Mercurial > repos > lparsons > cutadapt

comparison macros.xml @ 19:49370cb85f0f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 6318c53e772ed592862729f3048ed9bd3a711969
author iuc
date Tue, 18 Dec 2018 14:09:53 -0500
parents 8f1df515eb87
children e4691e1589d3
comparison
equal deleted inserted replaced
18:5c7e7d905b33 19:49370cb85f0f
5 ## Read1 trimming 5 ## Read1 trimming
6 6
7 #for $a in $library.r1.adapters 7 #for $a in $library.r1.adapters
8 #if $a.adapter_source.adapter_source_list == 'builtin': 8 #if $a.adapter_source.adapter_source_list == 'builtin':
9 -a "${a.adapter_source.adapter.fields.name}"='${a.adapter_source.adapter}' 9 -a "${a.adapter_source.adapter.fields.name}"='${a.adapter_source.adapter}'
10 #else if $a.adapter_source.adapter_source_list == 'file':
11 -a file:'${a.adapter_source.adapter_file}'
10 #else if str($a.adapter_source.adapter_name) != "": 12 #else if str($a.adapter_source.adapter_name) != "":
11 -a '${a.adapter_source.adapter_name}'='${a.adapter_source.adapter}' 13 -a '${a.adapter_source.adapter_name}'='${a.adapter_source.adapter}'
12 #else 14 #else
13 -a '${a.adapter_source.adapter}' 15 -a '${a.adapter_source.adapter}'
14 #end if 16 #end if
15 #end for 17 #end for
16 #for $aa in $library.r1.anywhere_adapters 18 #for $aa in $library.r1.anywhere_adapters
17 #if $aa.anywhere_adapter_source.anywhere_adapter_source_list == 'builtin': 19 #if $aa.anywhere_adapter_source.anywhere_adapter_source_list == 'builtin':
18 -b ${aa.anywhere_adapter_source.anywhere_adapter.fields.name}"='${aa.anywhere_adapter_source.anywhere_adapter}' 20 -b ${aa.anywhere_adapter_source.anywhere_adapter.fields.name}"='${aa.anywhere_adapter_source.anywhere_adapter}'
21 #else if $aa.anywhere_adapter_source.anywhere_adapter_source_list == 'file':
22 -b file:'${aa.anywhere_adapter_source.anywhere_adapter_file}'
19 #else if str($aa.anywhere_adapter_source.anywhere_adapter_name) != "": 23 #else if str($aa.anywhere_adapter_source.anywhere_adapter_name) != "":
20 -b '${aa.anywhere_adapter_source.anywhere_adapter_name}'='${aa.anywhere_adapter_source.anywhere_adapter}' 24 -b '${aa.anywhere_adapter_source.anywhere_adapter_name}'='${aa.anywhere_adapter_source.anywhere_adapter}'
21 #else 25 #else
22 -b '${aa.anywhere_adapter_source.anywhere_adapter}' 26 -b '${aa.anywhere_adapter_source.anywhere_adapter}'
23 #end if 27 #end if
24 #end for 28 #end for
25 #for $fa in $library.r1.front_adapters 29 #for $fa in $library.r1.front_adapters
26 #if $fa.front_adapter_source.front_adapter_source_list == 'builtin': 30 #if $fa.front_adapter_source.front_adapter_source_list == 'builtin':
27 -g "${fa.front_adapter_source.front_adapter.fields.name}"='${fa.front_adapter_source.front_adapter}' 31 -g "${fa.front_adapter_source.front_adapter.fields.name}"='${fa.front_adapter_source.front_adapter}'
32 #else if $fa.front_adapter_source.front_adapter_source_list == 'file':
33 -g file:'${fa.front_adapter_source.front_adapter_file}'
28 #else if str($fa.front_adapter_source.front_adapter_name) != "": 34 #else if str($fa.front_adapter_source.front_adapter_name) != "":
29 -g '${fa.front_adapter_source.front_adapter_name}'='${fa.front_adapter_source.front_adapter}' 35 -g '${fa.front_adapter_source.front_adapter_name}'='${fa.front_adapter_source.front_adapter}'
30 #else 36 #else
31 -g '${fa.front_adapter_source.front_adapter}' 37 -g '${fa.front_adapter_source.front_adapter}'
32 #end if 38 #end if
64 ## Read2 trimming 70 ## Read2 trimming
65 71
66 #for $a in $library.r2.adapters2 72 #for $a in $library.r2.adapters2
67 #if $a.adapter_source2.adapter_source_list2 == 'builtin': 73 #if $a.adapter_source2.adapter_source_list2 == 'builtin':
68 -A "${a.adapter_source2.adapter2.fields.name}"='${a.adapter_source2.adapter2}' 74 -A "${a.adapter_source2.adapter2.fields.name}"='${a.adapter_source2.adapter2}'
75 #else if $a.adapter_source2.adapter_source_list2 == 'file':
76 -A file:'${a.adapter_source2.adapter_file2}'
69 #else if str($a.adapter_source2.adapter_name2) != "": 77 #else if str($a.adapter_source2.adapter_name2) != "":
70 -A '${a.adapter_source2.adapter_name2}'='${a.adapter_source2.adapter2}' 78 -A '${a.adapter_source2.adapter_name2}'='${a.adapter_source2.adapter2}'
71 #else 79 #else
72 -A '${a.adapter_source2.adapter2}' 80 -A '${a.adapter_source2.adapter2}'
73 #end if 81 #end if
74 #end for 82 #end for
75 #for $aa in $library.r2.anywhere_adapters2 83 #for $aa in $library.r2.anywhere_adapters2
76 #if $aa.anywhere_adapter_source2.anywhere_adapter_source_list2 == 'builtin': 84 #if $aa.anywhere_adapter_source2.anywhere_adapter_source_list2 == 'builtin':
77 -B "${aa.anywhere_adapter_source2.anywhere_adapter2.fields.name}"='${aa.anywhere_adapter_source2.anywhere_adapter2}' 85 -B "${aa.anywhere_adapter_source2.anywhere_adapter2.fields.name}"='${aa.anywhere_adapter_source2.anywhere_adapter2}'
86 #else if $aa.anywhere_adapter_source2.anywhere_adapter_source_list2 == 'file':
87 -B file:'${aa.anywhere_adapter_source2.anywhere_adapter_file2}'
78 #else if str($aa.anywhere_adapter_source2.anywhere_adapter_name2) != "": 88 #else if str($aa.anywhere_adapter_source2.anywhere_adapter_name2) != "":
79 -B '${aa.anywhere_adapter_source2.anywhere_adapter_name2}'='${aa.anywhere_adapter_source2.anywhere_adapter2}' 89 -B '${aa.anywhere_adapter_source2.anywhere_adapter_name2}'='${aa.anywhere_adapter_source2.anywhere_adapter2}'
80 #else 90 #else
81 -B '${aa.anywhere_adapter_source2.anywhere_adapter2}' 91 -B '${aa.anywhere_adapter_source2.anywhere_adapter2}'
82 #end if 92 #end if
83 #end for 93 #end for
84 #for $fa in $library.r2.front_adapters2 94 #for $fa in $library.r2.front_adapters2
85 #if $fa.front_adapter_source2.front_adapter_source_list2 == 'builtin': 95 #if $fa.front_adapter_source2.front_adapter_source_list2 == 'builtin':
86 -G "${fa.front_adapter_source2.front_adapter2.fields.name}"='${fa.front_adapter_source2.front_adapter2}' 96 -G "${fa.front_adapter_source2.front_adapter2.fields.name}"='${fa.front_adapter_source2.front_adapter2}'
97 #else if $fa.front_adapter_source2.front_adapter_source_list2 == 'file':
98 -G file:'${fa.front_adapter_source2.front_adapter_file2}'
87 #else if str($fa.front_adapter_source2.front_adapter_name2) != "": 99 #else if str($fa.front_adapter_source2.front_adapter_name2) != "":
88 -G '${fa.front_adapter_source2.front_adapter_name2}'='${fa.front_adapter_source2.front_adapter2}' 100 -G '${fa.front_adapter_source2.front_adapter_name2}'='${fa.front_adapter_source2.front_adapter2}'
89 #else 101 #else
90 -G '${fa.front_adapter_source2.front_adapter2}' 102 -G '${fa.front_adapter_source2.front_adapter2}'
91 #end if 103 #end if
116 <repeat name="adapters" title="3' (End) Adapters" help="Sequence of an adapter ligated to the 3' end (paired data: of the first read). The adapter and subsequent bases are trimmed. If a '$' character is appended ('anchoring'), the adapter is only found if it is a suffix of the read. To search for a linked adapter, separate the 2 sequences with 3 dots (ADAPTER1...ADAPTER2), see Help below."> 128 <repeat name="adapters" title="3' (End) Adapters" help="Sequence of an adapter ligated to the 3' end (paired data: of the first read). The adapter and subsequent bases are trimmed. If a '$' character is appended ('anchoring'), the adapter is only found if it is a suffix of the read. To search for a linked adapter, separate the 2 sequences with 3 dots (ADAPTER1...ADAPTER2), see Help below.">
117 <conditional name="adapter_source"> 129 <conditional name="adapter_source">
118 <param name="adapter_source_list" type="select" label="Source" > 130 <param name="adapter_source_list" type="select" label="Source" >
119 <option value="builtin" selected="True">Standard (select from the list below)</option> 131 <option value="builtin" selected="True">Standard (select from the list below)</option>
120 <option value="user">Enter custom sequence</option> 132 <option value="user">Enter custom sequence</option>
133 <option value="file">File From History</option>
121 </param> 134 </param>
122 135
123 <when value="user"> 136 <when value="user">
124 <param name="adapter_name" type="text" value="" optional="True" label="Enter custom 3' adapter name (Optional if Multiple output is 'No')" /> 137 <param name="adapter_name" type="text" value="" optional="True" label="Enter custom 3' adapter name (Optional if Multiple output is 'No')" />
125 <param name="adapter" argument="-a" type="text" value="AATTGGCC" label="Enter custom 3' adapter sequence" /> 138 <param name="adapter" argument="-a" type="text" value="AATTGGCC" label="Enter custom 3' adapter sequence" />
129 <param name="adapter" argument="-a" type="select" label="Choose 3' adapter"> 142 <param name="adapter" argument="-a" type="select" label="Choose 3' adapter">
130 <options from_data_table="adapters"> 143 <options from_data_table="adapters">
131 <filter type="sort_by" column="1" /> 144 <filter type="sort_by" column="1" />
132 </options> 145 </options>
133 </param> 146 </param>
147 </when>
148
149 <when value="file">
150 <param name="adapter_file" argument="-a" format="fasta" type="data" help="Should be of datatype FASTA" label="Choose file containing 3' adapters" />
134 </when> 151 </when>
135 </conditional> 152 </conditional>
136 </repeat> 153 </repeat>
137 154
138 <repeat name="front_adapters" title="5' (Front) Adapters" help="Sequence of an adapter ligated to the 5' end (paired data: of the first read). The adapter and any preceding bases are trimmed. Partial matches at the 5' end are allowed. If a '^' character is prepended ('anchoring'), the adapter is only found if it is a prefix of the read. To search for a linked adapter, separate the 2 sequences with 3 dots (ADAPTER1...ADAPTER2), see Help below."> 155 <repeat name="front_adapters" title="5' (Front) Adapters" help="Sequence of an adapter ligated to the 5' end (paired data: of the first read). The adapter and any preceding bases are trimmed. Partial matches at the 5' end are allowed. If a '^' character is prepended ('anchoring'), the adapter is only found if it is a prefix of the read. To search for a linked adapter, separate the 2 sequences with 3 dots (ADAPTER1...ADAPTER2), see Help below.">
139 <conditional name="front_adapter_source"> 156 <conditional name="front_adapter_source">
140 <param name="front_adapter_source_list" type="select" label="Source"> 157 <param name="front_adapter_source_list" type="select" label="Source">
141 <option value="builtin" selected="True">Standard (select from the list below)</option> 158 <option value="builtin" selected="True">Standard (select from the list below)</option>
142 <option value="user">Enter custom sequence</option> 159 <option value="user">Enter custom sequence</option>
160 <option value="file">File From History</option>
143 </param> 161 </param>
144 162
145 <when value="user"> 163 <when value="user">
146 <param name="front_adapter_name" type="text" value="" optional="True" label="Enter custom 5' adapter name (Optional if Multiple output is 'No')" /> 164 <param name="front_adapter_name" type="text" value="" optional="True" label="Enter custom 5' adapter name (Optional if Multiple output is 'No')" />
147 <param name="front_adapter" argument="-g" type="text" value="AATTGGCC" label="Enter custom 5' adapter sequence" /> 165 <param name="front_adapter" argument="-g" type="text" value="AATTGGCC" label="Enter custom 5' adapter sequence" />
150 <param name="front_adapter" argument="-g" type="select" label="Choose 5' adapter"> 168 <param name="front_adapter" argument="-g" type="select" label="Choose 5' adapter">
151 <options from_data_table="adapters"> 169 <options from_data_table="adapters">
152 <filter type="sort_by" column="1" /> 170 <filter type="sort_by" column="1" />
153 </options> 171 </options>
154 </param> 172 </param>
173 </when>
174 <when value="file">
175 <param name="front_adapter_file" argument="-g" format="fasta" type="data" help="Should be of datatype &quot;FASTA&quot;" label="Choose file containing 5' adapters" />
155 </when> 176 </when>
156 </conditional> 177 </conditional>
157 </repeat> 178 </repeat>
158 179
159 <repeat name="anywhere_adapters" title="5' or 3' (Anywhere) Adapters" help="Sequence of an adapter that may be ligated to the 5' or 3' end (paired data: of the first read). Both types of matches as described under 3' und 5' Adapters are allowed. If the first base of the read is part of the match, the behavior is as with 5' Adapters, otherwise as with 3' Adapters. This option is mostly for rescuing failed library preparations - do not use if you know which end your adapter was ligated to!"> 180 <repeat name="anywhere_adapters" title="5' or 3' (Anywhere) Adapters" help="Sequence of an adapter that may be ligated to the 5' or 3' end (paired data: of the first read). Both types of matches as described under 3' und 5' Adapters are allowed. If the first base of the read is part of the match, the behavior is as with 5' Adapters, otherwise as with 3' Adapters. This option is mostly for rescuing failed library preparations - do not use if you know which end your adapter was ligated to!">
160 <conditional name="anywhere_adapter_source"> 181 <conditional name="anywhere_adapter_source">
161 <param name="anywhere_adapter_source_list" type="select" label="Source"> 182 <param name="anywhere_adapter_source_list" type="select" label="Source">
162 <option value="builtin" selected="True">Standard (select from the list below)</option> 183 <option value="builtin" selected="True">Standard (select from the list below)</option>
163 <option value="user">Enter custom sequence</option> 184 <option value="user">Enter custom sequence</option>
185 <option value="file">File From History</option>
164 </param> 186 </param>
165 187
166 <when value="user"> 188 <when value="user">
167 <param name="anywhere_adapter_name" type="text" value="" optional="True" label="Enter custom 5' or 3' adapter name (Optional if Multiple output is 'No')" /> 189 <param name="anywhere_adapter_name" type="text" value="" optional="True" label="Enter custom 5' or 3' adapter name (Optional if Multiple output is 'No')" />
168 <param name="anywhere_adapter" argument="-b" type="text" value="AATTGGCC" label="Enter custom 5' or 3' adapter sequence" /> 190 <param name="anywhere_adapter" argument="-b" type="text" value="AATTGGCC" label="Enter custom 5' or 3' adapter sequence" />
171 <param name="anywhere_adapter" argument="-b" type="select" label="Choose 5' or 3' adapter"> 193 <param name="anywhere_adapter" argument="-b" type="select" label="Choose 5' or 3' adapter">
172 <options from_data_table="adapters"> 194 <options from_data_table="adapters">
173 <filter type="sort_by" column="1" /> 195 <filter type="sort_by" column="1" />
174 </options> 196 </options>
175 </param> 197 </param>
198 </when>
199 <when value="file">
200 <param name="anywhere_adapter_file" argument="-b" format="fasta" type="data" help="Should be of datatype &quot;FASTA&quot;" label="Choose file containing 3' or 5' adapters" />
176 </when> 201 </when>
177 </conditional> 202 </conditional>
178 </repeat> 203 </repeat>
179 204
180 <param name="cut" argument="-u" type="integer" value="0" optional="True" label="Cut bases from reads before adapter trimming" help="Remove bases from each read (first read only if paired). If positive, remove bases from the beginning. If negative, remove bases from the end. This is applied *before* adapter trimming." /> 205 <param name="cut" argument="-u" type="integer" value="0" optional="True" label="Cut bases from reads before adapter trimming" help="Remove bases from each read (first read only if paired). If positive, remove bases from the beginning. If negative, remove bases from the end. This is applied *before* adapter trimming." />
194 <repeat name="adapters2" title="3' (End) Adapters" help="Sequence of an adapter ligated to the 3' end of the second read in each pair. The adapter and subsequent bases are trimmed. If a '$' character is appended ('anchoring'), the adapter is only found if it is a suffix of the read. To search for a linked adapter, separate the 2 sequences with 3 dots (ADAPTER1...ADAPTER2), see Help below."> 219 <repeat name="adapters2" title="3' (End) Adapters" help="Sequence of an adapter ligated to the 3' end of the second read in each pair. The adapter and subsequent bases are trimmed. If a '$' character is appended ('anchoring'), the adapter is only found if it is a suffix of the read. To search for a linked adapter, separate the 2 sequences with 3 dots (ADAPTER1...ADAPTER2), see Help below.">
195 <conditional name="adapter_source2"> 220 <conditional name="adapter_source2">
196 <param name="adapter_source_list2" type="select" label="Source" > 221 <param name="adapter_source_list2" type="select" label="Source" >
197 <option value="builtin" selected="True">Standard (select from the list below)</option> 222 <option value="builtin" selected="True">Standard (select from the list below)</option>
198 <option value="user">Enter custom sequence</option> 223 <option value="user">Enter custom sequence</option>
224 <option value="file">File From History</option>
199 </param> 225 </param>
200 226
201 <when value="user"> 227 <when value="user">
202 <param name="adapter_name2" type="text" value="" optional="True" label="Enter custom 3' adapter name (Optional)" /> 228 <param name="adapter_name2" type="text" value="" optional="True" label="Enter custom 3' adapter name (Optional)" />
203 <param name="adapter2" argument="-A" type="text" label="Enter custom 3' adapter sequence" value="AATTGGCC" /> 229 <param name="adapter2" argument="-A" type="text" label="Enter custom 3' adapter sequence" value="AATTGGCC" />
207 <param name="adapter2" argument="-A" type="select" label="Choose 3' adapter"> 233 <param name="adapter2" argument="-A" type="select" label="Choose 3' adapter">
208 <options from_data_table="adapters"> 234 <options from_data_table="adapters">
209 <filter type="sort_by" column="1" /> 235 <filter type="sort_by" column="1" />
210 </options> 236 </options>
211 </param> 237 </param>
238 </when>
239 <when value="file">
240 <param name="adapter_file2" argument="-a" format="fasta" type="data" help="Should be of datatype &quot;FASTA&quot;" label="Choose file containing 3' adapters" />
212 </when> 241 </when>
213 </conditional> 242 </conditional>
214 </repeat> 243 </repeat>
215 244
216 <repeat name="front_adapters2" title="5' (Front) Adapters" help="Sequence of an adapter ligated to the 5' end of the second read in each pair. The adapter and any preceding bases are trimmed. Partial matches at the 5' end are allowed. If a '^' character is prepended ('anchoring'), the adapter is only found if it is a prefix of the read. To search for a linked adapter, separate the 2 sequences with 3 dots (ADAPTER1...ADAPTER2), see Help below."> 245 <repeat name="front_adapters2" title="5' (Front) Adapters" help="Sequence of an adapter ligated to the 5' end of the second read in each pair. The adapter and any preceding bases are trimmed. Partial matches at the 5' end are allowed. If a '^' character is prepended ('anchoring'), the adapter is only found if it is a prefix of the read. To search for a linked adapter, separate the 2 sequences with 3 dots (ADAPTER1...ADAPTER2), see Help below.">
217 <conditional name="front_adapter_source2"> 246 <conditional name="front_adapter_source2">
218 <param name="front_adapter_source_list2" type="select" label="Source"> 247 <param name="front_adapter_source_list2" type="select" label="Source">
219 <option value="builtin" selected="True">Standard (select from the list below)</option> 248 <option value="builtin" selected="True">Standard (select from the list below)</option>
220 <option value="user">Enter custom sequence</option> 249 <option value="user">Enter custom sequence</option>
250 <option value="file">File From History</option>
221 </param> 251 </param>
222 252
223 <when value="user"> 253 <when value="user">
224 <param name="front_adapter_name2" type="text" value="" label="Enter custom 5' adapter name (Optional)" /> 254 <param name="front_adapter_name2" type="text" value="" label="Enter custom 5' adapter name (Optional)" />
225 <param name="front_adapter2" argument="-G" type="text" value="AATTGGCC" label="Enter custom 5' adapter sequence" /> 255 <param name="front_adapter2" argument="-G" type="text" value="AATTGGCC" label="Enter custom 5' adapter sequence" />
228 <param name="front_adapter2" argument="-G" type="select" label="Choose 5' adapter"> 258 <param name="front_adapter2" argument="-G" type="select" label="Choose 5' adapter">
229 <options from_data_table="adapters"> 259 <options from_data_table="adapters">
230 <filter type="sort_by" column="1" /> 260 <filter type="sort_by" column="1" />
231 </options> 261 </options>
232 </param> 262 </param>
263 </when>
264 <when value="file">
265 <param name="front_adapter_file2" argument="-g" format="fasta" type="data" help="Should be of datatype &quot;FASTA&quot;" label="Choose file containing 5' adapters" />
233 </when> 266 </when>
234 </conditional> 267 </conditional>
235 </repeat> 268 </repeat>
236 269
237 <repeat name="anywhere_adapters2" title="5' or 3' (Anywhere) Adapters" help="Sequence of an adapter that may be ligated to the 5' or 3' end of the second read in each pair. Both types of matches as described under under 3' und 5' Adapters are allowed. If the first base of the read is part of the match, the behavior is as with 5' Adapters, otherwise as with 3' Adapters. This option is mostly for rescuing failed library preparations - do not use if you know which end your adapter was ligated to!"> 270 <repeat name="anywhere_adapters2" title="5' or 3' (Anywhere) Adapters" help="Sequence of an adapter that may be ligated to the 5' or 3' end of the second read in each pair. Both types of matches as described under under 3' und 5' Adapters are allowed. If the first base of the read is part of the match, the behavior is as with 5' Adapters, otherwise as with 3' Adapters. This option is mostly for rescuing failed library preparations - do not use if you know which end your adapter was ligated to!">
238 <conditional name="anywhere_adapter_source2"> 271 <conditional name="anywhere_adapter_source2">
239 <param name="anywhere_adapter_source_list2" type="select" label="Source"> 272 <param name="anywhere_adapter_source_list2" type="select" label="Source">
240 <option value="builtin" selected="True">Standard (select from the list below)</option> 273 <option value="builtin" selected="True">Standard (select from the list below)</option>
241 <option value="user">Enter custom sequence</option> 274 <option value="user">Enter custom sequence</option>
275 <option value="file">File From History</option>
242 </param> 276 </param>
243 277
244 <when value="user"> 278 <when value="user">
245 <param name="anywhere_adapter_name2" type="text" value="" optional="True" label="Enter custom 5' or 3' adapter name (Optional)" /> 279 <param name="anywhere_adapter_name2" type="text" value="" optional="True" label="Enter custom 5' or 3' adapter name (Optional)" />
246 <param name="anywhere_adapter2" argument="-B" type="text" label="Enter custom 5' or 3' adapter sequence" value="AATTGGCC" /> 280 <param name="anywhere_adapter2" argument="-B" type="text" label="Enter custom 5' or 3' adapter sequence" value="AATTGGCC" />
249 <param name="anywhere_adapter2" argument="-B" type="select" label="Choose 5' or 3' adapter"> 283 <param name="anywhere_adapter2" argument="-B" type="select" label="Choose 5' or 3' adapter">
250 <options from_data_table="adapters"> 284 <options from_data_table="adapters">
251 <filter type="sort_by" column="1" /> 285 <filter type="sort_by" column="1" />
252 </options> 286 </options>
253 </param> 287 </param>
288 </when>
289 <when value="file">
290 <param name="anywhere_adapter_file2" argument="-b" format="fasta" type="data" help="Should be of datatype &quot;FASTA&quot;" label="Choose file containing 3' or 5' adapters" />
254 </when> 291 </when>
255 </conditional> 292 </conditional>
256 </repeat> 293 </repeat>
257 294
258 <param name="cut2" argument="-U" type="integer" value="0" optional="True" label="Cut bases from the second read in each pair." help="Remove bases from the beginning or end of each read before trimming adapters. If positive, the bases are removed from the beginning of each read. If negative, the bases are removed from the end of each read." /> 295 <param name="cut2" argument="-U" type="integer" value="0" optional="True" label="Cut bases from the second read in each pair." help="Remove bases from the beginning or end of each read before trimming adapters. If positive, the bases are removed from the beginning of each read. If negative, the bases are removed from the end of each read." />