Mercurial > repos > lparsons > cutadapt

comparison macros.xml @ 11:8665bcc8b847 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutadapt commit 07c4e473990f522bbe8254ddeded47ed5f3b2fe4
author iuc
date Mon, 05 Mar 2018 11:02:48 -0500
parents
children 78e1cf88d133
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10:01d94df2e32a 11:8665bcc8b847
1 <macros>
2
3 <token name="@read1_options@"><![CDATA[
4
5 ## Read1 trimming
6
7 #for $a in $library.r1.adapters
8 #if $a.adapter_source.adapter_source_list == 'builtin':
9 -a "${a.adapter_source.adapter.fields.name}"='${a.adapter_source.adapter}'
10 #else if str($a.adapter_source.adapter_name) != "":
11 -a '${a.adapter_source.adapter_name}'='${a.adapter_source.adapter}'
12 #else
13 -a '${a.adapter_source.adapter}'
14 #end if
15 #end for
16 #for $aa in $library.r1.anywhere_adapters
17 #if $aa.anywhere_adapter_source.anywhere_adapter_source_list == 'builtin':
18 -b ${aa.anywhere_adapter_source.anywhere_adapter.fields.name}"='${aa.anywhere_adapter_source.anywhere_adapter}'
19 #else if str($aa.anywhere_adapter_source.anywhere_adapter_name) != "":
20 -b '${aa.anywhere_adapter_source.anywhere_adapter_name}'='${aa.anywhere_adapter_source.anywhere_adapter}'
21 #else
22 -b '${aa.anywhere_adapter_source.anywhere_adapter}'
23 #end if
24 #end for
25 #for $fa in $library.r1.front_adapters
26 #if $fa.front_adapter_source.front_adapter_source_list == 'builtin':
27 -g "${fa.front_adapter_source.front_adapter.fields.name}"='${fa.front_adapter_source.front_adapter}'
28 #else if str($fa.front_adapter_source.front_adapter_name) != "":
29 -g '${fa.front_adapter_source.front_adapter_name}'='${fa.front_adapter_source.front_adapter}'
30 #else
31 -g '${fa.front_adapter_source.front_adapter}'
32 #end if
33 #end for
34
35 #if str($library.r1.cut) != '0':
36 -u $library.r1.cut
37 #end if
38
39 ## Additional Outputs
40
41 #if $output_options.info_file:
42 --info-file=$info_file
43 #end if
44 #if $output_options.rest_file:
45 --rest-file=$rest_output
46 #end if
47 #if $output_options.wildcard_file:
48 --wildcard-file=$wild_output
49 #end if
50 #if $output_options.too_short_file:
51 --too-short-output=$too_short_output
52 #end if
53 #if $output_options.too_long_file:
54 --too-long-output=$too_long_output
55 #end if
56 #if $output_options.untrimmed_file:
57 --untrimmed-output=$untrimmed_output
58 #end if
59
60 ]]></token>
61
62 <token name="@read2_options@"><![CDATA[
63
64 ## Read2 trimming
65
66 #for $a in $library.r2.adapters2
67 #if $a.adapter_source2.adapter_source_list2 == 'builtin':
68 -A "${a.adapter_source2.adapter2.fields.name}"='${a.adapter_source2.adapter2}'
69 #else if str($a.adapter_source2.adapter_name2) != "":
70 -A '${a.adapter_source2.adapter_name2}'='${a.adapter_source2.adapter2}'
71 #else
72 -A '${a.adapter_source2.adapter2}'
73 #end if
74 #end for
75 #for $aa in $library.r2.anywhere_adapters2
76 #if $aa.anywhere_adapter_source2.anywhere_adapter_source_list2 == 'builtin':
77 -B "${aa.anywhere_adapter_source2.anywhere_adapter2.fields.name}"='${aa.anywhere_adapter_source2.anywhere_adapter2}'
78 #else if str($aa.anywhere_adapter_source2.anywhere_adapter_name2) != "":
79 -B '${aa.anywhere_adapter_source2.anywhere_adapter_name2}'='${aa.anywhere_adapter_source2.anywhere_adapter2}'
80 #else
81 -B '${aa.anywhere_adapter_source2.anywhere_adapter2}'
82 #end if
83 #end for
84 #for $fa in $library.r2.front_adapters2
85 #if $fa.front_adapter_source2.front_adapter_source_list2 == 'builtin':
86 -G "${fa.front_adapter_source2.front_adapter2.fields.name}"='${fa.front_adapter_source2.front_adapter2}'
87 #else if str($fa.front_adapter_source2.front_adapter_name2) != "":
88 -G '${fa.front_adapter_source2.front_adapter_name2}'='${fa.front_adapter_source2.front_adapter2}'
89 #else
90 -G '${fa.front_adapter_source2.front_adapter2}'
91 #end if
92 #end for
93
94 #if str($library.r2.cut2) != '0':
95 -U $library.r2.cut2
96 #end if
97
98 ## Additional Outputs - Read 2
99
100 #if $output_options.too_short_file:
101 --too-short-paired-output=$too_short_paired_output
102 #end if
103 #if $output_options.too_long_file:
104 --too-long-paired-output=$too_long_paired_output
105 #end if
106 #if $output_options.untrimmed_file:
107 --untrimmed-paired-output=$untrimmed_paired_output
108 #end if
109
110 ]]></token>
111
112 <xml name="single_end_options" >
113
114 <section name="r1" title="Read 1 Options" expanded="True">
115
116 <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.">
117 <conditional name="adapter_source">
118 <param name="adapter_source_list" type="select" label="Source" >
119 <option value="builtin" selected="True">Standard (select from the list below)</option>
120 <option value="user">Enter custom sequence</option>
121 </param>
122
123 <when value="user">
124 <param name="adapter_name" type="text" value="" optional="True" label="Enter custom 3' adapter name (Optional)" />
125 <param name="adapter" argument="-a" type="text" value="AATTGGCC" label="Enter custom 3' adapter sequence" />
126 </when>
127
128 <when value="builtin">
129 <param name="adapter" argument="-a" type="select" label="Choose 3' adapter">
130 <options from_data_table="adapters">
131 <filter type="sort_by" column="1" />
132 </options>
133 </param>
134 </when>
135 </conditional>
136 </repeat>
137
138 <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.">
139 <conditional name="front_adapter_source">
140 <param name="front_adapter_source_list" type="select" label="Source">
141 <option value="builtin" selected="True">Standard (select from the list below)</option>
142 <option value="user">Enter custom sequence</option>
143 </param>
144
145 <when value="user">
146 <param name="front_adapter_name" type="text" value="" optional="True" label="Enter custom 5' adapter name (Optional)" />
147 <param name="front_adapter" argument="-g" type="text" value="AATTGGCC" label="Enter custom 5' adapter sequence" />
148 </when>
149 <when value="builtin">
150 <param name="front_adapter" argument="-g" type="select" label="Choose 5' adapter">
151 <options from_data_table="adapters">
152 <filter type="sort_by" column="1" />
153 </options>
154 </param>
155 </when>
156 </conditional>
157 </repeat>
158
159 <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!">
160 <conditional name="anywhere_adapter_source">
161 <param name="anywhere_adapter_source_list" type="select" label="Source">
162 <option value="builtin" selected="True">Standard (select from the list below)</option>
163 <option value="user">Enter custom sequence</option>
164 </param>
165
166 <when value="user">
167 <param name="anywhere_adapter_name" type="text" value="" optional="True" label="Enter custom 5' or 3' adapter name (Optional)" />
168 <param name="anywhere_adapter" argument="-b" type="text" value="AATTGGCC" label="Enter custom 5' or 3' adapter sequence" />
169 </when>
170 <when value="builtin">
171 <param name="anywhere_adapter" argument="-b" type="select" label="Choose 5' or 3' adapter">
172 <options from_data_table="adapters">
173 <filter type="sort_by" column="1" />
174 </options>
175 </param>
176 </when>
177 </conditional>
178 </repeat>
179
180 <param name="cut" argument="-u" 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." />
181
182 </section>
183
184 </xml>
185
186 <xml name="paired_end_options" >
187
188 <!-- Read 1 Options -->
189 <expand macro="single_end_options" />
190
191 <!-- Read 2 Options -->
192 <section name="r2" title="Read 2 Options" expanded="True">
193
194 <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.">
195 <conditional name="adapter_source2">
196 <param name="adapter_source_list2" type="select" label="Source" >
197 <option value="builtin" selected="True">Standard (select from the list below)</option>
198 <option value="user">Enter custom sequence</option>
199 </param>
200
201 <when value="user">
202 <param name="adapter_name2" type="text" value="" optional="True" label="Enter custom 3' adapter name (Optional)" />
203 <param name="adapter2" argument="-A" type="text" label="Enter custom 3' adapter sequence" value="AATTGGCC" />
204 </when>
205
206 <when value="builtin">
207 <param name="adapter2" argument="-A" type="select" label="Choose 3' adapter">
208 <options from_data_table="adapters">
209 <filter type="sort_by" column="1" />
210 </options>
211 </param>
212 </when>
213 </conditional>
214 </repeat>
215
216 <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.">
217 <conditional name="front_adapter_source2">
218 <param name="front_adapter_source_list2" type="select" label="Source">
219 <option value="builtin" selected="True">Standard (select from the list below)</option>
220 <option value="user">Enter custom sequence</option>
221 </param>
222
223 <when value="user">
224 <param name="front_adapter_name2" type="text" value="" label="Enter custom 5' adapter name (Optional)" />
225 <param name="front_adapter2" argument="-G" type="text" value="AATTGGCC" label="Enter custom 5' adapter sequence" />
226 </when>
227 <when value="builtin">
228 <param name="front_adapter2" argument="-G" type="select" label="Choose 5' adapter">
229 <options from_data_table="adapters">
230 <filter type="sort_by" column="1" />
231 </options>
232 </param>
233 </when>
234 </conditional>
235 </repeat>
236
237 <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!">
238 <conditional name="anywhere_adapter_source2">
239 <param name="anywhere_adapter_source_list2" type="select" label="Source">
240 <option value="builtin" selected="True">Standard (select from the list below)</option>
241 <option value="user">Enter custom sequence</option>
242 </param>
243
244 <when value="user">
245 <param name="anywhere_adapter_name2" type="text" value="" optional="True" label="Enter custom 5' or 3' adapter name (Optional)" />
246 <param name="anywhere_adapter2" argument="-B" type="text" label="Enter custom 5' or 3' adapter sequence" value="AATTGGCC" />
247 </when>
248 <when value="builtin">
249 <param name="anywhere_adapter2" argument="-B" type="select" label="Choose 5' or 3' adapter">
250 <options from_data_table="adapters">
251 <filter type="sort_by" column="1" />
252 </options>
253 </param>
254 </when>
255 </conditional>
256 </repeat>
257
258 <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." />
259
260 </section>
261
262 </xml>
263
264 </macros>