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comparison read_group_macros.xml @ 5:42bb952b4e3c draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
author devteam
date Tue, 21 Jul 2015 13:01:59 -0400
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children e23b0cdeeba6
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4:1fc845afa3ac 5:42bb952b4e3c
1 <macros>
2 <!-- Import this at the top of your command block and then
3 define rg_auto_name. -->
4 <token name="@define_read_group_helpers@">
5 #import re
6 #def identifier_or_name($input1)
7 #if hasattr($input1, 'element_identifier')
8 #return $input1.element_identifier
9 #else
10 #return $input1.name.rstrip('.gz').rstrip('.fastq').rstrip('.fq')
11 #end if
12 #end def
13
14 #def clean(name)
15 #set $name_clean = re.sub('[^\w\-_\.]', '_', $name)
16 #return $name_clean
17 #end def
18
19 #def read_group_name_default($input1, $input2=None)
20 #if $input2 is None
21 #return $clean($identifier_or_name($input1))
22 #else
23 #import itertools
24 #set $input_name1 = $clean($identifier_or_name($input1))
25 #set $input_name2 = $clean($identifier_or_name($input2))
26 #set $common_prefix = ''.join([c[0] for c in itertools.takewhile(lambda x: all(x[0] == y for y in x), itertools.izip(*[$input_name1, $input_name2]))])
27 #if len($common_prefix) > 3
28 #return $common_prefix
29 #else
30 #return $input_name1
31 #end if
32 #end if
33 #end def
34
35 #def format_read_group(prefix, value, quote='', arg='')
36 #if $value
37 #return $arg + $quote + $prefix + $value + $quote
38 #else
39 #return ''
40 #end if
41 #end def
42
43 #def rg_param(name)
44 #if $varExists("rg")
45 #return $rg.get($name, None)
46 #else
47 #return $getVar($name, None)
48 #end if
49 #end def
50
51 #set $use_rg = True
52 </token>
53 <!-- preconditions use_rg and rg_auto_name have been
54 defined.
55 -->
56 <token name="@set_read_group_vars@">
57 #if $use_rg
58 #if $rg_param('read_group_id_conditional') is None
59 #set $rg_id = $rg_auto_name
60 #elif $rg_param('read_group_id_conditional').do_auto_name
61 #set $rg_id = $rg_auto_name
62 #else
63 #set $rg_id = str($rg_param('read_group_id_conditional').ID)
64 #end if
65
66 #if $rg_param('read_group_sm_conditional') is None
67 #set $rg_sm = ''
68 #elif $rg_param('read_group_sm_conditional').do_auto_name
69 #set $rg_sm = $rg_auto_name
70 #else
71 #set $rg_sm = str($rg_param('read_group_sm_conditional').SM)
72 #end if
73
74 #if $rg_param('PL')
75 #set $rg_pl = str($rg_param('PL'))
76 #else
77 #set $rg_pl = ''
78 #end if
79
80 #if $rg_param('read_group_lb_conditional') is None
81 #set $rg_lb = ''
82 #elif $rg_param('read_group_lb_conditional')do_auto_name
83 #set $rg_lb = $rg_auto_name
84 #else
85 #set $rg_lb = str($rg_param('read_group_lb_conditional').LB)
86 #end if
87
88 #if $rg_param('CN')
89 #set $rg_cn = str($rg_param('CN'))
90 #else
91 #set $rg_cn = ''
92 #end if
93
94 #if $rg_param("DS")
95 #set $rg_ds = str($rg_param("DS"))
96 #else
97 #set $rg_ds = ''
98 #end if
99
100 #if $rg_param("DT")
101 #set $rg_dt = str($rg_param("DT"))
102 #else
103 #set $rg_dt = ''
104 #end if
105
106 #if $rg_param("FO")
107 #set $rg_fo = str($rg_param("FO"))
108 #else
109 #set $rg_fo = ''
110 #end if
111
112 #if $rg_param("KS")
113 #set $rg_ks = str($rg_param("KS"))
114 #else
115 #set $rg_ks = ''
116 #end if
117
118 #if $rg_param("PG")
119 #set $rg_pg = str($rg_param("PG"))
120 #else
121 #set $rg_pg = ''
122 #end if
123
124 #if str($rg_param("PI"))
125 #set $rg_pi = str($rg_param("PI"))
126 #else
127 #set $rg_pi = ''
128 #end if
129
130 #if $rg_param("PU")
131 #set $rg_pu = str($rg_param("PU"))
132 #else
133 #set $rg_pu = ''
134 #end if
135 #end if
136 </token>
137 <token name="@set_use_rg_var@">
138 #set $use_rg = str($rg.rg_selector) != "do_not_set"
139 </token>
140 <xml name="read_group_auto_name_conditional">
141 <param name="do_auto_name" type="boolean" label="Auto-assign" help="Use dataset name or collection information to automatically assign this value" checked="no" />
142 <when value="true">
143 </when>
144 <when value="false">
145 <yield />
146 </when>
147 </xml>
148 <xml name="read_group_id_param">
149 <param name="ID" type="text" value="" size="20" label="Read group identifier (ID)" help="This value must be unique among multiple samples in your experiment" optional="false">
150 <validator type="empty_field" />
151 </param>
152 </xml>
153 <xml name="read_group_id_conditional">
154 <conditional name="read_group_id_conditional">
155 <expand macro="read_group_auto_name_conditional">
156 <expand macro="read_group_id_param" />
157 </expand>
158 </conditional>
159 </xml>
160 <xml name="read_group_sm_param">
161 <param name="SM" type="text" value="" size="20" label="Read group sample name (SM)" help="This value should be descriptive. Use pool name where a pool is being sequenced" />
162 </xml>
163 <xml name="read_group_sm_conditional">
164 <conditional name="read_group_sm_conditional">
165 <expand macro="read_group_auto_name_conditional">
166 <expand macro="read_group_sm_param" />
167 </expand>
168 </conditional>
169 </xml>
170 <!-- Above SM param is optional (for SAM/BAM spec, this is required
171 as per Picard.
172 -->
173 <xml name="read_group_sm_param_required">
174 <param name="SM" type="text" value="" size="20" label="Read group sample name (SM)" optional="false" help="This value should be descriptive. Use pool name where a pool is being sequenced">
175 <validator type="empty_field" />
176 </param>
177 </xml>
178 <xml name="read_group_sm_required_conditional">
179 <conditional name="read_group_sm_conditional">
180 <expand macro="read_group_auto_name_conditional">
181 <expand macro="read_group_sm_param" />
182 </expand>
183 </conditional>
184 </xml>
185 <xml name="read_group_pl_param">
186 <param name="PL" type="select" label="Platform/technology used to produce the reads (PL)">
187 <option value="CAPILLARY">CAPILLARY</option>
188 <option value="LS454">LS454</option>
189 <option selected="True" value="ILLUMINA">ILLUMINA</option>
190 <option value="SOLID">SOLID</option>
191 <option value="HELICOS">HELICOS</option>
192 <option value="IONTORRENT">IONTORRENT</option>
193 <option value="PACBIO">PACBIO</option>
194 </param>
195 </xml>
196 <xml name="read_group_lb_param">
197 <param name="LB" type="text" size="25" label="Library name (LB)" optional="true" />
198 </xml>
199 <xml name="read_group_lb_conditional">
200 <conditional name="read_group_lb_conditional">
201 <expand macro="read_group_auto_name_conditional">
202 <expand macro="read_group_lb_param" />
203 </expand>
204 </conditional>
205 </xml>
206 <xml name="read_group_lb_required_param">
207 <param name="LB" type="text" size="25" label="Library name (LB)" optional="false">
208 <validator type="empty_field" />
209 </param>
210 </xml>
211 <xml name="read_group_lb_required_conditional">
212 <conditional name="read_group_lb_conditional">
213 <expand macro="read_group_auto_name_conditional">
214 <expand macro="read_group_lb_required_param" />
215 </expand>
216 </conditional>
217 </xml>
218 <xml name="read_group_cn_param">
219 <param name="CN" type="text" size="25" label="Sequencing center that produced the read (CN)" />
220 </xml>
221 <xml name="read_group_ds_param">
222 <param name="DS" type="text" size="25" label="Description (DS)" />
223 </xml>
224 <xml name="read_group_dt_param">
225 <param name="DT" type="text" size="25" label="Date that run was produced (DT)" help="ISO8601 format date or date/time, like YYYY-MM-DD" />
226 </xml>
227 <xml name="read_group_fo_param">
228 <param name="FO" type="text" size="25" optional="true" label="Flow order (FO)" help="The array of nucleotide bases that correspond to the nucleotides used for each flow of each read. Multi-base flows are encoded in IUPAC format, and non-nucleotide flows by various other characters. Format: /\*|[ACMGRSVTWYHKDBN]+/">
229 <validator type="regex" message="Invalid flow order">\*|[ACMGRSVTWYHKDBN]+$</validator>
230 </param>
231 </xml>
232 <xml name="read_group_ks_param">
233 <param name="KS" type="text" size="25" label="The array of nucleotide bases that correspond to the key sequence of each read (KS)" />
234 </xml>
235 <xml name="read_group_pg_param">
236 <param name="PG" type="text" size="25" label="Programs used for processing the read group (PG)" />
237 </xml>
238 <xml name="read_group_pi_param">
239 <param name="PI" type="integer" optional="true" label="Predicted median insert size (PI)" />
240 </xml>
241 <xml name="read_group_pu_param">
242 <param name="PU" type="text" size="25" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="True" />
243 </xml>
244 <xml name="read_group_pu_required_param">
245 <param name="PU" type="text" size="25" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="False" />
246 </xml>
247 <!-- Only ID is required - all groups available -->
248 <xml name="read_group_inputs_spec">
249 <expand macro="read_group_id_conditional" />
250 <expand macro="read_group_sm_conditional" />
251 <expand macro="read_group_pl_param" />
252 <expand macro="read_group_lb_conditional" />
253 <expand macro="read_group_cn_param" />
254 <expand macro="read_group_ds_param" />
255 <expand macro="read_group_dt_param" />
256 <expand macro="read_group_fo_param" />
257 <expand macro="read_group_ks_param" />
258 <expand macro="read_group_pg_param" />
259 <expand macro="read_group_pi_param" />
260 <expand macro="read_group_pu_param" />
261 </xml>
262 <!-- ID, SM, LB, PU, PL all required - not ks, pg, or fo params. -->
263 <xml name="read_group_inputs_picard">
264 <expand macro="read_group_id_conditional" />
265 <expand macro="read_group_sm_required_conditional" />
266 <expand macro="read_group_lb_required_conditional" />
267 <expand macro="read_group_pl_param" />
268 <expand macro="read_group_pu_required_param" />
269 <expand macro="read_group_cn_param" />
270 <expand macro="read_group_ds_param" />
271 <expand macro="read_group_pi_param" />
272 <expand macro="read_group_dt_param" />
273 </xml>
274 <xml name="read_group_conditional">
275 <conditional name="rg">
276 <param name="rg_selector" type="select" label="Set read groups information?" help="Specifying read group information can greatly simplify your downstream analyses by allowing combining multiple datasets.">
277 <option value="set">Set read groups (SAM/BAM specification)</option>
278 <option value="set_picard">Set read groups (Picard style)</option>
279 <option value="set_id_auto">Automatically assign ID</option>
280 <option value="do_not_set" selected="True">Do not set</option>
281 </param>
282 <when value="set_picard">
283 <expand macro="read_group_inputs_picard" />
284 </when>
285 <when value="set">
286 <expand macro="read_group_inputs_spec" />
287 </when>
288 <when value="set_id_auto">
289 </when>
290 <when value="do_not_set">
291 </when>
292 </conditional>
293 </xml>
294 </macros>