Mercurial > repos > lparsons > cutadapt

comparison macros.xml @ 24:288f97432497 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit b26a2d90a1c70476fd2de33cd9fd739100f54fcf"
author iuc
date Wed, 02 Jun 2021 22:47:34 +0000
parents c4b82dce8335
children 4e5056fefd88
comparison
equal deleted inserted replaced
23:c4b82dce8335 24:288f97432497
1 <macros> 1 <macros>
2 2 <token name="@TOOL_VERSION@">3.4</token>
3 <token name="@GALAXY_TOOL_VERSION@">galaxy0</token>
4 <xml name="edam_ontology">
5 <edam_topics>
6 <edam_topic>topic_0632</edam_topic>
7 </edam_topics>
8 <edam_operations>
9 <edam_operation>operation_0231</edam_operation>
10 </edam_operations>
11 </xml>
12 <xml name="requirements">
13 <requirements>
14 <requirement type="package" version="@TOOL_VERSION@">cutadapt</requirement>
15 </requirements>
16 </xml>
17 <xml name="citations">
18 <citations>
19 <citation type="doi">10.14806/ej.17.1.200</citation>
20 </citations>
21 </xml>
22 <xml name="xrefs">
23 <xrefs>
24 <xref type='bio.tools'>cutadapt</xref>
25 </xrefs>
26 </xml>
3 <token name="@read1_options@"><![CDATA[ 27 <token name="@read1_options@"><![CDATA[
4 28
5 ## Read1 trimming 29 ## Read1 trimming
6 30
7 #for $a in $library.r1.adapters 31 #for $a in $library.r1.adapters
8 #if $a.adapter_source.adapter_source_list == 'builtin': 32 #if $a.adapter_source.adapter_source_list == 'builtin':
9 -a '${a.adapter_source.adapter.fields.name}'='${a.adapter_source.adapter}' 33 -a '${a.adapter_source.adapter.fields.name}'='${a.adapter_source.adapter}${adapter_options.internal}'
10 #else if $a.adapter_source.adapter_source_list == 'file': 34 #else if $a.adapter_source.adapter_source_list == 'file':
11 -a file:'${a.adapter_source.adapter_file}' 35 -a file:'${a.adapter_source.adapter_file}${adapter_options.internal}'
12 #else if str($a.adapter_source.adapter_name) != "": 36 #else if str($a.adapter_source.adapter_name) != "":
13 -a '${a.adapter_source.adapter_name}'='${a.adapter_source.adapter}' 37 -a '${a.adapter_source.adapter_name}'='${a.adapter_source.adapter}${adapter_options.internal}'
14 #else 38 #else
15 -a '${a.adapter_source.adapter}' 39 -a '${a.adapter_source.adapter}${adapter_options.internal}'
16 #end if 40 #end if
17 #end for 41 #end for
18 #for $aa in $library.r1.anywhere_adapters 42 #for $aa in $library.r1.anywhere_adapters
19 #if $aa.anywhere_adapter_source.anywhere_adapter_source_list == 'builtin': 43 #if $aa.anywhere_adapter_source.anywhere_adapter_source_list == 'builtin':
20 -b '${aa.anywhere_adapter_source.anywhere_adapter.fields.name}'='${aa.anywhere_adapter_source.anywhere_adapter}' 44 -b '${aa.anywhere_adapter_source.anywhere_adapter.fields.name}'='${aa.anywhere_adapter_source.anywhere_adapter}'
26 -b '${aa.anywhere_adapter_source.anywhere_adapter}' 50 -b '${aa.anywhere_adapter_source.anywhere_adapter}'
27 #end if 51 #end if
28 #end for 52 #end for
29 #for $fa in $library.r1.front_adapters 53 #for $fa in $library.r1.front_adapters
30 #if $fa.front_adapter_source.front_adapter_source_list == 'builtin': 54 #if $fa.front_adapter_source.front_adapter_source_list == 'builtin':
31 -g '${fa.front_adapter_source.front_adapter.fields.name}'='${fa.front_adapter_source.front_adapter}' 55 -g '${fa.front_adapter_source.front_adapter.fields.name}'='${adapter_options.internal}${fa.front_adapter_source.front_adapter}'
32 #else if $fa.front_adapter_source.front_adapter_source_list == 'file': 56 #else if $fa.front_adapter_source.front_adapter_source_list == 'file':
33 -g file:'${fa.front_adapter_source.front_adapter_file}' 57 -g file:'${adapter_options.internal}${fa.front_adapter_source.front_adapter_file}'
34 #else if str($fa.front_adapter_source.front_adapter_name) != "": 58 #else if str($fa.front_adapter_source.front_adapter_name) != "":
35 -g '${fa.front_adapter_source.front_adapter_name}'='${fa.front_adapter_source.front_adapter}' 59 -g '${fa.front_adapter_source.front_adapter_name}'='${adapter_options.internal}${fa.front_adapter_source.front_adapter}'
36 #else 60 #else
37 -g '${fa.front_adapter_source.front_adapter}' 61 -g '${adapter_options.internal}${fa.front_adapter_source.front_adapter}'
38 #end if 62 #end if
39 #end for 63 #end for
40 64
41 #if str($library.r1.cut) != '0': 65 #if str($library.r1.cut) != '0':
42 -u $library.r1.cut 66 -u $library.r1.cut
43 #end if 67 #end if
44 68
45 ## Additional Outputs 69 ## Additional Outputs
46 70
47 #if $output_options.info_file: 71 #if 'info_file' in $output_selector:
48 --info-file=$info_file 72 --info-file=$info_file
49 #end if 73 #end if
50 #if $output_options.rest_file: 74 #if 'rest_file' in $output_selector:
51 --rest-file='${rest_output}' 75 --rest-file='${rest_output}'
52 #end if 76 #end if
53 #if $output_options.wildcard_file: 77 #if 'wildcard_file' in $output_selector:
54 --wildcard-file='${wild_output}' 78 --wildcard-file='${wild_output}'
55 #end if 79 #end if
56 #if $output_options.too_short_file: 80 #if 'too_short_file' in $output_selector:
57 --too-short-output='${too_short_output}' 81 --too-short-output='${too_short_output}'
58 #end if 82 #end if
59 #if $output_options.too_long_file: 83 #if 'too_long_file' in $output_selector:
60 --too-long-output='${too_long_output}' 84 --too-long-output='${too_long_output}'
61 #end if 85 #end if
62 #if $output_options.untrimmed_file: 86 #if 'untrimmed_file' in $output_selector:
63 --untrimmed-output='${untrimmed_output}' 87 --untrimmed-output='${untrimmed_output}'
64 #end if 88 #end if
65 89
66 ]]></token> 90 ]]></token>
67 91
69 93
70 ## Read2 trimming 94 ## Read2 trimming
71 95
72 #for $a in $library.r2.adapters2 96 #for $a in $library.r2.adapters2
73 #if $a.adapter_source2.adapter_source_list2 == 'builtin': 97 #if $a.adapter_source2.adapter_source_list2 == 'builtin':
74 -A '${a.adapter_source2.adapter2.fields.name}'='${a.adapter_source2.adapter2}' 98 -A '${a.adapter_source2.adapter2.fields.name}'='${a.adapter_source2.adapter2}${adapter_options.internal}'
75 #else if $a.adapter_source2.adapter_source_list2 == 'file': 99 #else if $a.adapter_source2.adapter_source_list2 == 'file':
76 -A file:'${a.adapter_source2.adapter_file2}' 100 -A file:'${a.adapter_source2.adapter_file2}${adapter_options.internal}'
77 #else if str($a.adapter_source2.adapter_name2) != "": 101 #else if str($a.adapter_source2.adapter_name2) != "":
78 -A '${a.adapter_source2.adapter_name2}'='${a.adapter_source2.adapter2}' 102 -A '${a.adapter_source2.adapter_name2}'='${a.adapter_source2.adapter2}${adapter_options.internal}'
79 #else 103 #else
80 -A '${a.adapter_source2.adapter2}' 104 -A '${a.adapter_source2.adapter2}${adapter_options.internal}'
81 #end if 105 #end if
82 #end for 106 #end for
83 #for $aa in $library.r2.anywhere_adapters2 107 #for $aa in $library.r2.anywhere_adapters2
84 #if $aa.anywhere_adapter_source2.anywhere_adapter_source_list2 == 'builtin': 108 #if $aa.anywhere_adapter_source2.anywhere_adapter_source_list2 == 'builtin':
85 -B '${aa.anywhere_adapter_source2.anywhere_adapter2.fields.name}'='${aa.anywhere_adapter_source2.anywhere_adapter2}' 109 -B '${aa.anywhere_adapter_source2.anywhere_adapter2.fields.name}'='${aa.anywhere_adapter_source2.anywhere_adapter2}'
91 -B '${aa.anywhere_adapter_source2.anywhere_adapter2}' 115 -B '${aa.anywhere_adapter_source2.anywhere_adapter2}'
92 #end if 116 #end if
93 #end for 117 #end for
94 #for $fa in $library.r2.front_adapters2 118 #for $fa in $library.r2.front_adapters2
95 #if $fa.front_adapter_source2.front_adapter_source_list2 == 'builtin': 119 #if $fa.front_adapter_source2.front_adapter_source_list2 == 'builtin':
96 -G '${fa.front_adapter_source2.front_adapter2.fields.name}'='${fa.front_adapter_source2.front_adapter2}' 120 -G '${fa.front_adapter_source2.front_adapter2.fields.name}'='${adapter_options.internal}${fa.front_adapter_source2.front_adapter2}'
97 #else if $fa.front_adapter_source2.front_adapter_source_list2 == 'file': 121 #else if $fa.front_adapter_source2.front_adapter_source_list2 == 'file':
98 -G file:'${fa.front_adapter_source2.front_adapter_file2}' 122 -G file:'${adapter_options.internal}${fa.front_adapter_source2.front_adapter_file2}'
99 #else if str($fa.front_adapter_source2.front_adapter_name2) != "": 123 #else if str($fa.front_adapter_source2.front_adapter_name2) != "":
100 -G '${fa.front_adapter_source2.front_adapter_name2}'='${fa.front_adapter_source2.front_adapter2}' 124 -G '${fa.front_adapter_source2.front_adapter_name2}'='${adapter_options.internal}${fa.front_adapter_source2.front_adapter2}'
101 #else 125 #else
102 -G '${fa.front_adapter_source2.front_adapter2}' 126 -G '${adapter_options.internal}${fa.front_adapter_source2.front_adapter2}'
103 #end if 127 #end if
104 #end for 128 #end for
105 129
106 #if str($library.r2.cut2) != '0': 130 #if str($library.r2.cut2) != '0':
107 -U $library.r2.cut2 131 -U $library.r2.cut2
108 #end if 132 #end if
109 133
110 ## Additional Outputs - Read 2 134 ## Additional Outputs - Read 2
111 135
112 #if $output_options.too_short_file: 136 #if 'too_short_file' in $output_selector:
113 --too-short-paired-output='${too_short_paired_output}' 137 --too-short-paired-output='${too_short_paired_output}'
114 #end if 138 #end if
115 #if $output_options.too_long_file: 139 #if 'too_long_file' in $output_selector:
116 --too-long-paired-output='${too_long_paired_output}' 140 --too-long-paired-output='${too_long_paired_output}'
117 #end if 141 #end if
118 #if $output_options.untrimmed_file: 142 #if 'untrimmed_file' in $output_selector:
119 --untrimmed-paired-output='${untrimmed_paired_output}' 143 --untrimmed-paired-output='${untrimmed_paired_output}'
120 #end if 144 #end if
121 145
122 ]]></token> 146 ]]></token>
123 147
179 <repeat name="adapters" title="3' (End) Adapters" help="Sequence of an adapter ligated to the 3' end (paired data: of the first read). The adapter and subsequent bases are trimmed. If a '$' 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."> 203 <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.">
180 <conditional name="adapter_source"> 204 <conditional name="adapter_source">
181 <param name="adapter_source_list" type="select" label="Source" > 205 <param name="adapter_source_list" type="select" label="Source" >
182 <option value="builtin" selected="True">Standard (select from the list below)</option> 206 <option value="builtin" selected="True">Standard (select from the list below)</option>
183 <option value="user">Enter custom sequence</option> 207 <option value="user">Enter custom sequence</option>
184 <option value="file">File From History</option> 208 <option value="file">File from history</option>
185 </param> 209 </param>
186 210
187 <when value="user"> 211 <when value="user">
188 <param name="adapter_name" type="text" value="" optional="True" label="Enter custom 3' adapter name (Optional if Multiple output is 'No')" /> 212 <param name="adapter_name" type="text" value="" optional="True" label="Enter custom 3' adapter name (Optional if Multiple output is 'No')" />
189 <expand macro="adapter" name="adapter" argument="-a" type="text" value="AATTGGCC" label="Enter custom 3' adapter sequence" /> 213 <expand macro="adapter" name="adapter" argument="-a" type="text" value="AATTGGCC" label="Enter custom 3' adapter sequence" />
202 <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."> 226 <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.">
203 <conditional name="front_adapter_source"> 227 <conditional name="front_adapter_source">
204 <param name="front_adapter_source_list" type="select" label="Source"> 228 <param name="front_adapter_source_list" type="select" label="Source">
205 <option value="builtin" selected="True">Standard (select from the list below)</option> 229 <option value="builtin" selected="True">Standard (select from the list below)</option>
206 <option value="user">Enter custom sequence</option> 230 <option value="user">Enter custom sequence</option>
207 <option value="file">File From History</option> 231 <option value="file">File from history</option>
208 </param> 232 </param>
209 233
210 <when value="user"> 234 <when value="user">
211 <param name="front_adapter_name" type="text" value="" optional="True" label="Enter custom 5' adapter name (Optional if Multiple output is 'No')" /> 235 <param name="front_adapter_name" type="text" value="" optional="True" label="Enter custom 5' adapter name (Optional if Multiple output is 'No')" />
212 <expand macro="adapter" name="front_adapter" argument="-g" value="AATTGGCC" label="Enter custom 5' adapter sequence" /> 236 <expand macro="adapter" name="front_adapter" argument="-g" value="AATTGGCC" label="Enter custom 5' adapter sequence" />
223 <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!"> 247 <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!">
224 <conditional name="anywhere_adapter_source"> 248 <conditional name="anywhere_adapter_source">
225 <param name="anywhere_adapter_source_list" type="select" label="Source"> 249 <param name="anywhere_adapter_source_list" type="select" label="Source">
226 <option value="builtin" selected="True">Standard (select from the list below)</option> 250 <option value="builtin" selected="True">Standard (select from the list below)</option>
227 <option value="user">Enter custom sequence</option> 251 <option value="user">Enter custom sequence</option>
228 <option value="file">File From History</option> 252 <option value="file">File from history</option>
229 </param> 253 </param>
230 254
231 <when value="user"> 255 <when value="user">
232 <param name="anywhere_adapter_name" type="text" value="" optional="True" label="Enter custom 5' or 3' adapter name (Optional if Multiple output is 'No')" /> 256 <param name="anywhere_adapter_name" type="text" value="" optional="True" label="Enter custom 5' or 3' adapter name (Optional if Multiple output is 'No')" />
233 <expand macro="adapter" name="anywhere_adapter" argument="-b" value="AATTGGCC" label="Enter custom 5' or 3' adapter sequence" /> 257 <expand macro="adapter" name="anywhere_adapter" argument="-b" value="AATTGGCC" label="Enter custom 5' or 3' adapter sequence" />
258 <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."> 282 <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.">
259 <conditional name="adapter_source2"> 283 <conditional name="adapter_source2">
260 <param name="adapter_source_list2" type="select" label="Source" > 284 <param name="adapter_source_list2" type="select" label="Source" >
261 <option value="builtin" selected="True">Standard (select from the list below)</option> 285 <option value="builtin" selected="True">Standard (select from the list below)</option>
262 <option value="user">Enter custom sequence</option> 286 <option value="user">Enter custom sequence</option>
263 <option value="file">File From History</option> 287 <option value="file">File from history</option>
264 </param> 288 </param>
265 289
266 <when value="user"> 290 <when value="user">
267 <param name="adapter_name2" type="text" value="" optional="True" label="Enter custom 3' adapter name (Optional)" /> 291 <param name="adapter_name2" type="text" value="" optional="True" label="Enter custom 3' adapter name (Optional)" />
268 <expand macro="adapter" name="adapter2" argument="-A" label="Enter custom 3' adapter sequence" value="AATTGGCC" /> 292 <expand macro="adapter" name="adapter2" argument="-A" label="Enter custom 3' adapter sequence" value="AATTGGCC" />
280 <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."> 304 <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.">
281 <conditional name="front_adapter_source2"> 305 <conditional name="front_adapter_source2">
282 <param name="front_adapter_source_list2" type="select" label="Source"> 306 <param name="front_adapter_source_list2" type="select" label="Source">
283 <option value="builtin" selected="True">Standard (select from the list below)</option> 307 <option value="builtin" selected="True">Standard (select from the list below)</option>
284 <option value="user">Enter custom sequence</option> 308 <option value="user">Enter custom sequence</option>
285 <option value="file">File From History</option> 309 <option value="file">File from history</option>
286 </param> 310 </param>
287 311
288 <when value="user"> 312 <when value="user">
289 <param name="front_adapter_name2" type="text" value="" label="Enter custom 5' adapter name (Optional)" /> 313 <param name="front_adapter_name2" type="text" value="" label="Enter custom 5' adapter name (Optional)" />
290 <expand macro="adapter" name="front_adapter2" argument="-G" value="AATTGGCC" label="Enter custom 5' adapter sequence" /> 314 <expand macro="adapter" name="front_adapter2" argument="-G" value="AATTGGCC" label="Enter custom 5' adapter sequence" />
301 <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!"> 325 <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!">
302 <conditional name="anywhere_adapter_source2"> 326 <conditional name="anywhere_adapter_source2">
303 <param name="anywhere_adapter_source_list2" type="select" label="Source"> 327 <param name="anywhere_adapter_source_list2" type="select" label="Source">
304 <option value="builtin" selected="True">Standard (select from the list below)</option> 328 <option value="builtin" selected="True">Standard (select from the list below)</option>
305 <option value="user">Enter custom sequence</option> 329 <option value="user">Enter custom sequence</option>
306 <option value="file">File From History</option> 330 <option value="file">File from history</option>
307 </param> 331 </param>
308 332
309 <when value="user"> 333 <when value="user">
310 <param name="anywhere_adapter_name2" type="text" value="" optional="True" label="Enter custom 5' or 3' adapter name (Optional)" /> 334 <param name="anywhere_adapter_name2" type="text" value="" optional="True" label="Enter custom 5' or 3' adapter name (Optional)" />
311 <expand macro="adapter" name="anywhere_adapter2" argument="-B" label="Enter custom 5' or 3' adapter sequence" value="AATTGGCC" /> 335 <expand macro="adapter" name="anywhere_adapter2" argument="-B" label="Enter custom 5' or 3' adapter sequence" value="AATTGGCC" />