_mean_quality_filter_treatments"> 331 <conditional name="max_mean_quality_filter_treatments">
269 <param name='apply_max_mean_quality_filter_treatments' 332 <param name='apply_max_mean_quality_filter_treatments'
270 type='boolean' checked="false" label="Filter 333 type='boolean' checked="false" truevalue="true"
334 falsevalue="false" label="Filter
271 sequences with too high mean score?" 335 sequences with too high mean score?"
272 help="By default, no treatment based on 336 help="By default, no treatment based on
273 a maximum mean score is made"/> 337 a maximum mean score is made"/>
274 <when value="true"> 338 <when value="true">
275 <param name="max_mean_quality_filter_treatment_value" 339 <param name="max_mean_quality_filter_treatment_value"
276 type="integer" 340 type="integer"
277 min="0" max="40" value="40" 341 min="0" max="40" value="40"
278 label="Maximum mean score threshold 342 label="Maximum mean score threshold
279 to conserve sequences" help=""/> 343 to conserve sequences" help="(-max_qual_mean)"/>
280 </when> 344 </when>
281 </conditional> 345 <when value="false" />
282 </when> 346 </conditional>
347 </when>
348 <when value="false" />
283 </conditional> 349 </conditional>
284 </when> 350 </when>
351 <when value="false" />
285 </conditional> 352 </conditional>
286 <conditional name="base_content_filter_treatments"> 353 <conditional name="base_content_filter_treatments">
287 <param name='apply_base_content_filter_treatments' 354 <param name='apply_base_content_filter_treatments'
288 type='boolean' checked="true" label="Filter sequences 355 type='boolean' checked="true" truevalue="true" falsevalue="false"
289 based on their base content?" help="By default, sequences 356 label="Filter sequences based on their base content?"
357 help="By default, sequences
290 with more than 2% of N bases are removed."/> 358 with more than 2% of N bases are removed."/>
291 <when value="true"> 359 <when value="true">
292 <conditional name="GC_perc_content_filter_treatments"> 360 <conditional name="GC_perc_content_filter_treatments">
293 <param name='apply_GC_perc_content_filter_treatments' 361 <param name='apply_GC_perc_content_filter_treatments'
294 type='boolean' checked="false" label="Filter 362 type='boolean' checked="false" truevalue="true"
363 falsevalue="false" label="Filter
295 sequences based on their GC percentage?" 364 sequences based on their GC percentage?"
296 help="By default, no treatment based on GC percentage 365 help="By default, no treatment based on GC percentage
297 is made."/> 366 is made."/>
298 <when value="true"> 367 <when value="true">
299 <conditional name="min_GC_perc_content_filter_treatments"> 368 <conditional name="min_GC_perc_content_filter_treatments">
300 <param name='apply_min_GC_perc_content_filter_treatments' 369 <param name='apply_min_GC_perc_content_filter_treatments'
301 type='boolean' checked="false" label="Filter 370 type='boolean' checked="false" truevalue="true"
371 falsevalue="false" label="Filter
302 sequences with too small GC percentage?" 372 sequences with too small GC percentage?"
303 help="By default, no treatment based on 373 help="By default, no treatment based on
304 GC percentage is made."/> 374 GC percentage is made."/>
305 <when value="true"> 375 <when value="true">
306 <param name="min_GC_perc_content_filter_treatment_value" 376 <param name="min_GC_perc_content_filter_treatment_value"
307 type="integer" min="0" 377 type="integer" min="0"
308 max="100" value="10" label="Minimal 378 max="100" value="10" label="Minimal
309 GC percentage threshold to conserve 379 GC percentage threshold to conserve
310 sequences" help=""/> 380 sequences" help="(-min_gc)"/>
311 </when> 381 </when>
382 <when value="false" />
312 </conditional> 383 </conditional>
313 <conditional name="max_GC_perc_content_filter_treatments"> 384 <conditional name="max_GC_perc_content_filter_treatments">
314 <param name='apply_max_GC_perc_content_filter_treatments' 385 <param name='apply_max_GC_perc_content_filter_treatments'
315 type='boolean' checked="false" label="Filter 386 type='boolean' checked="false" truevalue="true"
387 falsevalue="false" label="Filter
316 sequences with too high GC percentage?" 388 sequences with too high GC percentage?"
317 help="By default, no treatment based on 389 help="By default, no treatment based on
318 GC percentage is made."/> 390 GC percentage is made."/>
319 <when value="true"> 391 <when value="true">
320 <param name="max_GC_perc_content_filter_treatment_value" 392 <param name="max_GC_perc_content_filter_treatment_value"
321 type="integer" min="0" 393 type="integer" min="0"
322 max="100" value="90" label="Maximal GC 394 max="100" value="90" label="Maximal GC
323 percentage threshold to conserve 395 percentage threshold to conserve
324 sequences" help=""/> 396 sequences" help="(-max_gc)"/>
325 </when> 397 </when>
326 </conditional> 398 <when value="false" />
327 </when> 399 </conditional>
400 </when>
401 <when value="false" />
328 </conditional> 402 </conditional>
329 <conditional name="N_number_content_filter_treatments"> 403 <conditional name="N_number_content_filter_treatments">
330 <param name='apply_N_number_content_filter_treatments' 404 <param name='apply_N_number_content_filter_treatments'
331 type='boolean' checked="false" label="Filter 405 type='boolean' checked="false" truevalue="true"
332 sequences based on their number of N bases?" 406 falsevalue="false" label="Filter sequences based
407 on their number of N bases?"
333 help="By default, no treatment based on N number 408 help="By default, no treatment based on N number
334 is made."/> 409 is made."/>
335 <when value="true"> 410 <when value="true">
336 <param name="N_number_content_filter_treatment_value" 411 <param name="N_number_content_filter_treatment_value"
337 type="integer" min="0" 412 type="integer" min="0"
338 max="3000" value="10" label="Maximal N number 413 max="3000" value="10" label="Maximal N number
339 threshold to conserve sequences" help=""/> 414 threshold to conserve sequences" help="(-ns_max_n)"/>
340 </when> 415 </when>
416 <when value="false" />
341 </conditional> 417 </conditional>
342 <conditional name="N_percentage_content_filter_treatments"> 418 <conditional name="N_percentage_content_filter_treatments">
343 <param name='apply_N_percentage_content_filter_treatments' 419 <param name='apply_N_percentage_content_filter_treatments'
344 type='boolean' checked="true" label="Filter sequences 420 type='boolean' checked="true" truevalue="true"
421 falsevalue="false" label="Filter sequences
345 based on their percentage of N bases?" help="By 422 based on their percentage of N bases?" help="By
346 default, sequences with more than 2% of N bases 423 default, sequences with more than 2% of N bases
347 are removed."/> 424 are removed."/>
348 <when value="true"> 425 <when value="true">
349 <param name="N_percentage_content_filter_treatment_value" 426 <param name="N_percentage_content_filter_treatment_value"
350 type="integer" min="0" max="100" 427 type="integer" min="0" max="100"
351 value="2" label="Maximal N percentage threshold 428 value="2" label="Maximal N percentage threshold
352 to conserve sequences" help=""/> 429 to conserve sequences" help="(-ns_max_p)"/>
353 </when> 430 </when>
431 <when value="false" />
354 </conditional> 432 </conditional>
355 <param name='apply_other_base_content_filter_treatments' 433 <param name='apply_other_base_content_filter_treatments'
356 type='boolean' checked="false" label="Filter sequences 434 type='boolean' truevalue="-noniupac" falsevalue=""
435 checked="false" label="Filter sequences
357 with characters other than A, T, C, G and N?" help="By 436 with characters other than A, T, C, G and N?" help="By
358 default, this treatment is not made."/> 437 default, this treatment is not made. (-noniupac)"/>
359 </when> 438 </when>
439 <when value="false" />
360 </conditional> 440 </conditional>
361 <conditional name="complexity_filter_treatments"> 441 <conditional name="complexity_filter_treatments">
362 <param name='apply_complexity_filter_treatments' type='boolean' 442 <param name='apply_complexity_filter_treatments' type='boolean'
363 checked="false" label="Filter sequences based on their 443 checked="false" truevalue="true" falsevalue="false"
444 label="Filter sequences based on their
364 complexity?" help="By default, no complexity filter is 445 complexity?" help="By default, no complexity filter is
365 applied"/> 446 applied"/>
366 <when value="true"> 447 <when value="true">
367 <param name="method_complexity_filter_treatments" type="select" 448 <param name="method_complexity_filter_treatments" type="select"
368 display="radio" label="Method to filter low complexity 449 display="radio" label="Method to filter low complexity
369 sequences" help=""> 450 sequences" help="(-lc_method)">
370 <option value="dust">Dust</option> 451 <option value="dust">Dust</option>
371 <option value="entropy" >Entropy</option> 452 <option value="entropy" >Entropy</option>
372 </param> 453 </param>
373 <param name="threshold_complexity_filter_treatments" type="integer" 454 <param name="threshold_complexity_filter_treatments" type="integer"
374 min="0" max="100" value="2" label="Threshold value used 455 min="0" max="100" value="2" label="Threshold value used
375 to filter sequences by sequence complexity" help="The 456 to filter sequences by sequence complexity" help="The
376 dust method uses the threshold as maximum allowed score 457 dust method uses the threshold as maximum allowed score
377 and the entropy method as minimum allowed value."/> 458 and the entropy method as minimum allowed value.(-lc_threshold)"/>
378 </when> 459 </when>
460 <when value="false" />
379 </conditional> 461 </conditional>
380 </when> 462 </when>
463 <when value="false" />
381 </conditional> 464 </conditional>
382 465
383 <conditional name="trimming_treatments"> 466 <conditional name="trimming_treatments">
384 <param name='apply_trimming_treatments' type='boolean' checked="true" 467 <param name='apply_trimming_treatments' type='boolean' checked="true"
385 label="Apply trimming treatments?" help=""/> 468 truevalue="true" falsevalue="false" label="Apply trimming
469 treatments?" help=""/>
386 <when value="true"> 470 <when value="true">
387 <conditional name="length_trimming_treatments"> 471 <conditional name="length_trimming_treatments">
388 <param name='apply_length_trimming_treatments' type='boolean' 472 <param name='apply_length_trimming_treatments' type='boolean'
389 checked="false" label="Trim all sequences from the 3'-end 473 checked="false" truevalue="true" falsevalue="false"
474 label="Trim all sequences from the 3'-end
390 to a length?" help="By default, no length trimming is made"/> 475 to a length?" help="By default, no length trimming is made"/>
391 <when value="true"> 476 <when value="true">
392 <param name="length_trimming_treatment_value" type="integer" min="0" max="3000" 477 <param name="length_trimming_treatment_value" type="integer" min="0" max="3000"
393 value="100" label="Length of sequences after 478 value="100" label="Length of sequences after
394 trimming" help=""/> 479 trimming" help="(-trim_to_len)"/>
395 </when> 480 </when>
481 <when value="false" />
396 </conditional> 482 </conditional>
397 <conditional name="position_trimming_treatments"> 483 <conditional name="position_trimming_treatments">
398 <param name='apply_position_trimming_treatments' type='boolean' 484 <param name='apply_position_trimming_treatments' type='boolean'
399 checked="false" label="Trim all sequences from the ends?" 485 checked="false" truevalue="true" falsevalue="false"
486 label="Trim all sequences from the ends?"
400 help="By default, no position trimming is made"/> 487 help="By default, no position trimming is made"/>
401 <when value="true"> 488 <when value="true">
402 <conditional name="nb_position_trimming_treatments"> 489 <conditional name="nb_position_trimming_treatments">
403 <param name='apply_nb_position_trimming_treatments' 490 <param name='apply_nb_position_trimming_treatments'
404 type='boolean' checked="false" label="Trim sequences 491 type='boolean' checked="false" label="Trim sequences
405 by a defined number of positions?" help="By default, 492 by a defined number of positions?" help="By default,
406 no position trimming is made"/> 493 no position trimming is made"/>
407 <when value="true"> 494 <when value="true">
408 <conditional name="left_position_trimming_treatments"> 495 <conditional name="left_position_trimming_treatments">
409 <param name='apply_left_position_trimming_treatments' 496 <param name='apply_left_position_trimming_treatments'
410 type='boolean' checked="false" label="Trim 497 type='boolean' checked="false" truevalue="true"
498 falsevalue="false" label="Trim
411 sequences at the 5'-end by a defined number 499 sequences at the 5'-end by a defined number
412 of positions?" help="By default, no position 500 of positions?" help="By default, no position
413 trimming is made"/> 501 trimming is made"/>
414 <when value="true"> 502 <when value="true">
415 <param name="left_position_trimming_treatment_value" 503 <param name="left_position_trimming_treatment_value"
416 type="integer" min="0" 504 type="integer" min="0"
417 max="3000" value="100" label="Number of 505 max="3000" value="100" label="Number of
418 positions to trim on 5'-end" help=""/> 506 positions to trim on 5'-end" help="(-trim_left)"/>
419 </when> 507 </when>
508 <when value="false" />
420 </conditional> 509 </conditional>
421 <conditional name="right_position_trimming_treatments"> 510 <conditional name="right_position_trimming_treatments">
422 <param name='apply_right_position_trimming_treatments' 511 <param name='apply_right_position_trimming_treatments'
423 type='boolean' checked="false" label="Trim 512 type='boolean' checked="false" truevalue="true"
513 falsevalue="false" label="Trim
424 sequences at the 3'-end by a defined number 514 sequences at the 3'-end by a defined number
425 of positions?" help="By default, no position 515 of positions?" help="By default, no position
426 trimming is made"/> 516 trimming is made"/>
427 <when value="true"> 517 <when value="true">
428 <param name="right_position_trimming_treatment_value" 518 <param name="right_position_trimming_treatment_value"
429 type="integer" min="0" 519 type="integer" min="0"
430 max="3000" value="100" label="Number 520 max="3000" value="100" label="Number
431 of positions to trim on 3'-end" 521 of positions to trim on 3'-end"
432 help=""/> 522 help="(-trim_right)"/>
433 </when> 523 </when>
434 </conditional> 524 <when value="false" />
435 </when> 525 </conditional>
526 </when>
527 <when value="false" />
436 </conditional> 528 </conditional>
437 <conditional name="percentage_position_trimming_treatments"> 529 <conditional name="percentage_position_trimming_treatments">
438 <param name='apply_percentage_position_trimming_treatments' 530 <param name='apply_percentage_position_trimming_treatments'
439 type='boolean' checked="false" label="Trim sequences 531 type='boolean' checked="false" truevalue="true"
532 falsevalue="false" label="Trim sequences
440 by a defined percentage of read length?" help="By 533 by a defined percentage of read length?" help="By
441 default, no position trimming is made. The trim 534 default, no position trimming is made. The trim
442 length is rounded towards the lower integer"/> 535 length is rounded towards the lower integer"/>
443 <when value="true"> 536 <when value="true">
444 <conditional name="left_percentage_position_trimming_treatments"> 537 <conditional name="left_percentage_position_trimming_treatments">
445 <param name='apply_left_percentage_position_trimming_treatments' 538 <param name='apply_left_percentage_position_trimming_treatments'
446 type='boolean' checked="false" label="Trim 539 type='boolean' checked="false" truevalue="true"
447 sequences at the 5'-end by a defined percentage 540 falsevalue="false" label="Trim sequences
541 at the 5'-end by a defined percentage
448 of read length?" help="By default, no position 542 of read length?" help="By default, no position
449 trimming is made. The trim length is rounded 543 trimming is made. The trim length is rounded
450 towards the lower integer"/> 544 towards the lower integer"/>
451 <when value="true"> 545 <when value="true">
452 <param name="left_percentage_position_trimming_treatment_value" 546 <param name="left_percentage_position_trimming_treatment_value"
453 type="integer" min="0" 547 type="integer" min="0"
454 max="100" value="2" label="Percentage 548 max="100" value="2" label="Percentage
455 of positions to trim on 5'-end" help=""/> 549 of positions to trim on 5'-end" help="(-trim_left_p)"/>
456 </when> 550 </when>
551 <when value="false" />
457 </conditional> 552 </conditional>
458 <conditional name="right_percentage_position_trimming_treatments"> 553 <conditional name="right_percentage_position_trimming_treatments">
459 <param name='apply_right_percentage_position_trimming_treatments' 554 <param name='apply_right_percentage_position_trimming_treatments'
460 type='boolean' checked="false" label="Trim 555 type='boolean' checked="false" truevalue="true"
556 falsevalue="false" label="Trim
461 sequences at the 3'-end by a defined percentage 557 sequences at the 3'-end by a defined percentage
462 of read length?" help="By default, no position 558 of read length?" help="By default, no position
463 trimming is made. The trim length is rounded 559 trimming is made. The trim length is rounded
464 towards the lower integer"/> 560 towards the lower integer"/>
465 <when value="true"> 561 <when value="true">
466 <param name="right_percentage_position_trimming_treatment_value" 562 <param name="right_percentage_position_trimming_treatment_value"
467 type="integer" min="0" 563 type="integer" min="0"
468 max="100" value="2" label="Percentage 564 max="100" value="2" label="Percentage
469 of positions to trim on 3'-end" help=""/> 565 of positions to trim on 3'-end" help="(-trim_right_p)"/>
470 </when> 566 </when>
471 </conditional> 567 <when value="false" />
472 </when> 568 </conditional>
569 </when>
570 <when value="false" />
473 </conditional> 571 </conditional>
474 </when> 572 </when>
573 <when value="false" />
475 </conditional> 574 </conditional>
476 <conditional name="tail_trimming_treatments"> 575 <conditional name="tail_trimming_treatments">
477 <param name='apply_tail_trimming_treatments' type='boolean' 576 <param name='apply_tail_trimming_treatments' type='boolean'
478 checked="false" label="Trim tails?" help="By default, no 577 checked="false" truevalue="true" falsevalue="false"
578 label="Trim tails?" help="By default, no
479 tail trimming is made"/> 579 tail trimming is made"/>
480 <when value="true"> 580 <when value="true">
481 <conditional name="a_t_tail_trimming_treatments"> 581 <conditional name="a_t_tail_trimming_treatments">
482 <param name='apply_a_t_tail_trimming_treatments' 582 <param name='apply_a_t_tail_trimming_treatments'
483 type='boolean' checked="false" label="Trim poly-A/T 583 type='boolean' checked="false" truevalue="true"
584 falsevalue="false" label="Trim poly-A/T
484 tail?" help="By default, no poly-A/T tail trimming 585 tail?" help="By default, no poly-A/T tail trimming
485 is made"/> 586 is made"/>
486 <when value="true"> 587 <when value="true">
487 <conditional name="left_a_t_tail_trimming_treatments"> 588 <conditional name="left_a_t_tail_trimming_treatments">
488 <param name='apply_left_a_t_tail_trimming_treatments' 589 <param name='apply_left_a_t_tail_trimming_treatments'
489 type='boolean' checked="false" label="Trim 590 type='boolean' checked="false" truevalue="true"
591 falsevalue="false" label="Trim
490 poly-A/T tail at the 5'-end?" help="By 592 poly-A/T tail at the 5'-end?" help="By
491 default, no 5'-end poly-A/T tail trimming 593 default, no 5'-end poly-A/T tail trimming
492 is made"/> 594 is made"/>
493 <when value="true"> 595 <when value="true">
494 <param name="left_a_t_tail_trimming_treatment_value" 596 <param name="left_a_t_tail_trimming_treatment_value"
495 type="integer" min="0" 597 type="integer" min="0"
496 max="3000" value="100" label="Minimum 598 max="3000" value="100" label="Minimum
497 length of poly-A/T to trim at the 5'-end" 599 length of poly-A/T to trim at the 5'-end"
498 help=""/> 600 help="(-trim_tail_left)"/>
499 </when> 601 </when>
602 <when value="false" />
500 </conditional> 603 </conditional>
501 <conditional name="right_a_t_tail_trimming_treatments"> 604 <conditional name="right_a_t_tail_trimming_treatments">
502 <param name='apply_right_a_t_tail_trimming_treatments' 605 <param name='apply_right_a_t_tail_trimming_treatments'
503 type='boolean' checked="false" label="Trim poly-A/T 606 type='boolean' checked="false" truevalue="true"
607 falsevalue="false" label="Trim poly-A/T
504 tail at the 5'-end?" help="By default, no 608 tail at the 5'-end?" help="By default, no
505 3'-end poly-A/T tail trimming is made"/> 609 3'-end poly-A/T tail trimming is made"/>
506 <when value="true"> 610 <when value="true">
507 <param name="right_a_t_tail_trimming_treatment_value" 611 <param name="right_a_t_tail_trimming_treatment_value"
508 type="integer" min="0" 612 type="integer" min="0"
509 max="3000" value="100" label="Minimum 613 max="3000" value="100" label="Minimum
510 length of poly-A/T to trim at the 5'-end" 614 length of poly-A/T to trim at the 5'-end"
511 help=""/> 615 help="(-trim_tail_right)"/>
512 </when> 616 </when>
513 </conditional> 617 <when value="false" />
514 </when> 618 </conditional>
619 </when>
620 <when value="false" />
515 </conditional> 621 </conditional>
516 <conditional name="ns_tail_trimming_treatments"> 622 <conditional name="ns_tail_trimming_treatments">
517 <param name='apply_ns_tail_trimming_treatments' type='boolean' 623 <param name='apply_ns_tail_trimming_treatments' type='boolean'
518 checked="false" label="Trim poly-N tail?" help="By 624 checked="false" truevalue="true" falsevalue="false"
625 label="Trim poly-N tail?" help="By
519 default, no poly-N tail trimming is made"/> 626 default, no poly-N tail trimming is made"/>
520 <when value="true"> 627 <when value="true">
521 <conditional name="left_ns_tail_trimming_treatments"> 628 <conditional name="left_ns_tail_trimming_treatments">
522 <param name='apply_left_ns_tail_trimming_treatments' 629 <param name='apply_left_ns_tail_trimming_treatments'
523 type='boolean' checked="false" label="Trim 630 type='boolean' checked="false" truevalue="true"
631 falsevalue="false" label="Trim
524 poly-N tail at the 5'-end?" help="By default, 632 poly-N tail at the 5'-end?" help="By default,
525 no 5'-end poly-N tail trimming is made"/> 633 no 5'-end poly-N tail trimming is made"/>
526 <when value="true"> 634 <when value="true">
527 <param name="left_ns_tail_trimming_treatment_value" 635 <param name="left_ns_tail_trimming_treatment_value"
528 type="integer" min="0" 636 type="integer" min="0"
529 max="3000" value="100" label="Minimum 637 max="3000" value="100" label="Minimum
530 length of poly-N to trim at the 5'-end" 638 length of poly-N to trim at the 5'-end"
531 help=""/> 639 help="(-trim_ns_left)"/>
532 </when> 640 </when>
641 <when value="false" />
533 </conditional> 642 </conditional>
534 <conditional name="right_ns_tail_trimming_treatments"> 643 <conditional name="right_ns_tail_trimming_treatments">
535 <param name='apply_right_ns_tail_trimming_treatments' 644 <param name='apply_right_ns_tail_trimming_treatments'
536 type='boolean' checked="false" label="Trim 645 type='boolean' checked="false" truevalue="true"
646 falsevalue="false" label="Trim
537 poly-N tail at the 5'-end?" help="By default, 647 poly-N tail at the 5'-end?" help="By default,
538 no 3'-end poly-N tail trimming is made"/> 648 no 3'-end poly-N tail trimming is made"/>
539 <when value="true"> 649 <when value="true">
540 <param name="right_ns_tail_trimming_treatment_value" 650 <param name="right_ns_tail_trimming_treatment_value"
541 type="integer" min="0" 651 type="integer" min="0"
542 max="3000" value="100" label="Minimum 652 max="3000" value="100" label="Minimum
543 length of poly-N to trim at the 5'-end" 653 length of poly-N to trim at the 5'-end"
544 help=""/> 654 help="(-trim_ns_right)"/>
545 </when> 655 </when>
546 </conditional> 656 <when value="false" />
547 </when> 657 </conditional>
658 </when>
659 <when value="false" />
548 </conditional> 660 </conditional>
549 </when> 661 </when>
662 <when value="false" />
550 </conditional> 663 </conditional>
551 <conditional name="quality_trimming_treatments"> 664 <conditional name="quality_trimming_treatments">
552 <param name='apply_quality_trimming_treatments' type='boolean' 665 <param name='apply_quality_trimming_treatments' type='boolean'
553 checked="true" label="Trim sequence by quality score?" 666 checked="true" truevalue="true" falsevalue="false"
667 label="Trim sequence by quality score?"
554 help="By default, a 3'-end trimming is made to remove ends 668 help="By default, a 3'-end trimming is made to remove ends
555 with a minimum quality score over 5 bp below 20"/> 669 with a minimum quality score over 5 bp below 20"/>
556 <when value="true"> 670 <when value="true">
557 <conditional name="left_quality_trimming_treatments"> 671 <conditional name="left_quality_trimming_treatments">
558 <param name='apply_left_quality_trimming_treatments' 672 <param name='apply_left_quality_trimming_treatments'
559 type='boolean' checked="false" label="Trim sequence 673 type='boolean' checked="false" truevalue="true"
674 falsevalue="false" label="Trim sequence
560 by quality score from the 5'-end?" help="By default, 675 by quality score from the 5'-end?" help="By default,
561 no 5'-end quality trimming is made"/> 676 no 5'-end quality trimming is made"/>
562 <when value="true"> 677 <when value="true">
563 <param name="left_quality_trimming_treatment_value" 678 <param name="left_quality_trimming_treatment_value"
564 type="integer" min="0" max="40" 679 type="integer" min="0" max="40"
565 value="20" label="Quality score threshold to 680 value="20" label="Quality score threshold to
566 trim positions" help=""/> 681 trim positions" help="(-trim_qual_left)"/>
567 </when> 682 </when>
683 <when value="false" />
568 </conditional> 684 </conditional>
569 <conditional name="right_quality_trimming_treatments"> 685 <conditional name="right_quality_trimming_treatments">
570 <param name='apply_right_quality_trimming_treatments' 686 <param name='apply_right_quality_trimming_treatments'
571 type='boolean' checked="true" label="Trim sequence 687 type='boolean' checked="true" truevalue="true"
688 falsevalue="false" label="Trim sequence
572 by quality score from the 3'-end?" help="By default, 689 by quality score from the 3'-end?" help="By default,
573 3'-end trimming is made based on a score of 20"/> 690 3'-end trimming is made based on a score of 20"/>
574 <when value="true"> 691 <when value="true">
575 <param name="right_quality_trimming_treatment_value" 692 <param name="right_quality_trimming_treatment_value"
576 type="integer" min="0" max="40" 693 type="integer" min="0" max="40"
577 value="20" label="Quality score threshold to 694 value="20" label="Quality score threshold to
578 trim positions" help=""/> 695 trim positions" help="(-trim_qual_right)"/>
579 </when> 696 </when>
697 <when value="false" />
580 </conditional> 698 </conditional>
581 <param name="type_quality_trimming_treatments" type="select" 699 <param name="type_quality_trimming_treatments" type="select"
582 display="radio" label="Type of quality score calculation 700 display="radio" label="Type of quality score calculation
583 to use" help="By default, min is used"> 701 to use" help="By default, min is used. (-trim_qual_type)">
584 <option value="min" selected="true">Mininum</option> 702 <option value="min" selected="true">Mininum</option>
585 <option value="mean" >Mean</option> 703 <option value="mean" >Mean</option>
586 <option value="max" >Max</option> 704 <option value="max" >Max</option>
587 <option value="sum" >Sum</option> 705 <option value="sum" >Sum</option>
588 </param> 706 </param>
589 <param name="rule_quality_trimming_treatments" type="select" 707 <param name="rule_quality_trimming_treatments" type="select"
590 display="radio" label="Rule tu use to compare quality 708 display="radio" label="Rule tu use to compare quality
591 score to calculated value" help="By default, 'less than' 709 score to calculated value" help="By default, 'less than'
592 is used"> 710 is used. (-trim_qual_rule)">
593 <option value="lt" selected="true">Less than</option> 711 <option value="lt" selected="true">Less than</option>
594 <option value="gt" >Greater than</option> 712 <option value="gt" >Greater than</option>
595 <option value="et" >Equal to</option> 713 <option value="et" >Equal to</option>
596 </param> 714 </param>
597 <param name="window_quality_trimming_treatments" type="integer" 715 <param name="window_quality_trimming_treatments" type="integer"
598 min="0" max="300" value="1" label="Size of the sliding 716 min="0" max="300" value="1" label="Size of the sliding
599 window used to calculated quality score by type" help="To 717 window used to calculated quality score by type" help="To
600 stop at the first base that fails the rule defined, use a 718 stop at the first base that fails the rule defined, use a
601 window size of 1 (default value)"/> 719 window size of 1 (default value). (-trim_qual_window)"/>
602 <param name="step_quality_trimming_treatments" type="integer" 720 <param name="step_quality_trimming_treatments" type="integer"
603 min="0" max="300" value="1" label="Step size used to move 721 min="0" max="300" value="1" label="Step size used to move
604 the sliding window" help="To move the window over all 722 the sliding window" help="To move the window over all
605 quality scores without missing any, the step size sould 723 quality scores without missing any, the step size sould
606 be less or equal to the window size. The default value 724 be less or equal to the window size. The default value
607 is 1."/> 725 is 1. (-trim_qual_step)"/>
608 </when> 726 </when>
727 <when value="false" />
609 </conditional> 728 </conditional>
610 </when> 729 </when>
730 <when value="false" />
611 </conditional> 731 </conditional>
732
733 <param name="graph_stats" type="select" multiple="True" label="Which statistics should be calculated included in the graph_data file" help="(-graph_stats)">
734 <option value="ld" selected="True">Length distribution</option>
735 <option value="gc" selected="True">GC content distribution</option>
736 <option value="qd" selected="True">Base quality distribution</option>
737 <option value="ns" selected="True">Occurence of N</option>
738 <option value="pt" selected="True">Poly-A/T tails</option>
739 <option value="ts" selected="True">Tag sequence check</option>
740 <option value="aq" selected="True">Assembly quality measure</option>
741 <option value="de" selected="True">Sequence duplication - exact only</option>
742 <option value="da" selected="True">Sequence duplication - exact + 5'/3'</option>
743 <option value="sc" selected="True">Sequence complexity</option>
744 <option value="dn" selected="True">Dinucleotide odds ratios, includes the PCA plots</option>
745 </param>
612 </inputs> 746 </inputs>
613 747
614 <outputs> 748 <outputs>
615 <data format="fastq" name="good_sequence_file" 749 <data format="fastq" name="good_sequence_file"
616 from_work_dir="good_sequences.fastq" 750 from_work_dir="good_sequences.fastq"
617 label="Good sequences of ${on_string} (PRINSEQ)" /> 751 label="Good sequences of ${on_string} (PRINSEQ)" >
752 <filter>seq_type['seq_type_opt'] == "single"</filter>
753 </data>
618 <data format="fastq" name="rejected_sequence_file" 754 <data format="fastq" name="rejected_sequence_file"
619 from_work_dir="rejected_sequences.fastq" 755 from_work_dir="rejected_sequences.fastq"
620 label="Rejected sequences of ${on_string} (PRINSEQ)" /> 756 label="Rejected sequences of ${on_string} (PRINSEQ)" >
757 <filter>seq_type['seq_type_opt'] == "single"</filter>
758 </data>
759
760 <data format="fastq" name="good_sequences_1_file"
761 from_work_dir="good_sequences_1.fastq"
762 label="Good sequences for R1 of ${on_string} (PRINSEQ)" >
763 <filter>seq_type['seq_type_opt'] == "paired"</filter>
764 </data>
765 <data format="fastq" name="good_sequences_1_singletons_file"
766 from_work_dir="good_sequences_1_singletons.fastq"
767 label="Good singleton sequences for R1 of ${on_string} (PRINSEQ)" >
768 <filter>seq_type['seq_type_opt'] == "paired"</filter>
769 </data>
770 <data format="fastq" name="rejected_sequence_1_file"
771 from_work_dir="rejected_sequences_1.fastq"
772 label="Rejected sequences for R1 of ${on_string} (PRINSEQ)" >
773 <filter>seq_type['seq_type_opt'] == "paired"</filter>
774 </data>
775 <data format="fastq" name="good_sequences_2_file"
776 from_work_dir="good_sequences_2.fastq"
777 label="Good sequences for R2 of ${on_string} (PRINSEQ)" >
778 <filter>seq_type['seq_type_opt'] == "paired"</filter>
779 </data>
780 <data format="fastq" name="good_sequences_2_singletons_file"
781 from_work_dir="good_sequences_2_singletons.fastq"
782 label="Good singleton sequences for R2 of ${on_string} (PRINSEQ)" >
783 <filter>seq_type['seq_type_opt'] == "paired"</filter>
784 </data>
785 <data format="fastq" name="rejected_sequence_2_file"
786 from_work_dir="rejected_sequences_2.fastq"
787 label="Rejected sequences for R2 of ${on_string} (PRINSEQ)" >
788 <filter>seq_type['seq_type_opt'] == "paired"</filter>
789 </data>
790
791 <data format="html" name="html_file"
792 from_work_dir="stats_html.html"
793 label="Summary of ${tool.name} on ${on_string} summary" />
621 </outputs> 794 </outputs>
622 795
623 <tests> 796 <tests>
624 <test> 797 <test>
625 <param name="sequence_to_control_file" value="prinseq_input_sequences.fastq"/> 798 <param name="sequence_to_control_file" value="prinseq_input_sequences.fastq"/>
680 853
681 ----- 854 -----
682 855
683 **Parameters** 856 **Parameters**
684 857
685 The parameters are numerous in PRINSEQ 858 The parameters are numerous in PRINSEQ given the wanted treatments.
686 859
687 - Filtering parameters to eliminate sequences 860 Several filter treatments are proposed:
688 - Filters based on sequence length 861
689 - Filters based on quality score 862 - Filters based on sequence length
690 - Filters based on base content 863 - Filters based on quality score
691 - Trimming parameters to eliminate sequence parts 864 - Filters based on base content
692 - Trim of ends 865
693 - Trim of tails 866 And several trimming treatments eliminate sequence parts:
694 - Trim based quality score 867 - Trim of ends
868 - Trim of tails
869 - Trim based quality score
870
871 All these treaments can be customed using the proposed parameters.
695 872
696 ----- 873 -----
697 874
698 **Output** 875 **Output**
699 876