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comparison stacks_denovomap.xml @ 5:34000c653ae5 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 05:43:39 -0500
parents 998dfec32bde
children 39d2b6c1c030
comparison
equal deleted inserted replaced
4:998dfec32bde 5:34000c653ae5
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_sequences: 13 #for $input_parent in $options_usage.parent_sequences:
14 14
15 #if $input_parent.ext == "fastqsanger": 15 #if $input_parent.is_of_type('fastqsanger'):
16 #set $data_path = splitext($input_parent.element_identifier)[0] 16 #set $data_path = splitext($input_parent.element_identifier)[0]
17 #set $data_path = re.sub(r'\.1$', '', $data_path) 17 #set $data_path = re.sub(r'\.1$', '', $data_path)
18 #set $data_path = $data_path + ".fq" 18 #set $data_path = $data_path + ".fq"
19 #else: 19 #else:
20 #set $data_path = splitext($input_parent.element_identifier)[0] 20 #set $data_path = splitext($input_parent.element_identifier)[0]
25 ln -s "${input_parent}" "${data_path}" && 25 ln -s "${input_parent}" "${data_path}" &&
26 #end for 26 #end for
27 27
28 #for $input_progeny in $options_usage.progeny_sequences: 28 #for $input_progeny in $options_usage.progeny_sequences:
29 #if $input_progeny: 29 #if $input_progeny:
30 #if $input_progeny.ext == "fastqsanger": 30 #if $input_progeny.is_of_type('fastqsanger'):
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 + ".fq" 33 #set $data_path = $data_path + ".fq"
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 == "fastqsanger": 46 #if $input_indiv.is_of_type('fastqsanger'):
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 + ".fq" 49 #set $data_path = $data_path + ".fq"
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_sequences: 69 #for $input_parent in $options_usage.parent_sequences:
70 #if $input_parent.ext == "fastqsanger": 70 #if $input_parent.is_of_type('fastqsanger'):
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 + ".fq" 73 #set $data_path = $data_path + ".fq"
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_sequences: 85 #for $input_progeny in $options_usage.progeny_sequences:
86 #if $input_progeny: 86 #if $input_progeny:
87 #if $input_progeny.ext == "fastqsanger": 87 #if $input_progeny.is_of_type('fastqsanger'):
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 + ".fq" 90 #set $data_path = $data_path + ".fq"
91 #else: 91 #else:
92 #set $data_path = splitext($input_progeny.element_identifier)[0] 92 #set $data_path = splitext($input_progeny.element_identifier)[0]
102 -P $assembly_options.P 102 -P $assembly_options.P
103 #end if 103 #end if
104 #else: 104 #else:
105 #for $i_indiv, $input_indiv in enumerate($options_usage.individual_sample): 105 #for $i_indiv, $input_indiv in enumerate($options_usage.individual_sample):
106 106
107 #if $input_indiv.ext == "fastqsanger": 107 #if $input_indiv.is_of_type('fastqsanger'):
108 #set $data_path = splitext($input_indiv.element_identifier)[0] 108 #set $data_path = splitext($input_indiv.element_identifier)[0]
109 #set $data_path = re.sub(r'\.1$', '', $data_path) 109 #set $data_path = re.sub(r'\.1$', '', $data_path)
110 #set $data_path = $data_path + ".fq" 110 #set $data_path = $data_path + ".fq"
111 #else: 111 #else:
112 #set $data_path = splitext($input_indiv.element_identifier)[0] 112 #set $data_path = splitext($input_indiv.element_identifier)[0]