Mercurial > repos > bgruening > bismark

comparison bismark_bowtie2_wrapper.xml @ 19:359f8b60d316 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit 36810f2b29fdaffc73c3f85c6ed2f91887b49e93"
author bgruening
date Fri, 04 Oct 2019 07:54:51 -0400
parents aa9bf0f29a9f
children 120b7b35e442
comparison
equal deleted inserted replaced
18:bb74e17e47d7 19:359f8b60d316
10 10
11 #if $singlePaired.sPaired == "single": 11 #if $singlePaired.sPaired == "single":
12 #if $singlePaired.input_singles.ext == "fasta": 12 #if $singlePaired.input_singles.ext == "fasta":
13 #set read1 = 'input_1.fa' 13 #set read1 = 'input_1.fa'
14 #elif $singlePaired.input_singles.ext in ["fastq.gz", "fastqsanger.gz"]: 14 #elif $singlePaired.input_singles.ext in ["fastq.gz", "fastqsanger.gz"]:
15 #if $params.pbat == "--pbat" 15 #if $params.settingsType == "custom" and $params.pbat == "--pbat"
16 #set read1 = 'input_1.fq' 16 #set read1 = 'input_1.fq'
17 #else 17 #else
18 #set read1 = 'input_1.fq.gz' 18 #set read1 = 'input_1.fq.gz'
19 #end if 19 #end if
20 #else 20 #else
21 #set read1 = 'input_1.fq' 21 #set read1 = 'input_1.fq'
22 #end if 22 #end if
23 23
24 #if $params.pbat == "--pbat" and $singlePaired.input_singles.ext in ["fastq.gz", "fastqsanger.gz"]: 24 #if $params.settingsType == "custom" and $params.pbat == "--pbat" and $singlePaired.input_singles.ext in ["fastq.gz", "fastqsanger.gz"]:
25 zcat '${singlePaired.input_singles}' > '${read1}' && 25 zcat '${singlePaired.input_singles}' > '${read1}' &&
26 #else 26 #else
27 ln -s '${singlePaired.input_singles}' '${read1}' && 27 ln -s '${singlePaired.input_singles}' '${read1}' &&
28 #end if 28 #end if
29 #else: 29 #else:
32 #for $mate_pair in $singlePaired.mate_list 32 #for $mate_pair in $singlePaired.mate_list
33 33
34 #if $mate_pair.input_mate1.ext == "fasta": 34 #if $mate_pair.input_mate1.ext == "fasta":
35 #set read1 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fa' 35 #set read1 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fa'
36 #elif $mate_pair.input_mate1.ext in ["fastq.gz", "fastqsanger.gz"]: 36 #elif $mate_pair.input_mate1.ext in ["fastq.gz", "fastqsanger.gz"]:
37 #if $params.pbat == "--pbat" 37 #if $params.settingsType == "custom" and $params.pbat == "--pbat"
38 #set read1 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fq' 38 #set read1 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fq'
39 #else 39 #else
40 #set read1 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fq.gz' 40 #set read1 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fq.gz'
41 #end if 41 #end if
42 #else 42 #else
43 #set read1 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fq' 43 #set read1 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_1.fq'
44 #end if 44 #end if
45 45
46 #if $params.pbat == "--pbat" and $mate_pair.input_mate1.ext in ["fastq.gz", "fastqsanger.gz"]: 46 #if $params.settingsType == "custom" and $params.pbat == "--pbat" and $mate_pair.input_mate1.ext in ["fastq.gz", "fastqsanger.gz"]:
47 zcat '${mate_pair.input_mate1}' > '${read1}' && 47 zcat '${mate_pair.input_mate1}' > '${read1}' &&
48 #else 48 #else
49 ln -s '${mate_pair.input_mate1}' '${read1}' && 49 ln -s '${mate_pair.input_mate1}' '${read1}' &&
50 #end if 50 #end if
51 51
52 #if $mate_pair.input_mate2.ext == "fasta": 52 #if $mate_pair.input_mate2.ext == "fasta":
53 #set read2 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fa' 53 #set read2 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fa'
54 #elif $mate_pair.input_mate2.ext in ["fastq.gz", "fastqsanger.gz"]: 54 #elif $mate_pair.input_mate2.ext in ["fastq.gz", "fastqsanger.gz"]:
55 #if $params.pbat == "--pbat" 55 #if $params.settingsType == "custom" and $params.pbat == "--pbat"
56 #set read2 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fq' 56 #set read2 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fq'
57 #else 57 #else
58 #set read2 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fq.gz' 58 #set read2 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fq.gz'
59 #end if 59 #end if
60 #else 60 #else
61 #set read2 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fq' 61 #set read2 = re.sub('[^\w\-_.]', '_', str($mate_pair.input_mate1.element_identifier)) + '_2.fq'
62 #end if 62 #end if
63 63
64 #if $params.pbat == "--pbat" and $mate_pair.input_mate2.ext in ["fastq.gz", "fastqsanger.gz"]: 64 #if $params.settingsType == "custom" and $params.pbat == "--pbat" and $mate_pair.input_mate2.ext in ["fastq.gz", "fastqsanger.gz"]:
65 zcat '${mate_pair.input_mate2}' > '${read2}' && 65 zcat '${mate_pair.input_mate2}' > '${read2}' &&
66 #else 66 #else
67 ln -s '${mate_pair.input_mate2}' '${read2}' && 67 ln -s '${mate_pair.input_mate2}' '${read2}' &&
68 #end if 68 #end if
69 69