Mercurial > repos > lparsons > cutadapt
comparison macros.xml @ 22:093678460093 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 916aaa04992e36f9324299949b86cccd12d3081d"
author | iuc |
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date | Sat, 04 Jul 2020 06:52:59 -0400 |
parents | e4691e1589d3 |
children | c4b82dce8335 |
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21:104d86c98776 | 22:093678460093 |
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4 | 4 |
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': | 10 #else if $a.adapter_source.adapter_source_list == 'file': |
11 -a file:'${a.adapter_source.adapter_file}' | 11 -a file:'${a.adapter_source.adapter_file}' |
12 #else if str($a.adapter_source.adapter_name) != "": | 12 #else if str($a.adapter_source.adapter_name) != "": |
13 -a '${a.adapter_source.adapter_name}'='${a.adapter_source.adapter}' | 13 -a '${a.adapter_source.adapter_name}'='${a.adapter_source.adapter}' |
14 #else | 14 #else |
15 -a '${a.adapter_source.adapter}' | 15 -a '${a.adapter_source.adapter}' |
16 #end if | 16 #end if |
17 #end for | 17 #end for |
18 #for $aa in $library.r1.anywhere_adapters | 18 #for $aa in $library.r1.anywhere_adapters |
19 #if $aa.anywhere_adapter_source.anywhere_adapter_source_list == 'builtin': | 19 #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}' | 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': | 21 #else if $aa.anywhere_adapter_source.anywhere_adapter_source_list == 'file': |
22 -b file:'${aa.anywhere_adapter_source.anywhere_adapter_file}' | 22 -b file:'${aa.anywhere_adapter_source.anywhere_adapter_file}' |
23 #else if str($aa.anywhere_adapter_source.anywhere_adapter_name) != "": | 23 #else if str($aa.anywhere_adapter_source.anywhere_adapter_name) != "": |
24 -b '${aa.anywhere_adapter_source.anywhere_adapter_name}'='${aa.anywhere_adapter_source.anywhere_adapter}' | 24 -b '${aa.anywhere_adapter_source.anywhere_adapter_name}'='${aa.anywhere_adapter_source.anywhere_adapter}' |
25 #else | 25 #else |
26 -b '${aa.anywhere_adapter_source.anywhere_adapter}' | 26 -b '${aa.anywhere_adapter_source.anywhere_adapter}' |
27 #end if | 27 #end if |
28 #end for | 28 #end for |
29 #for $fa in $library.r1.front_adapters | 29 #for $fa in $library.r1.front_adapters |
30 #if $fa.front_adapter_source.front_adapter_source_list == 'builtin': | 30 #if $fa.front_adapter_source.front_adapter_source_list == 'builtin': |
31 -g "${fa.front_adapter_source.front_adapter.fields.name}"='${fa.front_adapter_source.front_adapter}' | 31 -g '${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': | 32 #else if $fa.front_adapter_source.front_adapter_source_list == 'file': |
33 -g file:'${fa.front_adapter_source.front_adapter_file}' | 33 -g file:'${fa.front_adapter_source.front_adapter_file}' |
34 #else if str($fa.front_adapter_source.front_adapter_name) != "": | 34 #else if str($fa.front_adapter_source.front_adapter_name) != "": |
35 -g '${fa.front_adapter_source.front_adapter_name}'='${fa.front_adapter_source.front_adapter}' | 35 -g '${fa.front_adapter_source.front_adapter_name}'='${fa.front_adapter_source.front_adapter}' |
36 #else | 36 #else |
69 | 69 |
70 ## Read2 trimming | 70 ## Read2 trimming |
71 | 71 |
72 #for $a in $library.r2.adapters2 | 72 #for $a in $library.r2.adapters2 |
73 #if $a.adapter_source2.adapter_source_list2 == 'builtin': | 73 #if $a.adapter_source2.adapter_source_list2 == 'builtin': |
74 -A "${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': | 75 #else if $a.adapter_source2.adapter_source_list2 == 'file': |
76 -A file:'${a.adapter_source2.adapter_file2}' | 76 -A file:'${a.adapter_source2.adapter_file2}' |
77 #else if str($a.adapter_source2.adapter_name2) != "": | 77 #else if str($a.adapter_source2.adapter_name2) != "": |
78 -A '${a.adapter_source2.adapter_name2}'='${a.adapter_source2.adapter2}' | 78 -A '${a.adapter_source2.adapter_name2}'='${a.adapter_source2.adapter2}' |
79 #else | 79 #else |
80 -A '${a.adapter_source2.adapter2}' | 80 -A '${a.adapter_source2.adapter2}' |
81 #end if | 81 #end if |
82 #end for | 82 #end for |
83 #for $aa in $library.r2.anywhere_adapters2 | 83 #for $aa in $library.r2.anywhere_adapters2 |
84 #if $aa.anywhere_adapter_source2.anywhere_adapter_source_list2 == 'builtin': | 84 #if $aa.anywhere_adapter_source2.anywhere_adapter_source_list2 == 'builtin': |
85 -B "${aa.anywhere_adapter_source2.anywhere_adapter2.fields.name}"='${aa.anywhere_adapter_source2.anywhere_adapter2}' | 85 -B '${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': | 86 #else if $aa.anywhere_adapter_source2.anywhere_adapter_source_list2 == 'file': |
87 -B file:'${aa.anywhere_adapter_source2.anywhere_adapter_file2}' | 87 -B file:'${aa.anywhere_adapter_source2.anywhere_adapter_file2}' |
88 #else if str($aa.anywhere_adapter_source2.anywhere_adapter_name2) != "": | 88 #else if str($aa.anywhere_adapter_source2.anywhere_adapter_name2) != "": |
89 -B '${aa.anywhere_adapter_source2.anywhere_adapter_name2}'='${aa.anywhere_adapter_source2.anywhere_adapter2}' | 89 -B '${aa.anywhere_adapter_source2.anywhere_adapter_name2}'='${aa.anywhere_adapter_source2.anywhere_adapter2}' |
90 #else | 90 #else |
91 -B '${aa.anywhere_adapter_source2.anywhere_adapter2}' | 91 -B '${aa.anywhere_adapter_source2.anywhere_adapter2}' |
92 #end if | 92 #end if |
93 #end for | 93 #end for |
94 #for $fa in $library.r2.front_adapters2 | 94 #for $fa in $library.r2.front_adapters2 |
95 #if $fa.front_adapter_source2.front_adapter_source_list2 == 'builtin': | 95 #if $fa.front_adapter_source2.front_adapter_source_list2 == 'builtin': |
96 -G "${fa.front_adapter_source2.front_adapter2.fields.name}"='${fa.front_adapter_source2.front_adapter2}' | 96 -G '${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': | 97 #else if $fa.front_adapter_source2.front_adapter_source_list2 == 'file': |
98 -G file:'${fa.front_adapter_source2.front_adapter_file2}' | 98 -G file:'${fa.front_adapter_source2.front_adapter_file2}' |
99 #else if str($fa.front_adapter_source2.front_adapter_name2) != "": | 99 #else if str($fa.front_adapter_source2.front_adapter_name2) != "": |
100 -G '${fa.front_adapter_source2.front_adapter_name2}'='${fa.front_adapter_source2.front_adapter2}' | 100 -G '${fa.front_adapter_source2.front_adapter_name2}'='${fa.front_adapter_source2.front_adapter2}' |
101 #else | 101 #else |
119 --untrimmed-paired-output='${untrimmed_paired_output}' | 119 --untrimmed-paired-output='${untrimmed_paired_output}' |
120 #end if | 120 #end if |
121 | 121 |
122 ]]></token> | 122 ]]></token> |
123 | 123 |
124 <xml name="adapter_sanitizer"> | |
125 <sanitizer> | |
126 <valid initial="string.digits"> | |
127 <add value="A"/><!--standard nucleotides--> | |
128 <add value="T"/> | |
129 <add value="C"/> | |
130 <add value="G"/> | |
131 | |
132 <add value="U"/><!--ambiguous nucleotides--> | |
133 <add value="R"/> | |
134 <add value="Y"/> | |
135 <add value="S"/> | |
136 <add value="W"/> | |
137 <add value="K"/> | |
138 <add value="M"/> | |
139 <add value="B"/> | |
140 <add value="D"/> | |
141 <add value="H"/> | |
142 <add value="V"/> | |
143 <add value="N"/> | |
144 | |
145 <add value="X"/><!-- don't match any nucleotide--> | |
146 | |
147 <add value="{"/><!--specify repeats .. needs digits which are added as default--> | |
148 <add value="}"/> | |
149 | |
150 <add value="^"/><!--anchoring--> | |
151 <add value="$"/> | |
152 <add value="."/> | |
153 <add value="("/><!--specify what to keep--> | |
154 <add value=")"/> | |
155 | |
156 </valid> | |
157 </sanitizer> | |
158 </xml> | |
159 | |
160 <xml name="adapter" token_name="" token_argument="" token_value="" token_label=""> | |
161 <param name="@NAME@" argument="@ARGUMENT@" type="text" value="@VALUE@" label="@LABEL@"> | |
162 <expand macro="adapter_sanitizer"/> | |
163 </param> | |
164 </xml> | |
165 | |
166 <xml name="adapter_select" token_name="" token_argument="" token_label=""> | |
167 <param name="@NAME@" argument="@ARGUMENT@" type="select" label="@LABEL@"> | |
168 <options from_data_table="adapters"> | |
169 <filter type="sort_by" column="1" /> | |
170 </options> | |
171 <expand macro="adapter_sanitizer"/> | |
172 </param> | |
173 </xml> | |
174 | |
124 <xml name="single_end_options" > | 175 <xml name="single_end_options" > |
125 | 176 |
126 <section name="r1" title="Read 1 Options" expanded="True"> | 177 <section name="r1" title="Read 1 Options" expanded="True"> |
127 | 178 |
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 '$' character is appended ('anchoring'), the adapter is only found if it is a suffix of the read. To search for a linked adapter, separate the 2 sequences with 3 dots (ADAPTER1...ADAPTER2), see Help below."> | 179 <repeat name="adapters" title="3' (End) Adapters" help="Sequence of an adapter ligated to the 3' end (paired data: of the first read). The adapter and subsequent bases are trimmed. If a '$' 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."> |
133 <option value="file">File From History</option> | 184 <option value="file">File From History</option> |
134 </param> | 185 </param> |
135 | 186 |
136 <when value="user"> | 187 <when value="user"> |
137 <param name="adapter_name" type="text" value="" optional="True" label="Enter custom 3' adapter name (Optional if Multiple output is 'No')" /> | 188 <param name="adapter_name" type="text" value="" optional="True" label="Enter custom 3' adapter name (Optional if Multiple output is 'No')" /> |
138 <param name="adapter" argument="-a" type="text" value="AATTGGCC" label="Enter custom 3' adapter sequence" /> | 189 <expand macro="adapter" name="adapter" argument="-a" type="text" value="AATTGGCC" label="Enter custom 3' adapter sequence" /> |
139 </when> | 190 </when> |
140 | 191 |
141 <when value="builtin"> | 192 <when value="builtin"> |
142 <param name="adapter" argument="-a" type="select" label="Choose 3' adapter"> | 193 <expand macro="adapter_select" name="adapter" argument="-a" label="Choose 3' adapter"/> |
143 <options from_data_table="adapters"> | |
144 <filter type="sort_by" column="1" /> | |
145 </options> | |
146 </param> | |
147 </when> | 194 </when> |
148 | 195 |
149 <when value="file"> | 196 <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" /> | 197 <param name="adapter_file" argument="-a" format="fasta" type="data" help="Should be of datatype FASTA" label="Choose file containing 3' adapters" /> |
151 </when> | 198 </when> |
160 <option value="file">File From History</option> | 207 <option value="file">File From History</option> |
161 </param> | 208 </param> |
162 | 209 |
163 <when value="user"> | 210 <when value="user"> |
164 <param name="front_adapter_name" type="text" value="" optional="True" label="Enter custom 5' adapter name (Optional if Multiple output is 'No')" /> | 211 <param name="front_adapter_name" type="text" value="" optional="True" label="Enter custom 5' adapter name (Optional if Multiple output is 'No')" /> |
165 <param name="front_adapter" argument="-g" type="text" value="AATTGGCC" label="Enter custom 5' adapter sequence" /> | 212 <expand macro="adapter" name="front_adapter" argument="-g" value="AATTGGCC" label="Enter custom 5' adapter sequence" /> |
166 </when> | 213 </when> |
167 <when value="builtin"> | 214 <when value="builtin"> |
168 <param name="front_adapter" argument="-g" type="select" label="Choose 5' adapter"> | 215 <expand macro="adapter_select" name="front_adapter" argument="-g" label="Choose 5' adapter"/> |
169 <options from_data_table="adapters"> | |
170 <filter type="sort_by" column="1" /> | |
171 </options> | |
172 </param> | |
173 </when> | 216 </when> |
174 <when value="file"> | 217 <when value="file"> |
175 <param name="front_adapter_file" argument="-g" format="fasta" type="data" help="Should be of datatype "FASTA"" label="Choose file containing 5' adapters" /> | 218 <param name="front_adapter_file" argument="-g" format="fasta" type="data" help="Should be of datatype "FASTA"" label="Choose file containing 5' adapters" /> |
176 </when> | 219 </when> |
177 </conditional> | 220 </conditional> |
185 <option value="file">File From History</option> | 228 <option value="file">File From History</option> |
186 </param> | 229 </param> |
187 | 230 |
188 <when value="user"> | 231 <when value="user"> |
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')" /> | 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')" /> |
190 <param name="anywhere_adapter" argument="-b" type="text" value="AATTGGCC" label="Enter custom 5' or 3' adapter sequence" /> | 233 <expand macro="adapter" name="anywhere_adapter" argument="-b" value="AATTGGCC" label="Enter custom 5' or 3' adapter sequence" /> |
191 </when> | 234 </when> |
192 <when value="builtin"> | 235 <when value="builtin"> |
193 <param name="anywhere_adapter" argument="-b" type="select" label="Choose 5' or 3' adapter"> | 236 <expand macro="adapter_select" name="anywhere_adapter" argument="-b" label="Choose 5' or 3' adapter"/> |
194 <options from_data_table="adapters"> | |
195 <filter type="sort_by" column="1" /> | |
196 </options> | |
197 </param> | |
198 </when> | 237 </when> |
199 <when value="file"> | 238 <when value="file"> |
200 <param name="anywhere_adapter_file" argument="-b" format="fasta" type="data" help="Should be of datatype "FASTA"" label="Choose file containing 3' or 5' adapters" /> | 239 <param name="anywhere_adapter_file" argument="-b" format="fasta" type="data" help="Should be of datatype "FASTA"" label="Choose file containing 3' or 5' adapters" /> |
201 </when> | 240 </when> |
202 </conditional> | 241 </conditional> |
224 <option value="file">File From History</option> | 263 <option value="file">File From History</option> |
225 </param> | 264 </param> |
226 | 265 |
227 <when value="user"> | 266 <when value="user"> |
228 <param name="adapter_name2" type="text" value="" optional="True" label="Enter custom 3' adapter name (Optional)" /> | 267 <param name="adapter_name2" type="text" value="" optional="True" label="Enter custom 3' adapter name (Optional)" /> |
229 <param name="adapter2" argument="-A" type="text" label="Enter custom 3' adapter sequence" value="AATTGGCC" /> | 268 <expand macro="adapter" name="adapter2" argument="-A" label="Enter custom 3' adapter sequence" value="AATTGGCC" /> |
230 </when> | 269 </when> |
231 | 270 |
232 <when value="builtin"> | 271 <when value="builtin"> |
233 <param name="adapter2" argument="-A" type="select" label="Choose 3' adapter"> | 272 <expand macro="adapter_select" name="adapter2" argument="-A" label="Choose 3' adapter"/> |
234 <options from_data_table="adapters"> | |
235 <filter type="sort_by" column="1" /> | |
236 </options> | |
237 </param> | |
238 </when> | 273 </when> |
239 <when value="file"> | 274 <when value="file"> |
240 <param name="adapter_file2" argument="-a" format="fasta" type="data" help="Should be of datatype "FASTA"" label="Choose file containing 3' adapters" /> | 275 <param name="adapter_file2" argument="-a" format="fasta" type="data" help="Should be of datatype "FASTA"" label="Choose file containing 3' adapters" /> |
241 </when> | 276 </when> |
242 </conditional> | 277 </conditional> |
250 <option value="file">File From History</option> | 285 <option value="file">File From History</option> |
251 </param> | 286 </param> |
252 | 287 |
253 <when value="user"> | 288 <when value="user"> |
254 <param name="front_adapter_name2" type="text" value="" label="Enter custom 5' adapter name (Optional)" /> | 289 <param name="front_adapter_name2" type="text" value="" label="Enter custom 5' adapter name (Optional)" /> |
255 <param name="front_adapter2" argument="-G" type="text" value="AATTGGCC" label="Enter custom 5' adapter sequence" /> | 290 <expand macro="adapter" name="front_adapter2" argument="-G" value="AATTGGCC" label="Enter custom 5' adapter sequence" /> |
256 </when> | 291 </when> |
257 <when value="builtin"> | 292 <when value="builtin"> |
258 <param name="front_adapter2" argument="-G" type="select" label="Choose 5' adapter"> | 293 <expand macro="adapter_select" name="front_adapter2" argument="-G" label="Choose 5' adapter"/> |
259 <options from_data_table="adapters"> | |
260 <filter type="sort_by" column="1" /> | |
261 </options> | |
262 </param> | |
263 </when> | 294 </when> |
264 <when value="file"> | 295 <when value="file"> |
265 <param name="front_adapter_file2" argument="-g" format="fasta" type="data" help="Should be of datatype "FASTA"" label="Choose file containing 5' adapters" /> | 296 <param name="front_adapter_file2" argument="-g" format="fasta" type="data" help="Should be of datatype "FASTA"" label="Choose file containing 5' adapters" /> |
266 </when> | 297 </when> |
267 </conditional> | 298 </conditional> |
275 <option value="file">File From History</option> | 306 <option value="file">File From History</option> |
276 </param> | 307 </param> |
277 | 308 |
278 <when value="user"> | 309 <when value="user"> |
279 <param name="anywhere_adapter_name2" type="text" value="" optional="True" label="Enter custom 5' or 3' adapter name (Optional)" /> | 310 <param name="anywhere_adapter_name2" type="text" value="" optional="True" label="Enter custom 5' or 3' adapter name (Optional)" /> |
280 <param name="anywhere_adapter2" argument="-B" type="text" label="Enter custom 5' or 3' adapter sequence" value="AATTGGCC" /> | 311 <expand macro="adapter" name="anywhere_adapter2" argument="-B" label="Enter custom 5' or 3' adapter sequence" value="AATTGGCC" /> |
281 </when> | 312 </when> |
282 <when value="builtin"> | 313 <when value="builtin"> |
283 <param name="anywhere_adapter2" argument="-B" type="select" label="Choose 5' or 3' adapter"> | 314 <expand macro="adapter_select" name="anywhere_adapter2" argument="-B" type="select" label="Choose 5' or 3' adapter"/> |
284 <options from_data_table="adapters"> | |
285 <filter type="sort_by" column="1" /> | |
286 </options> | |
287 </param> | |
288 </when> | 315 </when> |
289 <when value="file"> | 316 <when value="file"> |
290 <param name="anywhere_adapter_file2" argument="-b" format="fasta" type="data" help="Should be of datatype "FASTA"" label="Choose file containing 3' or 5' adapters" /> | 317 <param name="anywhere_adapter_file2" argument="-b" format="fasta" type="data" help="Should be of datatype "FASTA"" label="Choose file containing 3' or 5' adapters" /> |
291 </when> | 318 </when> |
292 </conditional> | 319 </conditional> |