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comparison macros.xml @ 27:de6cebe3c043 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 5eacc4a26d9cd55d1d34d1c35ab200733da6948f"
author iuc
date Mon, 01 Nov 2021 12:14:05 +0000
parents 44e2cc14f75b
children c053d4cad713
comparison
equal deleted inserted replaced
26:44e2cc14f75b 27:de6cebe3c043
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">3.4</token> 2 <token name="@TOOL_VERSION@">3.5</token>
3 <token name="@VERSION_SUFFIX@">2</token> 3 <token name="@VERSION_SUFFIX@">0</token>
4 <token name="@FASTQ_TYPES@">fastq.gz,fastq,fasta</token> 4 <token name="@FASTQ_TYPES@">fastq.gz,fastq,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>
29 29
30 ## Read1 trimming 30 ## Read1 trimming
31 31
32 #for $a in $library.r1.adapters 32 #for $a in $library.r1.adapters
33 #if $a.adapter_source.adapter_source_list == 'builtin': 33 #if $a.adapter_source.adapter_source_list == 'builtin':
34 -a '${a.adapter_source.adapter.fields.name}'='${a.adapter_source.adapter}${adapter_options.internal}' 34 -a '${a.adapter_source.adapter.fields.name}'='${a.adapter_source.adapter}${adapter_options.internal}${a.single_noindels}'
35 #else if $a.adapter_source.adapter_source_list == 'file': 35 #else if $a.adapter_source.adapter_source_list == 'file':
36 -a file:'${a.adapter_source.adapter_file}${adapter_options.internal}' 36 -a file:'${a.adapter_source.adapter_file}${adapter_options.internal}${a.single_noindels}'
37 #else if str($a.adapter_source.adapter_name) != "": 37 #else if str($a.adapter_source.adapter_name) != "":
38 -a '${a.adapter_source.adapter_name}'='${a.adapter_source.adapter}${adapter_options.internal}' 38 -a '${a.adapter_source.adapter_name}'='${a.adapter_source.adapter}${adapter_options.internal}${a.single_noindels}'
39 #else 39 #else
40 -a '${a.adapter_source.adapter}${adapter_options.internal}' 40 -a '${a.adapter_source.adapter}${adapter_options.internal}${a.single_noindels}'
41 #end if 41 #end if
42 #end for 42 #end for
43 #for $aa in $library.r1.anywhere_adapters 43 #for $aa in $library.r1.anywhere_adapters
44 #if $aa.anywhere_adapter_source.anywhere_adapter_source_list == 'builtin': 44 #if $aa.anywhere_adapter_source.anywhere_adapter_source_list == 'builtin':
45 -b '${aa.anywhere_adapter_source.anywhere_adapter.fields.name}'='${aa.anywhere_adapter_source.anywhere_adapter}' 45 -b '${aa.anywhere_adapter_source.anywhere_adapter.fields.name}'='${aa.anywhere_adapter_source.anywhere_adapter}${aa.single_noindels}'
46 #else if $aa.anywhere_adapter_source.anywhere_adapter_source_list == 'file': 46 #else if $aa.anywhere_adapter_source.anywhere_adapter_source_list == 'file':
47 -b file:'${aa.anywhere_adapter_source.anywhere_adapter_file}' 47 -b file:'${aa.anywhere_adapter_source.anywhere_adapter_file}${aa.single_noindels}'
48 #else if str($aa.anywhere_adapter_source.anywhere_adapter_name) != "": 48 #else if str($aa.anywhere_adapter_source.anywhere_adapter_name) != "":
49 -b '${aa.anywhere_adapter_source.anywhere_adapter_name}'='${aa.anywhere_adapter_source.anywhere_adapter}' 49 -b '${aa.anywhere_adapter_source.anywhere_adapter_name}'='${aa.anywhere_adapter_source.anywhere_adapter}${aa.single_noindels}'
50 #else 50 #else
51 -b '${aa.anywhere_adapter_source.anywhere_adapter}' 51 -b '${aa.anywhere_adapter_source.anywhere_adapter}${aa.single_noindels}'
52 #end if 52 #end if
53 #end for 53 #end for
54 #for $fa in $library.r1.front_adapters 54 #for $fa in $library.r1.front_adapters
55 #if $fa.front_adapter_source.front_adapter_source_list == 'builtin': 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}' 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': 57 #else if $fa.front_adapter_source.front_adapter_source_list == 'file':
58 -g file:'${adapter_options.internal}${fa.front_adapter_source.front_adapter_file}' 58 -g file:'${adapter_options.internal}${fa.front_adapter_source.front_adapter_file}${fa.single_noindels}'
59 #else if str($fa.front_adapter_source.front_adapter_name) != "": 59 #else if str($fa.front_adapter_source.front_adapter_name) != "":
60 -g '${fa.front_adapter_source.front_adapter_name}'='${adapter_options.internal}${fa.front_adapter_source.front_adapter}' 60 -g '${fa.front_adapter_source.front_adapter_name}'='${adapter_options.internal}${fa.front_adapter_source.front_adapter}${fa.single_noindels}'
61 #else 61 #else
62 -g '${adapter_options.internal}${fa.front_adapter_source.front_adapter}' 62 -g '${adapter_options.internal}${fa.front_adapter_source.front_adapter}${fa.single_noindels}'
63 #end if 63 #end if
64 #end for 64 #end for
65 65
66 #if str($library.r1.cut) != '0': 66 #if str($library.r1.cut) != '0':
67 -u $library.r1.cut 67 -u $library.r1.cut
94 94
95 ## Read2 trimming 95 ## Read2 trimming
96 96
97 #for $a in $library.r2.adapters2 97 #for $a in $library.r2.adapters2
98 #if $a.adapter_source2.adapter_source_list2 == 'builtin': 98 #if $a.adapter_source2.adapter_source_list2 == 'builtin':
99 -A '${a.adapter_source2.adapter2.fields.name}'='${a.adapter_source2.adapter2}${adapter_options.internal}' 99 -A '${a.adapter_source2.adapter2.fields.name}'='${a.adapter_source2.adapter2}${adapter_options.internal}${a.single_noindels}'
100 #else if $a.adapter_source2.adapter_source_list2 == 'file': 100 #else if $a.adapter_source2.adapter_source_list2 == 'file':
101 -A file:'${a.adapter_source2.adapter_file2}${adapter_options.internal}' 101 -A file:'${a.adapter_source2.adapter_file2}${adapter_options.internal}${a.single_noindels}'
102 #else if str($a.adapter_source2.adapter_name2) != "": 102 #else if str($a.adapter_source2.adapter_name2) != "":
103 -A '${a.adapter_source2.adapter_name2}'='${a.adapter_source2.adapter2}${adapter_options.internal}' 103 -A '${a.adapter_source2.adapter_name2}'='${a.adapter_source2.adapter2}${adapter_options.internal}${a.single_noindels}'
104 #else 104 #else
105 -A '${a.adapter_source2.adapter2}${adapter_options.internal}' 105 -A '${a.adapter_source2.adapter2}${adapter_options.internal}${a.single_noindels}'
106 #end if 106 #end if
107 #end for 107 #end for
108 #for $aa in $library.r2.anywhere_adapters2 108 #for $aa in $library.r2.anywhere_adapters2
109 #if $aa.anywhere_adapter_source2.anywhere_adapter_source_list2 == 'builtin': 109 #if $aa.anywhere_adapter_source2.anywhere_adapter_source_list2 == 'builtin':
110 -B '${aa.anywhere_adapter_source2.anywhere_adapter2.fields.name}'='${aa.anywhere_adapter_source2.anywhere_adapter2}' 110 -B '${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': 111 #else if $aa.anywhere_adapter_source2.anywhere_adapter_source_list2 == 'file':
112 -B file:'${aa.anywhere_adapter_source2.anywhere_adapter_file2}' 112 -B file:'${aa.anywhere_adapter_source2.anywhere_adapter_file2}${aa.single_noindels}'
113 #else if str($aa.anywhere_adapter_source2.anywhere_adapter_name2) != "": 113 #else if str($aa.anywhere_adapter_source2.anywhere_adapter_name2) != "":
114 -B '${aa.anywhere_adapter_source2.anywhere_adapter_name2}'='${aa.anywhere_adapter_source2.anywhere_adapter2}' 114 -B '${aa.anywhere_adapter_source2.anywhere_adapter_name2}'='${aa.anywhere_adapter_source2.anywhere_adapter2}${aa.single_noindels}'
115 #else 115 #else
116 -B '${aa.anywhere_adapter_source2.anywhere_adapter2}' 116 -B '${aa.anywhere_adapter_source2.anywhere_adapter2}'
117 #end if 117 #end if
118 #end for 118 #end for
119 #for $fa in $library.r2.front_adapters2 119 #for $fa in $library.r2.front_adapters2
120 #if $fa.front_adapter_source2.front_adapter_source_list2 == 'builtin': 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}' 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': 122 #else if $fa.front_adapter_source2.front_adapter_source_list2 == 'file':
123 -G file:'${adapter_options.internal}${fa.front_adapter_source2.front_adapter_file2}' 123 -G file:'${adapter_options.internal}${fa.front_adapter_source2.front_adapter_file2}${fa.single_noindels}'
124 #else if str($fa.front_adapter_source2.front_adapter_name2) != "": 124 #else if str($fa.front_adapter_source2.front_adapter_name2) != "":
125 -G '${fa.front_adapter_source2.front_adapter_name2}'='${adapter_options.internal}${fa.front_adapter_source2.front_adapter2}' 125 -G '${fa.front_adapter_source2.front_adapter_name2}'='${adapter_options.internal}${fa.front_adapter_source2.front_adapter2}${fa.single_noindels}'
126 #else 126 #else
127 -G '${adapter_options.internal}${fa.front_adapter_source2.front_adapter2}' 127 -G '${adapter_options.internal}${fa.front_adapter_source2.front_adapter2}${fa.single_noindels}'
128 #end if 128 #end if
129 #end for 129 #end for
130 130
131 #if str($library.r2.cut2) != '0': 131 #if str($library.r2.cut2) != '0':
132 -U $library.r2.cut2 132 -U $library.r2.cut2
220 220
221 <when value="file"> 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" /> 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> 223 </when>
224 </conditional> 224 </conditional>
225 <param name="single_noindels" type="boolean" truevalue=";noindels" falsevalue="" checked="false" label="Disallow indels for this adapter"/>
225 </repeat> 226 </repeat>
226 227
227 <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."> 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.">
228 <conditional name="front_adapter_source"> 229 <conditional name="front_adapter_source">
229 <param name="front_adapter_source_list" type="select" label="Source"> 230 <param name="front_adapter_source_list" type="select" label="Source">
241 </when> 242 </when>
242 <when value="file"> 243 <when value="file">
243 <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" /> 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" />
244 </when> 245 </when>
245 </conditional> 246 </conditional>
247 <param name="single_noindels" type="boolean" truevalue=";noindels" falsevalue="" checked="false" label="Disallow indels for this adapter"/>
246 </repeat> 248 </repeat>
247 249
248 <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!"> 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!">
249 <conditional name="anywhere_adapter_source"> 251 <conditional name="anywhere_adapter_source">
250 <param name="anywhere_adapter_source_list" type="select" label="Source"> 252 <param name="anywhere_adapter_source_list" type="select" label="Source">
262 </when> 264 </when>
263 <when value="file"> 265 <when value="file">
264 <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" /> 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" />
265 </when> 267 </when>
266 </conditional> 268 </conditional>
269 <param name="single_noindels" type="boolean" truevalue=";noindels" falsevalue="" checked="false" label="Disallow indels for this adapter"/>
267 </repeat> 270 </repeat>
268 271
269 <param name="cut" 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." /> 272 <param name="cut" 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." />
270 273
271 </section> 274 </section>
298 </when> 301 </when>
299 <when value="file"> 302 <when value="file">
300 <param name="adapter_file2" argument="-a" format="fasta" type="data" help="Should be of datatype &quot;FASTA&quot;" label="Choose file containing 3' adapters" /> 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" />
301 </when> 304 </when>
302 </conditional> 305 </conditional>
306 <param name="single_noindels" type="boolean" truevalue=";noindels" falsevalue="" checked="false" label="Disallow indels for this adapter"/>
303 </repeat> 307 </repeat>
304 308
305 <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."> 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.">
306 <conditional name="front_adapter_source2"> 310 <conditional name="front_adapter_source2">
307 <param name="front_adapter_source_list2" type="select" label="Source"> 311 <param name="front_adapter_source_list2" type="select" label="Source">
319 </when> 323 </when>
320 <when value="file"> 324 <when value="file">
321 <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" /> 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" />
322 </when> 326 </when>
323 </conditional> 327 </conditional>
328 <param name="single_noindels" type="boolean" truevalue=";noindels" falsevalue="" checked="false" label="Disallow indels for this adapter"/>
324 </repeat> 329 </repeat>
325 330
326 <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!"> 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!">
327 <conditional name="anywhere_adapter_source2"> 332 <conditional name="anywhere_adapter_source2">
328 <param name="anywhere_adapter_source_list2" type="select" label="Source"> 333 <param name="anywhere_adapter_source_list2" type="select" label="Source">
340 </when> 345 </when>
341 <when value="file"> 346 <when value="file">
342 <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" /> 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" />
343 </when> 348 </when>
344 </conditional> 349 </conditional>
350 <param name="single_noindels" type="boolean" truevalue=";noindels" falsevalue="" checked="false" label="Disallow indels for this adapter"/>
345 </repeat> 351 </repeat>
346 352
347 <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." /> 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." />
348 354 <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>
349 </section> 360 </section>
350 361
351 </xml> 362 </xml>
352 363
353 <xml name="inherit_format_1"> 364 <xml name="inherit_format_1">