Mercurial > repos > lparsons > cutadapt

comparison macros.xml @ 22:093678460093 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 916aaa04992e36f9324299949b86cccd12d3081d"
author iuc
date Sat, 04 Jul 2020 06:52:59 -0400
parents e4691e1589d3
children c4b82dce8335
comparison
equal deleted inserted replaced
21:104d86c98776 22:093678460093
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 &quot;FASTA&quot;" label="Choose file containing 5' adapters" /> 218 <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" />
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 &quot;FASTA&quot;" 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 &quot;FASTA&quot;" 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 &quot;FASTA&quot;" label="Choose file containing 3' adapters" /> 275 <param name="adapter_file2" argument="-a" format="fasta" type="data" help="Should be of datatype &quot;FASTA&quot;" 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 &quot;FASTA&quot;" label="Choose file containing 5' adapters" /> 296 <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" />
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 &quot;FASTA&quot;" 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 &quot;FASTA&quot;" label="Choose file containing 3' or 5' adapters" />
291 </when> 318 </when>
292 </conditional> 319 </conditional>