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comparison macros.xml @ 35:9845c649f41b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit c37e2aeba811fd041c08f0e119a3cbe90bfa7418
author iuc
date Sun, 17 Dec 2023 18:52:25 +0000
parents 8c0175e03cee
children 64172f1c1202
comparison
equal deleted inserted replaced
34:8c0175e03cee 35:9845c649f41b
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">4.4</token> 2 <token name="@TOOL_VERSION@">4.6</token>
3 <token name="@VERSION_SUFFIX@">0</token> 3 <token name="@VERSION_SUFFIX@">0</token>
4 <token name="@FASTQ_TYPES@">fastq.gz,fastq,fasta</token> 4 <token name="@FASTQ_TYPES@">fastq.bz2,fastq.gz,fastq,fasta.bz2,fasta.gz,fasta</token>
5 <xml name="edam_ontology"> 5 <xml name="edam_ontology">
6 <edam_topics> 6 <edam_topics>
7 <edam_topic>topic_0632</edam_topic> 7 <edam_topic>topic_0632</edam_topic>
8 </edam_topics> 8 </edam_topics>
9 <edam_operations> 9 <edam_operations>
23 <xml name="xrefs"> 23 <xml name="xrefs">
24 <xrefs> 24 <xrefs>
25 <xref type='bio.tools'>cutadapt</xref> 25 <xref type='bio.tools'>cutadapt</xref>
26 </xrefs> 26 </xrefs>
27 </xml> 27 </xml>
28
29 <!-- parametrized token - you need to set `$ADAPTER_ARGUMENT` -->
30 <token name="@adapter_cli@">
31 #if $a.adapter_source.adapter_source_list == 'builtin':
32 $ADAPTER_ARGUMENT '${a.adapter_source.adapter.fields.name}'='${a.adapter_source.adapter}${a.single_noindels}'
33 #else if $a.adapter_source.adapter_source_list == 'file':
34 $ADAPTER_ARGUMENT file:'${a.adapter_source.adapter_file}${a.single_noindels}'
35 #else if str($a.adapter_source.adapter_name) != "":
36 $ADAPTER_ARGUMENT '${a.adapter_source.adapter_name}'='${a.adapter_source.adapter}${a.single_noindels}'
37 #else
38 $ADAPTER_ARGUMENT '${a.adapter_source.adapter}${a.single_noindels}'
39 #end if
40 </token>
41
28 <token name="@read1_options@"><![CDATA[ 42 <token name="@read1_options@"><![CDATA[
29 43
30 ## Read1 trimming 44 ## Read1 trimming
31 45
46 #set ADAPTER_ARGUMENT="-a"
32 #for $a in $library.r1.adapters 47 #for $a in $library.r1.adapters
33 #if $a.adapter_source.adapter_source_list == 'builtin': 48 @adapter_cli@
34 -a '${a.adapter_source.adapter.fields.name}'='${a.adapter_source.adapter}${adapter_options.internal}${a.single_noindels}' 49 #end for
35 #else if $a.adapter_source.adapter_source_list == 'file': 50
36 -a file:'${a.adapter_source.adapter_file}${adapter_options.internal}${a.single_noindels}' 51 #set ADAPTER_ARGUMENT="-b"
37 #else if str($a.adapter_source.adapter_name) != "": 52 #for $a in $library.r1.anywhere_adapters
38 -a '${a.adapter_source.adapter_name}'='${a.adapter_source.adapter}${adapter_options.internal}${a.single_noindels}' 53 @adapter_cli@
39 #else 54 #end for
40 -a '${a.adapter_source.adapter}${adapter_options.internal}${a.single_noindels}' 55
41 #end if 56 #set ADAPTER_ARGUMENT="-g"
42 #end for 57 #for $a in $library.r1.front_adapters
43 #for $aa in $library.r1.anywhere_adapters 58 @adapter_cli@
44 #if $aa.anywhere_adapter_source.anywhere_adapter_source_list == 'builtin': 59 #end for
45 -b '${aa.anywhere_adapter_source.anywhere_adapter.fields.name}'='${aa.anywhere_adapter_source.anywhere_adapter}${aa.single_noindels}' 60
46 #else if $aa.anywhere_adapter_source.anywhere_adapter_source_list == 'file': 61 #if str($cut) != '0':
47 -b file:'${aa.anywhere_adapter_source.anywhere_adapter_file}${aa.single_noindels}' 62 -u $cut
48 #else if str($aa.anywhere_adapter_source.anywhere_adapter_name) != "":
49 -b '${aa.anywhere_adapter_source.anywhere_adapter_name}'='${aa.anywhere_adapter_source.anywhere_adapter}${aa.single_noindels}'
50 #else
51 -b '${aa.anywhere_adapter_source.anywhere_adapter}${aa.single_noindels}'
52 #end if
53 #end for
54 #for $fa in $library.r1.front_adapters
55 #if $fa.front_adapter_source.front_adapter_source_list == 'builtin':
56 -g '${fa.front_adapter_source.front_adapter.fields.name}'='${adapter_options.internal}${fa.front_adapter_source.front_adapter}${fa.single_noindels}'
57 #else if $fa.front_adapter_source.front_adapter_source_list == 'file':
58 -g file:'${adapter_options.internal}${fa.front_adapter_source.front_adapter_file}${fa.single_noindels}'
59 #else if str($fa.front_adapter_source.front_adapter_name) != "":
60 -g '${fa.front_adapter_source.front_adapter_name}'='${adapter_options.internal}${fa.front_adapter_source.front_adapter}${fa.single_noindels}'
61 #else
62 -g '${adapter_options.internal}${fa.front_adapter_source.front_adapter}${fa.single_noindels}'
63 #end if
64 #end for
65
66 #if str($library.r1.cut) != '0':
67 -u $library.r1.cut
68 #end if 63 #end if
69 64
70 ## Additional Outputs 65 ## Additional Outputs
71 66
72 #if 'info_file' in $output_selector: 67 #if 'info_file' in $output_selector:
92 87
93 <token name="@read2_options@"><![CDATA[ 88 <token name="@read2_options@"><![CDATA[
94 89
95 ## Read2 trimming 90 ## Read2 trimming
96 91
92 #set ADAPTER_ARGUMENT="-A"
97 #for $a in $library.r2.adapters2 93 #for $a in $library.r2.adapters2
98 #if $a.adapter_source2.adapter_source_list2 == 'builtin': 94 @adapter_cli@
99 -A '${a.adapter_source2.adapter2.fields.name}'='${a.adapter_source2.adapter2}${adapter_options.internal}${a.single_noindels}' 95 #end for
100 #else if $a.adapter_source2.adapter_source_list2 == 'file': 96 #set ADAPTER_ARGUMENT="-B"
101 -A file:'${a.adapter_source2.adapter_file2}${adapter_options.internal}${a.single_noindels}' 97 #for $a in $library.r2.anywhere_adapters2
102 #else if str($a.adapter_source2.adapter_name2) != "": 98 @adapter_cli@
103 -A '${a.adapter_source2.adapter_name2}'='${a.adapter_source2.adapter2}${adapter_options.internal}${a.single_noindels}' 99 #end for
104 #else 100 #set ADAPTER_ARGUMENT="-G"
105 -A '${a.adapter_source2.adapter2}${adapter_options.internal}${a.single_noindels}' 101 #for $a in $library.r2.front_adapters2
106 #end if 102 @adapter_cli@
107 #end for
108 #for $aa in $library.r2.anywhere_adapters2
109 #if $aa.anywhere_adapter_source2.anywhere_adapter_source_list2 == 'builtin':
110 -B '${aa.anywhere_adapter_source2.anywhere_adapter2.fields.name}'='${aa.anywhere_adapter_source2.anywhere_adapter2}${aa.single_noindels}'
111 #else if $aa.anywhere_adapter_source2.anywhere_adapter_source_list2 == 'file':
112 -B file:'${aa.anywhere_adapter_source2.anywhere_adapter_file2}${aa.single_noindels}'
113 #else if str($aa.anywhere_adapter_source2.anywhere_adapter_name2) != "":
114 -B '${aa.anywhere_adapter_source2.anywhere_adapter_name2}'='${aa.anywhere_adapter_source2.anywhere_adapter2}${aa.single_noindels}'
115 #else
116 -B '${aa.anywhere_adapter_source2.anywhere_adapter2}'
117 #end if
118 #end for
119 #for $fa in $library.r2.front_adapters2
120 #if $fa.front_adapter_source2.front_adapter_source_list2 == 'builtin':
121 -G '${fa.front_adapter_source2.front_adapter2.fields.name}'='${adapter_options.internal}${fa.front_adapter_source2.front_adapter2}${fa.single_noindels}'
122 #else if $fa.front_adapter_source2.front_adapter_source_list2 == 'file':
123 -G file:'${adapter_options.internal}${fa.front_adapter_source2.front_adapter_file2}${fa.single_noindels}'
124 #else if str($fa.front_adapter_source2.front_adapter_name2) != "":
125 -G '${fa.front_adapter_source2.front_adapter_name2}'='${adapter_options.internal}${fa.front_adapter_source2.front_adapter2}${fa.single_noindels}'
126 #else
127 -G '${adapter_options.internal}${fa.front_adapter_source2.front_adapter2}${fa.single_noindels}'
128 #end if
129 #end for 103 #end for
130 104
131 #if str($library.r2.cut2) != '0': 105 #if str($library.r2.cut2) != '0':
132 -U $library.r2.cut2 106 -U $library.r2.cut2
133 #end if 107 #end if
180 154
181 </valid> 155 </valid>
182 </sanitizer> 156 </sanitizer>
183 </xml> 157 </xml>
184 158
185 <xml name="adapter" token_name="" token_argument="" token_value="" token_label=""> 159 <xml name="adapter_conditional" tokens="adapter_type,argument">
186 <param name="@NAME@" argument="@ARGUMENT@" type="text" value="@VALUE@" label="@LABEL@"> 160 <conditional name="adapter_source">
187 <expand macro="adapter_sanitizer"/> 161 <param name="adapter_source_list" type="select" label="Source" >
188 </param> 162 <option value="builtin" selected="true">Standard (select from the list below)</option>
189 </xml> 163 <option value="user">Enter custom sequence</option>
190 164 <option value="file">File from history</option>
191 <xml name="adapter_select" token_name="" token_argument="" token_label=""> 165 </param>
192 <param name="@NAME@" argument="@ARGUMENT@" type="select" label="@LABEL@"> 166 <when value="user">
193 <options from_data_table="adapters"> 167 <param name="adapter_name" type="text" value="" optional="true" label="Custom @ADAPTER_TYPE@ adapter name" help="Optional if 'Multiple output' is selected in the Outputs selector'" />
194 <filter type="sort_by" column="1" /> 168 <param name="adapter" argument="@ARGUMENT@" type="text" value="AATTGGCC" label="Custom @ADAPTER_TYPE@ adapter sequence">
195 </options> 169 <expand macro="adapter_sanitizer"/>
196 <expand macro="adapter_sanitizer"/> 170 </param>
197 </param> 171 </when>
172 <when value="builtin">
173 <param name="adapter" argument="@ARGUMENT@" type="select" label="@ADAPTER_TYPE@ adapter">
174 <options from_data_table="adapters">
175 <filter type="sort_by" column="1" />
176 </options>
177 <expand macro="adapter_sanitizer"/>
178 </param>
179 </when>
180 <when value="file">
181 <param name="adapter_file" argument="@ARGUMENT@" format="fasta" type="data" label="File containing @ADAPTER_TYPE@ adapters" help="Should be of datatype FASTA" />
182 </when>
183 </conditional>
184 <param name="single_noindels" type="boolean" truevalue=";noindels" falsevalue="" checked="false" label="Disallow indels for this adapter"/>
198 </xml> 185 </xml>
199 186
200 <xml name="single_end_options" > 187 <xml name="single_end_options" >
201 188 <section name="r1" title="Read 1 Options" expanded="true">
202 <section name="r1" title="Read 1 Options" expanded="True">
203
204 <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."> 189 <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.">
205 <conditional name="adapter_source"> 190 <expand macro="adapter_conditional" argument="-a" adapter_type="3'"/>
206 <param name="adapter_source_list" type="select" label="Source" > 191 </repeat>
207 <option value="builtin" selected="True">Standard (select from the list below)</option>
208 <option value="user">Enter custom sequence</option>
209 <option value="file">File from history</option>
210 </param>
211
212 <when value="user">
213 <param name="adapter_name" type="text" value="" optional="True" label="Enter custom 3' adapter name (Optional if Multiple output is 'No')" />
214 <expand macro="adapter" name="adapter" argument="-a" type="text" value="AATTGGCC" label="Enter custom 3' adapter sequence" />
215 </when>
216
217 <when value="builtin">
218 <expand macro="adapter_select" name="adapter" argument="-a" label="Choose 3' adapter"/>
219 </when>
220
221 <when value="file">
222 <param name="adapter_file" argument="-a" format="fasta" type="data" help="Should be of datatype FASTA" label="Choose file containing 3' adapters" />
223 </when>
224 </conditional>
225 <param name="single_noindels" type="boolean" truevalue=";noindels" falsevalue="" checked="false" label="Disallow indels for this adapter"/>
226 </repeat>
227
228 <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."> 192 <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.">
229 <conditional name="front_adapter_source"> 193 <expand macro="adapter_conditional" argument="-g" adapter_type="5'"/>
230 <param name="front_adapter_source_list" type="select" label="Source"> 194 </repeat>
231 <option value="builtin" selected="True">Standard (select from the list below)</option>
232 <option value="user">Enter custom sequence</option>
233 <option value="file">File from history</option>
234 </param>
235
236 <when value="user">
237 <param name="front_adapter_name" type="text" value="" optional="True" label="Enter custom 5' adapter name (Optional if Multiple output is 'No')" />
238 <expand macro="adapter" name="front_adapter" argument="-g" value="AATTGGCC" label="Enter custom 5' adapter sequence" />
239 </when>
240 <when value="builtin">
241 <expand macro="adapter_select" name="front_adapter" argument="-g" label="Choose 5' adapter"/>
242 </when>
243 <when value="file">
244 <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" />
245 </when>
246 </conditional>
247 <param name="single_noindels" type="boolean" truevalue=";noindels" falsevalue="" checked="false" label="Disallow indels for this adapter"/>
248 </repeat>
249
250 <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!"> 195 <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!">
251 <conditional name="anywhere_adapter_source"> 196 <expand macro="adapter_conditional" argument="-b" adapter_type="5' or 3'"/>
252 <param name="anywhere_adapter_source_list" type="select" label="Source"> 197 </repeat>
253 <option value="builtin" selected="True">Standard (select from the list below)</option>
254 <option value="user">Enter custom sequence</option>
255 <option value="file">File from history</option>
256 </param>
257
258 <when value="user">
259 <param name="anywhere_adapter_name" type="text" value="" optional="True" label="Enter custom 5' or 3' adapter name (Optional if Multiple output is 'No')" />
260 <expand macro="adapter" name="anywhere_adapter" argument="-b" value="AATTGGCC" label="Enter custom 5' or 3' adapter sequence" />
261 </when>
262 <when value="builtin">
263 <expand macro="adapter_select" name="anywhere_adapter" argument="-b" label="Choose 5' or 3' adapter"/>
264 </when>
265 <when value="file">
266 <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" />
267 </when>
268 </conditional>
269 <param name="single_noindels" type="boolean" truevalue=";noindels" falsevalue="" checked="false" label="Disallow indels for this adapter"/>
270 </repeat>
271
272 <param argument="--cut" 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." />
273
274 </section> 198 </section>
275
276 </xml> 199 </xml>
277 200
278 <xml name="paired_end_options" > 201 <xml name="paired_end_options" >
279 202
280 <!-- Read 1 Options --> 203 <!-- Read 1 Options -->
281 <expand macro="single_end_options" /> 204 <expand macro="single_end_options" />
282 205
283 <!-- Read 2 Options --> 206 <!-- Read 2 Options -->
284 <section name="r2" title="Read 2 Options" expanded="True"> 207 <section name="r2" title="Read 2 Options" expanded="true">
285
286 <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."> 208 <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.">
287 <conditional name="adapter_source2"> 209 <expand macro="adapter_conditional" argument="-A" adapter_type="3'"/>
288 <param name="adapter_source_list2" type="select" label="Source" > 210 </repeat>
289 <option value="builtin" selected="True">Standard (select from the list below)</option>
290 <option value="user">Enter custom sequence</option>
291 <option value="file">File from history</option>
292 </param>
293
294 <when value="user">
295 <param name="adapter_name2" type="text" value="" optional="True" label="Enter custom 3' adapter name (Optional)" />
296 <expand macro="adapter" name="adapter2" argument="-A" label="Enter custom 3' adapter sequence" value="AATTGGCC" />
297 </when>
298
299 <when value="builtin">
300 <expand macro="adapter_select" name="adapter2" argument="-A" label="Choose 3' adapter"/>
301 </when>
302 <when value="file">
303 <param name="adapter_file2" argument="-a" format="fasta" type="data" help="Should be of datatype &quot;FASTA&quot;" label="Choose file containing 3' adapters" />
304 </when>
305 </conditional>
306 <param name="single_noindels" type="boolean" truevalue=";noindels" falsevalue="" checked="false" label="Disallow indels for this adapter"/>
307 </repeat>
308
309 <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."> 211 <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.">
310 <conditional name="front_adapter_source2"> 212 <expand macro="adapter_conditional" argument="-G" adapter_type="5'"/>
311 <param name="front_adapter_source_list2" type="select" label="Source"> 213 </repeat>
312 <option value="builtin" selected="True">Standard (select from the list below)</option>
313 <option value="user">Enter custom sequence</option>
314 <option value="file">File from history</option>
315 </param>
316
317 <when value="user">
318 <param name="front_adapter_name2" type="text" value="" label="Enter custom 5' adapter name (Optional)" />
319 <expand macro="adapter" name="front_adapter2" argument="-G" value="AATTGGCC" label="Enter custom 5' adapter sequence" />
320 </when>
321 <when value="builtin">
322 <expand macro="adapter_select" name="front_adapter2" argument="-G" label="Choose 5' adapter"/>
323 </when>
324 <when value="file">
325 <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" />
326 </when>
327 </conditional>
328 <param name="single_noindels" type="boolean" truevalue=";noindels" falsevalue="" checked="false" label="Disallow indels for this adapter"/>
329 </repeat>
330
331 <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!"> 214 <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!">
332 <conditional name="anywhere_adapter_source2"> 215 <expand macro="adapter_conditional" argument="-B" adapter_type="5' or 3'"/>
333 <param name="anywhere_adapter_source_list2" type="select" label="Source"> 216 </repeat>
334 <option value="builtin" selected="True">Standard (select from the list below)</option> 217
335 <option value="user">Enter custom sequence</option> 218 <!-- read modification -->
336 <option value="file">File from history</option> 219 <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." />
337 </param> 220 <param name="quality_cutoff2" argument="-Q" type="text" optional="true" label="Optional separate quality cutoff for Read 2" help="Trim low-quality bases from 5' and/or 3' ends of each read before adapter removal. If one value is given, only the 3' end is trimmed. If two comma-separated cutoffs are given, the 5' end is trimmed with the first cutoff, the 3' end with the second. Leave blank to use the same value as for Read 1">
338 221 <sanitizer>
339 <when value="user"> 222 <valid initial="string.digits"><add value="," /></valid>
340 <param name="anywhere_adapter_name2" type="text" value="" optional="True" label="Enter custom 5' or 3' adapter name (Optional)" /> 223 </sanitizer>
341 <expand macro="adapter" name="anywhere_adapter2" argument="-B" label="Enter custom 5' or 3' adapter sequence" value="AATTGGCC" /> 224 <validator type="regex">[0-9]+(,[0-9])?</validator>
342 </when> 225 </param>
343 <when value="builtin"> 226 <!-- read filtering-->
344 <expand macro="adapter_select" name="anywhere_adapter2" argument="-B" type="select" label="Choose 5' or 3' adapter"/> 227 <param name="minimum_length2" type="integer" min="0" value="" optional="true" label="Minimum length (R2)" />
345 </when> 228 <param name="maximum_length2" type="integer" min="0" value="" optional="true" label="Maximum length (R2)" />
346 <when value="file">
347 <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" />
348 </when>
349 </conditional>
350 <param name="single_noindels" type="boolean" truevalue=";noindels" falsevalue="" checked="false" label="Disallow indels for this adapter"/>
351 </repeat>
352
353 <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." />
354 <param name="quality_cutoff2" type="text" optional="true" label="Optional separate quality cutoff for Read 2" help="Trim low-quality bases from 5' and/or 3' ends of each read before adapter removal. If one value is given, only the 3' end is trimmed. If two comma-separated cutoffs are given, the 5' end is trimmed with the first cutoff, the 3' end with the second. Leave blank to use the same value as for Read 1">
355 <sanitizer>
356 <valid initial="string.digits"><add value="," /></valid>
357 </sanitizer>
358 <validator type="regex">[0-9,]+</validator>
359 </param>
360 </section> 229 </section>
361
362 </xml> 230 </xml>
363 231
364 <xml name="inherit_format_1"> 232 <xml name="inherit_format_1">
365 <actions> 233 <actions>
366 <conditional name="library.type"> 234 <conditional name="library.type">