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comparison stacks_refmap.xml @ 5:12aa3ad29980 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 9401451df4a985ef5686864eaadafa077ffc0877
author iuc
date Mon, 27 Feb 2017 05:44:36 -0500
parents 827c8c6ec4c1
children c209e3f3359b
comparison
equal deleted inserted replaced
4:827c8c6ec4c1 5:12aa3ad29980
9 #from os.path import splitext 9 #from os.path import splitext
10 #import re 10 #import re
11 11
12 #if str( $options_usage.rad_analysis_type ) == "genetic": 12 #if str( $options_usage.rad_analysis_type ) == "genetic":
13 #for $input_parent in $options_usage.parent_alignments: 13 #for $input_parent in $options_usage.parent_alignments:
14 #if $input_parent.ext == "sam": 14 #if $input_parent.is_of_type('sam'):
15 #set $data_path = splitext($input_parent.element_identifier)[0] 15 #set $data_path = splitext($input_parent.element_identifier)[0]
16 #set $data_path = re.sub(r'\.1$', '', $data_path) 16 #set $data_path = re.sub(r'\.1$', '', $data_path)
17 #set $data_path = $data_path + ".sam" 17 #set $data_path = $data_path + ".sam"
18 #else: 18 #else:
19 #set $data_path = splitext($input_parent.element_identifier)[0] 19 #set $data_path = splitext($input_parent.element_identifier)[0]
25 #end for 25 #end for
26 26
27 #for $input_progeny in $options_usage.progeny_alignments: 27 #for $input_progeny in $options_usage.progeny_alignments:
28 28
29 #if $input_progeny: 29 #if $input_progeny:
30 #if $input_progeny.ext == "sam": 30 #if $input_progeny.is_of_type('sam'):
31 #set $data_path = splitext($input_progeny.element_identifier)[0] 31 #set $data_path = splitext($input_progeny.element_identifier)[0]
32 #set $data_path = re.sub(r'\.1$', '', $data_path) 32 #set $data_path = re.sub(r'\.1$', '', $data_path)
33 #set $data_path = $data_path + ".sam" 33 #set $data_path = $data_path + ".sam"
34 #else: 34 #else:
35 #set $data_path = splitext($input_progeny.element_identifier)[0] 35 #set $data_path = splitext($input_progeny.element_identifier)[0]
41 #end if 41 #end if
42 #end for 42 #end for
43 #else: 43 #else:
44 #for $input_indiv in $options_usage.individual_sample: 44 #for $input_indiv in $options_usage.individual_sample:
45 45
46 #if $input_indiv.ext == "sam": 46 #if $input_indiv.is_of_type('sam'):
47 #set $data_path = splitext($input_indiv.element_identifier)[0] 47 #set $data_path = splitext($input_indiv.element_identifier)[0]
48 #set $data_path = re.sub(r'\.1$', '', $data_path) 48 #set $data_path = re.sub(r'\.1$', '', $data_path)
49 #set $data_path = $data_path + ".sam" 49 #set $data_path = $data_path + ".sam"
50 #else: 50 #else:
51 #set $data_path = splitext($input_indiv.element_identifier)[0] 51 #set $data_path = splitext($input_indiv.element_identifier)[0]
65 65
66 -T \${GALAXY_SLOTS:-1} 66 -T \${GALAXY_SLOTS:-1}
67 67
68 #if str( $options_usage.rad_analysis_type ) == "genetic": 68 #if str( $options_usage.rad_analysis_type ) == "genetic":
69 #for $input_parent in $options_usage.parent_alignments: 69 #for $input_parent in $options_usage.parent_alignments:
70 #if $input_parent.ext == "sam": 70 #if $input_parent.is_of_type('sam'):
71 #set $data_path = splitext($input_parent.element_identifier)[0] 71 #set $data_path = splitext($input_parent.element_identifier)[0]
72 #set $data_path = re.sub(r'\.1$', '', $data_path) 72 #set $data_path = re.sub(r'\.1$', '', $data_path)
73 #set $data_path = $data_path + ".sam" 73 #set $data_path = $data_path + ".sam"
74 #else: 74 #else:
75 #set $data_path = splitext($input_parent.element_identifier)[0] 75 #set $data_path = splitext($input_parent.element_identifier)[0]
82 82
83 -A $options_usage.cross_type 83 -A $options_usage.cross_type
84 84
85 #for $input_progeny in $options_usage.progeny_alignments: 85 #for $input_progeny in $options_usage.progeny_alignments:
86 #if $input_progeny: 86 #if $input_progeny:
87 #if $input_progeny.ext == "sam": 87 #if $input_progeny.is_of_type('sam'):
88 #set $data_path = splitext($input_progeny.element_identifier)[0] 88 #set $data_path = splitext($input_progeny.element_identifier)[0]
89 #set $data_path = re.sub(r'\.1$', '', $data_path) 89 #set $data_path = re.sub(r'\.1$', '', $data_path)
90 #set $data_path = $data_path + ".sam" 90 #set $data_path = $data_path + ".sam"
91 #else: 91 #else:
92 #set $data_path = splitext($input_progeny.element_identifier)[0] 92 #set $data_path = splitext($input_progeny.element_identifier)[0]
98 #end if 98 #end if
99 #end for 99 #end for
100 #else: 100 #else:
101 #for $input_indiv in $options_usage.individual_sample: 101 #for $input_indiv in $options_usage.individual_sample:
102 102
103 #if $input_indiv.ext == "sam": 103 #if $input_indiv.is_of_type('sam'):
104 #set $data_path = splitext($input_indiv.element_identifier)[0] 104 #set $data_path = splitext($input_indiv.element_identifier)[0]
105 #set $data_path = re.sub(r'\.1$', '', $data_path) 105 #set $data_path = re.sub(r'\.1$', '', $data_path)
106 #set $data_path = $data_path + ".sam" 106 #set $data_path = $data_path + ".sam"
107 #else: 107 #else:
108 #set $data_path = splitext($input_indiv.element_identifier)[0] 108 #set $data_path = splitext($input_indiv.element_identifier)[0]