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comparison sickle.xml @ 4:3825840482cb draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit a8611c912a8265de6f64a3e17cea63c87fa48b8e
author iuc
date Mon, 23 Jan 2017 06:06:52 -0500
parents 3862781b4445
children 6a4d7d95fbdc
comparison
equal deleted inserted replaced
3:3862781b4445 4:3825840482cb
10 sickle 10 sickle
11 11
12 #if str($readtype.single_or_paired) == "se": 12 #if str($readtype.single_or_paired) == "se":
13 se -f "${readtype.input_single}" -o "$output_single" 13 se -f "${readtype.input_single}" -o "$output_single"
14 14
15 #if $readtype.is_of_type("fastq", "fastqsanger"): 15 #if $readtype.input_single.is_of_type('fastqillumina'):
16 -t sanger
17 #else if $readtype.input_single.is_of_type('fastqillumina'):
18 -t illumina 16 -t illumina
19 #else if $readtype.input_single.is_of_type('fastqsolexa'): 17 #else if $readtype.input_single.is_of_type('fastqsolexa'):
20 -t solexa 18 -t solexa
19 #else:
20 -t sanger
21 #end if 21 #end if
22 #end if 22 #end if
23 23
24 #if str($readtype.single_or_paired) == "pe_combo": 24 #if str($readtype.single_or_paired) == "pe_combo":
25 #if $readtype.output_n: 25 #if $readtype.output_n:
26 pe -c "${readtype.input_combo}" -M "$output_combo" 26 pe -c "${readtype.input_combo}" -M "$output_combo"
27 #else 27 #else
28 pe -c "${readtype.input_combo}" -m "$output_combo" -s "$output_combo_single" 28 pe -c "${readtype.input_combo}" -m "$output_combo" -s "$output_combo_single"
29 #end if 29 #end if
30 30
31 #if $readtype.input_combo.is_of_type("fastq", "fastqsanger"): 31 #if $readtype.input_combo.is_of_type('fastqillumina'):
32 -t sanger
33 #else if $readtype.input_combo.is_of_type('fastqillumina'):
34 -t illumina 32 -t illumina
35 #else if $readtype.input_combo.is_of_type('fastqsolexa'): 33 #else if $readtype.input_combo.is_of_type('fastqsolexa'):
36 -t solexa 34 -t solexa
35 #else:
36 -t sanger
37 #end if 37 #end if
38 #end if 38 #end if
39 39
40 #if str($readtype.single_or_paired) == "pe_sep": 40 #if str($readtype.single_or_paired) == "pe_sep":
41 pe -f "${readtype.input_paired1}" -r "${readtype.input_paired2}" -o "$output_paired1" -p "$output_paired2" -s "$output_paired_single" 41 pe -f "${readtype.input_paired1}" -r "${readtype.input_paired2}" -o "$output_paired1" -p "$output_paired2" -s "$output_paired_single"
42 42
43 #if $readtype.input_paired1.is_of_type("fastq", "fastqsanger"): 43 #if $readtype.input_paired1.is_of_type('fastqillumina'):
44 -t sanger
45 #else if $readtype.input_paired1.is_of_type('fastqillumina'):
46 -t illumina 44 -t illumina
47 #else if $readtype.input_paired1.is_of_type('fastqsolexa'): 45 #else if $readtype.input_paired1.is_of_type('fastqsolexa'):
48 -t solexa 46 -t solexa
47 #else:
48 -t sanger
49 #end if 49 #end if
50 #end if 50 #end if
51 51
52 #if str($readtype.single_or_paired) == "pe_collection": 52 #if str($readtype.single_or_paired) == "pe_collection":
53 pe -f "${readtype.input_paired.forward}" -r "${readtype.input_paired.reverse}" -o "${output_paired_coll.forward}" -p "${output_paired_coll.reverse}" -s "$output_paired_coll_single" 53 pe -f "${readtype.input_paired.forward}" -r "${readtype.input_paired.reverse}" -o "${output_paired_coll.forward}" -p "${output_paired_coll.reverse}" -s "$output_paired_coll_single"
54 54
55 #if $readtype.input_paired.forward.is_of_type("fastq", "fastqsanger"): 55 #if $readtype.input_paired.forward.is_of_type('fastqillumina'):
56 -t sanger
57 #else if $readtype.input_paired.forward.is_of_type('fastqillumina'):
58 -t illumina 56 -t illumina
59 #else if $readtype.input_paired.forward.is_of_type('fastqsolexa'): 57 #else if $readtype.input_paired.forward.is_of_type('fastqsolexa'):
60 -t solexa 58 -t solexa
59 #else:
60 -t sanger
61 #end if 61 #end if
62 #end if 62 #end if
63 63
64 #if str($qual_threshold) != "": 64 #if str($qual_threshold) != "":
65 -q $qual_threshold 65 -q $qual_threshold