Mercurial > repos > devteam > bwa

annotate read_group_macros.xml @ 23:3fe632431b68 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 777181bd04849dab271ee2cc95e45c182947d308"
author iuc
date Tue, 19 May 2020 11:29:11 -0400
parents 01ac0a5fedc3
children e188dc7a68e6
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
1 <macros>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
2 <!-- Import this at the top of your command block and then
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
3 define rg_auto_name. -->
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
4 <token name="@define_read_group_helpers@">
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
5 #def identifier_or_name($input1)
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
6 #if hasattr($input1, 'element_identifier')
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
7 #return $input1.element_identifier
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
8 #else
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
9 #return $input1.name.rstrip('.gz').rstrip('.fastq').rstrip('.fq')
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
10 #end if
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
11 #end def
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
12
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
13 #def clean(name)
6
09a7281d24c5 planemo upload commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
14 #import re
5
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
15 #set $name_clean = re.sub('[^\w\-_\.]', '_', $name)
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
16 #return $name_clean
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
17 #end def
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
18
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
19 #def read_group_name_default($input1, $input2=None)
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
20 #if $input2 is None
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
21 #return $clean($identifier_or_name($input1))
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
22 #else
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
23 #import itertools
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
24 #set $input_name1 = $clean($identifier_or_name($input1))
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
25 #set $input_name2 = $clean($identifier_or_name($input2))
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
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, $input_name2]))])
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
27 #if len($common_prefix) > 3
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
28 #return $common_prefix
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
29 #else
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
30 #return $input_name1
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
31 #end if
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
32 #end if
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
33 #end def
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
34
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
35 #def format_read_group(prefix, value, quote='', arg='')
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
36 #if $value
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
37 #return $arg + $quote + $prefix + $value + $quote
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
38 #else
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
39 #return ''
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
40 #end if
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
41 #end def
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
42
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
43 #def rg_param(name)
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
44 #if $varExists("rg")
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
45 #return $rg.get($name, None)
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
46 #else
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
47 #return $getVar($name, None)
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
48 #end if
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
49 #end def
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
50
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
51 #set $use_rg = True
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
52 </token>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
53 <!-- preconditions use_rg and rg_auto_name have been
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
54 defined.
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
55 -->
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
56 <token name="@set_read_group_vars@">
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
57 #if $use_rg
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
58 #if $rg_param('read_group_id_conditional') is None
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
59 #set $rg_id = $rg_auto_name
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
60 #elif $rg_param('read_group_id_conditional').do_auto_name
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
61 #set $rg_id = $rg_auto_name
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
62 #else
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
63 #set $rg_id = str($rg_param('read_group_id_conditional').ID)
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
64 #end if
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
65
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
66 #if $rg_param('read_group_sm_conditional') is None
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
67 #set $rg_sm = ''
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
68 #elif $rg_param('read_group_sm_conditional').do_auto_name
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
69 #set $rg_sm = $rg_auto_name
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
70 #else
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
71 #set $rg_sm = str($rg_param('read_group_sm_conditional').SM)
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
72 #end if
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
73
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
74 #if $rg_param('PL')
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
75 #set $rg_pl = str($rg_param('PL'))
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
76 #else
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
77 #set $rg_pl = ''
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
78 #end if
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
79
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
80 #if $rg_param('read_group_lb_conditional') is None
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
81 #set $rg_lb = ''
6
09a7281d24c5 planemo upload commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
82 #elif $rg_param('read_group_lb_conditional').do_auto_name
5
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
83 #set $rg_lb = $rg_auto_name
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
84 #else
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
85 #set $rg_lb = str($rg_param('read_group_lb_conditional').LB)
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
86 #end if
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
87
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
88 #if $rg_param('CN')
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
89 #set $rg_cn = str($rg_param('CN'))
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
90 #else
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
91 #set $rg_cn = ''
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
92 #end if
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
93
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
94 #if $rg_param("DS")
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
95 #set $rg_ds = str($rg_param("DS"))
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
96 #else
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
97 #set $rg_ds = ''
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
98 #end if
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
99
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
100 #if $rg_param("DT")
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
101 #set $rg_dt = str($rg_param("DT"))
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
102 #else
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
103 #set $rg_dt = ''
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
104 #end if
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
105
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
106 #if $rg_param("FO")
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
107 #set $rg_fo = str($rg_param("FO"))
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
108 #else
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
109 #set $rg_fo = ''
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
110 #end if
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
111
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
112 #if $rg_param("KS")
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
113 #set $rg_ks = str($rg_param("KS"))
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
114 #else
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
115 #set $rg_ks = ''
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
116 #end if
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
117
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
118 #if $rg_param("PG")
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
119 #set $rg_pg = str($rg_param("PG"))
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
120 #else
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
121 #set $rg_pg = ''
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
122 #end if
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
123
8
ca29c55c78e7 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit a1517c9d22029095120643bbe2c8fa53754dd2b7
devteam
parents: 7
diff changeset
124 #if $rg_param("PI") != None
5
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
125 #set $rg_pi = str($rg_param("PI"))
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
126 #else
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
127 #set $rg_pi = ''
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
128 #end if
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
129
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
130 #if $rg_param("PU")
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
131 #set $rg_pu = str($rg_param("PU"))
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
132 #else
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
133 #set $rg_pu = ''
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
134 #end if
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
135 #end if
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
136 </token>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
137 <token name="@set_use_rg_var@">
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
138 #set $use_rg = str($rg.rg_selector) != "do_not_set"
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
139 </token>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
140 <xml name="read_group_auto_name_conditional">
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
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" />
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
142 <when value="true">
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
143 </when>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
144 <when value="false">
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
145 <yield />
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
146 </when>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
147 </xml>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
148 <xml name="read_group_id_param">
7
d8c9597bfb09 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit ddb8bdb9d62399f086b06b3469450d0aad2113bd
devteam
parents: 6
diff changeset
149 <param name="ID" type="text" value="" label="Read group identifier (ID)" help="This value must be unique among multiple samples in your experiment" optional="false">
6
09a7281d24c5 planemo upload commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 5
diff changeset
150 <validator type="empty_field" />
5
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
151 </param>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
152 </xml>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
153 <xml name="read_group_id_conditional">
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
154 <conditional name="read_group_id_conditional">
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
155 <expand macro="read_group_auto_name_conditional">
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
156 <expand macro="read_group_id_param" />
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
157 </expand>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
158 </conditional>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
159 </xml>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
160 <xml name="read_group_sm_param">
7
d8c9597bfb09 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit ddb8bdb9d62399f086b06b3469450d0aad2113bd
devteam
parents: 6
diff changeset
161 <param name="SM" type="text" value="" label="Read group sample name (SM)" help="This value should be descriptive. Use pool name where a pool is being sequenced" />
5
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
162 </xml>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
163 <xml name="read_group_sm_conditional">
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
164 <conditional name="read_group_sm_conditional">
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
165 <expand macro="read_group_auto_name_conditional">
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
166 <expand macro="read_group_sm_param" />
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
167 </expand>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
168 </conditional>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
169 </xml>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
170 <!-- Above SM param is optional (for SAM/BAM spec, this is required
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
171 as per Picard.
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
172 -->
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
173 <xml name="read_group_sm_param_required">
7
d8c9597bfb09 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit ddb8bdb9d62399f086b06b3469450d0aad2113bd
devteam
parents: 6
diff changeset
174 <param name="SM" type="text" value="" label="Read group sample name (SM)" optional="false" help="This value should be descriptive. Use pool name where a pool is being sequenced">
5
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
175 <validator type="empty_field" />
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
176 </param>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
177 </xml>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
178 <xml name="read_group_sm_required_conditional">
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
179 <conditional name="read_group_sm_conditional">
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
180 <expand macro="read_group_auto_name_conditional">
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
181 <expand macro="read_group_sm_param" />
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
182 </expand>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
183 </conditional>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
184 </xml>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
185 <xml name="read_group_pl_param">
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
186 <param name="PL" type="select" label="Platform/technology used to produce the reads (PL)">
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
187 <option value="CAPILLARY">CAPILLARY</option>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
188 <option value="LS454">LS454</option>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
189 <option selected="True" value="ILLUMINA">ILLUMINA</option>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
190 <option value="SOLID">SOLID</option>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
191 <option value="HELICOS">HELICOS</option>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
192 <option value="IONTORRENT">IONTORRENT</option>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
193 <option value="PACBIO">PACBIO</option>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
194 </param>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
195 </xml>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
196 <xml name="read_group_lb_param">
7
d8c9597bfb09 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit ddb8bdb9d62399f086b06b3469450d0aad2113bd
devteam
parents: 6
diff changeset
197 <param name="LB" type="text" label="Library name (LB)" optional="true" />
5
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
198 </xml>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
199 <xml name="read_group_lb_conditional">
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
200 <conditional name="read_group_lb_conditional">
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
201 <expand macro="read_group_auto_name_conditional">
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
202 <expand macro="read_group_lb_param" />
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
203 </expand>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
204 </conditional>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
205 </xml>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
206 <xml name="read_group_lb_required_param">
7
d8c9597bfb09 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit ddb8bdb9d62399f086b06b3469450d0aad2113bd
devteam
parents: 6
diff changeset
207 <param name="LB" type="text" label="Library name (LB)" optional="false">
5
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
208 <validator type="empty_field" />
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
209 </param>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
210 </xml>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
211 <xml name="read_group_lb_required_conditional">
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
212 <conditional name="read_group_lb_conditional">
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
213 <expand macro="read_group_auto_name_conditional">
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
214 <expand macro="read_group_lb_required_param" />
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
215 </expand>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
216 </conditional>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
217 </xml>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
218 <xml name="read_group_cn_param">
7
d8c9597bfb09 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit ddb8bdb9d62399f086b06b3469450d0aad2113bd
devteam
parents: 6
diff changeset
219 <param name="CN" type="text" label="Sequencing center that produced the read (CN)" />
5
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
220 </xml>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
221 <xml name="read_group_ds_param">
7
d8c9597bfb09 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit ddb8bdb9d62399f086b06b3469450d0aad2113bd
devteam
parents: 6
diff changeset
222 <param name="DS" type="text" label="Description (DS)" />
5
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
223 </xml>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
224 <xml name="read_group_dt_param">
7
d8c9597bfb09 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit ddb8bdb9d62399f086b06b3469450d0aad2113bd
devteam
parents: 6
diff changeset
225 <param name="DT" type="text" label="Date that run was produced (DT)" help="ISO8601 format date or date/time, like YYYY-MM-DD" />
5
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
226 </xml>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
227 <xml name="read_group_fo_param">
7
d8c9597bfb09 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit ddb8bdb9d62399f086b06b3469450d0aad2113bd
devteam
parents: 6
diff changeset
228 <param name="FO" type="text" 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]+/">
5
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
229 <validator type="regex" message="Invalid flow order">\*|[ACMGRSVTWYHKDBN]+$</validator>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
230 </param>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
231 </xml>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
232 <xml name="read_group_ks_param">
7
d8c9597bfb09 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit ddb8bdb9d62399f086b06b3469450d0aad2113bd
devteam
parents: 6
diff changeset
233 <param name="KS" type="text" label="The array of nucleotide bases that correspond to the key sequence of each read (KS)" />
5
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
234 </xml>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
235 <xml name="read_group_pg_param">
7
d8c9597bfb09 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit ddb8bdb9d62399f086b06b3469450d0aad2113bd
devteam
parents: 6
diff changeset
236 <param name="PG" type="text" label="Programs used for processing the read group (PG)" />
5
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
237 </xml>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
238 <xml name="read_group_pi_param">
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
239 <param name="PI" type="integer" optional="true" label="Predicted median insert size (PI)" />
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
240 </xml>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
241 <xml name="read_group_pu_param">
7
d8c9597bfb09 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit ddb8bdb9d62399f086b06b3469450d0aad2113bd
devteam
parents: 6
diff changeset
242 <param name="PU" type="text" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="True" />
5
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
243 </xml>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
244 <xml name="read_group_pu_required_param">
22
01ac0a5fedc3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 393a497b224cd86285052e5ca2f41edc01125503
iuc
parents: 8
diff changeset
245 <param name="PU" type="text" value="run" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="False" />
5
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
246 </xml>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
247 <!-- Only ID is required - all groups available -->
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
248 <xml name="read_group_inputs_spec">
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
249 <expand macro="read_group_id_conditional" />
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
250 <expand macro="read_group_sm_conditional" />
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
251 <expand macro="read_group_pl_param" />
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
252 <expand macro="read_group_lb_conditional" />
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
253 <expand macro="read_group_cn_param" />
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
254 <expand macro="read_group_ds_param" />
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
255 <expand macro="read_group_dt_param" />
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
256 <expand macro="read_group_fo_param" />
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
257 <expand macro="read_group_ks_param" />
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
258 <expand macro="read_group_pg_param" />
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
259 <expand macro="read_group_pi_param" />
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
260 <expand macro="read_group_pu_param" />
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
261 </xml>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
262 <!-- ID, SM, LB, PU, PL all required - not ks, pg, or fo params. -->
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
263 <xml name="read_group_inputs_picard">
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
264 <expand macro="read_group_id_conditional" />
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
265 <expand macro="read_group_sm_required_conditional" />
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
266 <expand macro="read_group_lb_required_conditional" />
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
267 <expand macro="read_group_pl_param" />
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
268 <expand macro="read_group_pu_required_param" />
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
269 <expand macro="read_group_cn_param" />
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
270 <expand macro="read_group_ds_param" />
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
271 <expand macro="read_group_pi_param" />
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
272 <expand macro="read_group_dt_param" />
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
273 </xml>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
274 <xml name="read_group_conditional">
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
275 <conditional name="rg">
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
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.">
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
277 <option value="set">Set read groups (SAM/BAM specification)</option>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
278 <option value="set_picard">Set read groups (Picard style)</option>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
279 <option value="set_id_auto">Automatically assign ID</option>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
280 <option value="do_not_set" selected="True">Do not set</option>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
281 </param>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
282 <when value="set_picard">
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
283 <expand macro="read_group_inputs_picard" />
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
284 </when>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
285 <when value="set">
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
286 <expand macro="read_group_inputs_spec" />
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
287 </when>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
288 <when value="set_id_auto">
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
289 </when>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
290 <when value="do_not_set">
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
291 </when>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
292 </conditional>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
293 </xml>
fbf460831036 planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
devteam
parents:
diff changeset
294 </macros>