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comparison sickle.xml @ 6:73d2fda8a179 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sickle commit 7f0dbcf650d20acd80d7082bdae9759d51a1480c"
author iuc
date Thu, 05 Sep 2019 13:13:56 -0400
parents 6a4d7d95fbdc
children 340de8627f41
comparison
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5:6a4d7d95fbdc 6:73d2fda8a179
1 <tool id="sickle" name="Sickle" version="1.33.1" profile="17.01"> 1 <tool id="sickle" name="Sickle" version="1.33.2" profile="17.01">
2 <description>windowed adaptive trimming of FASTQ data</description> 2 <description>windowed adaptive trimming of FASTQ data</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.33">sickle</requirement>
5 <!-- conda dependency -->
6 <requirement type="package" version="1.33">sickle-trim</requirement> 4 <requirement type="package" version="1.33">sickle-trim</requirement>
7 </requirements> 5 </requirements>
8 <version_command>sickle --version | head -n 1</version_command> 6 <version_command>sickle --version | head -n 1</version_command>
9 <command><![CDATA[ 7 <command><![CDATA[
10 ## Link in the input files, which also determines the type of the output 8 ## Link in the input files, which also determines the type of the output
11 #set compressed = "" 9 #set compressed = ""
12 #if str($readtype.single_or_paired) == "se": 10 #if str($readtype.single_or_paired) == "se":
13 #if $readtype.input_single.is_of_type('fastq.gz'): 11 #if $readtype.input_single.is_of_type('fastq.gz'):
14 #set read1 = "input_1.fastq.gz" 12 #set read1 = "input_1.fastq.gz"
15 #set compressed = "-g" 13 #set compressed = "-g"
16 #else 14 #else
17 #set read1 = "input_1.fastq" 15 #set read1 = "input_1.fastq"
18 #end if 16 #end if
19 ln -f -s '${readtype.input_single}' ${read1} && 17 ln -f -s '${readtype.input_single}' ${read1} &&
20 #else if str($readtype.single_or_paired) == "pe_combo": 18 #else if str($readtype.single_or_paired) == "pe_combo":
21 #if $readtype.input_combo.is_of_type('fastq.gz'): 19 #if $readtype.input_combo.is_of_type('fastq.gz'):
22 #set read1 = "input_1.fastq.gz" 20 #set read1 = "input_1.fastq.gz"
23 #set compressed = "-g" 21 #set compressed = "-g"
24 #else 22 #else
25 #set read1 = "input_1.fastq" 23 #set read1 = "input_1.fastq"
26 #end if 24 #end if
27 ln -f -s '${readtype.input_combo}' ${read1} && 25 ln -f -s '${readtype.input_combo}' ${read1} &&
28 #else if str($readtype.single_or_paired) == "pe_sep": 26 #else if str($readtype.single_or_paired) == "pe_sep":
29 #if $readtype.input_paired1.is_of_type('fastq.gz'): 27 #if $readtype.input_paired1.is_of_type('fastq.gz'):
30 #set read1 = "input_1.fastq.gz" 28 #set read1 = "input_1.fastq.gz"
31 #set compressed = "-g" 29 #set compressed = "-g"
32 #else 30 #else
33 #set read1 = "input_1.fastq" 31 #set read1 = "input_1.fastq"
34 #end if 32 #end if
35 ln -f -s '${readtype.input_paired1}' ${read1} && 33 ln -f -s '${readtype.input_paired1}' ${read1} &&
36 34
37 #if $readtype.input_paired2.is_of_type('fastq.gz'): 35 #if $readtype.input_paired2.is_of_type('fastq.gz'):
38 #set read2 = "input_2.fastq.gz" 36 #set read2 = "input_2.fastq.gz"
39 #else 37 #else
40 #set read2 = "input_2.fastq" 38 #set read2 = "input_2.fastq"
41 #end if 39 #end if
42 ln -f -s '${readtype.input_paired2}' ${read2} && 40 ln -f -s '${readtype.input_paired2}' ${read2} &&
43 #else 41 #else
44 #if $readtype.input_paired.forward.is_of_type('fastq.gz'): 42 #if $readtype.input_paired.forward.is_of_type('fastq.gz'):
45 #set read1 = "input_1.fastq.gz" 43 #set read1 = "input_1.fastq.gz"
46 #set compressed = "-g" 44 #set compressed = "-g"
47 #else 45 #else
48 #set read1 = "input_1.fastq" 46 #set read1 = "input_1.fastq"
49 #end if 47 #end if
50 ln -f -s '${readtype.input_paired.forward}' ${read1} && 48 ln -f -s '${readtype.input_paired.forward}' ${read1} &&
51 49
52 #if $readtype.input_paired.reverse.is_of_type('fastq.gz'): 50 #if $readtype.input_paired.reverse.is_of_type('fastq.gz'):
53 #set read2 = "input_2.fastq.gz" 51 #set read2 = "input_2.fastq.gz"
54 #else 52 #else
55 #set read2 = "input_2.fastq" 53 #set read2 = "input_2.fastq"
56 #end if 54 #end if
57 ln -f -s '${readtype.input_paired.reverse}' ${read2} && 55 ln -f -s '${readtype.input_paired.reverse}' ${read2} &&
58 #end if 56 #end if
59 57
60 sickle 58 sickle
61 59
62 #if str($readtype.single_or_paired) == "se": 60 #if str($readtype.single_or_paired) == "se":
63 se -f ${read1} -o '${output_single}' 61 se -f ${read1} -o '${output_single}'
64 62
65 #if $readtype.input_single.is_of_type('fastqillumina', 'fastqillumina.gz'): 63 #if $readtype.input_single.is_of_type('fastqillumina', 'fastqillumina.gz'):
66 -t illumina 64 -t illumina
67 #else if $readtype.input_single.is_of_type('fastqsolexa', 'fastqsolexa.gz'): 65 #else if $readtype.input_single.is_of_type('fastqsolexa', 'fastqsolexa.gz'):
68 -t solexa 66 -t solexa
69 #else: 67 #else:
70 -t sanger 68 -t sanger
71 #end if 69 #end if
72 #else if str($readtype.single_or_paired) == "pe_combo": 70 #else if str($readtype.single_or_paired) == "pe_combo":
73 #if $readtype.output_n: 71 #if $readtype.output_n:
74 pe -c ${read1} -M '${output_combo}' 72 pe -c ${read1} -M '${output_combo}'
75 #else 73 #else
76 pe -c ${read1} -m '${output_combo}' -s '${output_combo_single}' 74 pe -c ${read1} -m '${output_combo}' -s '${output_combo_single}'
77 #end if 75 #end if
78 76
79 #if $readtype.input_combo.is_of_type('fastqillumina', 'fastqillumina.gz'): 77 #if $readtype.input_combo.is_of_type('fastqillumina', 'fastqillumina.gz'):
80 -t illumina 78 -t illumina
81 #else if $readtype.input_combo.is_of_type('fastqsolexa', 'fastqsolexa.gz'): 79 #else if $readtype.input_combo.is_of_type('fastqsolexa', 'fastqsolexa.gz'):
82 -t solexa 80 -t solexa
83 #else: 81 #else:
84 -t sanger 82 -t sanger
85 #end if 83 #end if
86 #else if str($readtype.single_or_paired) == "pe_sep": 84 #else if str($readtype.single_or_paired) == "pe_sep":
87 pe -f ${read1} -r ${read2} -o '${output_paired1}' -p '${output_paired2}' -s '${output_paired_single}' 85 pe -f ${read1} -r ${read2} -o '${output_paired1}' -p '${output_paired2}' -s '${output_paired_single}'
88 86
89 #if $readtype.input_paired1.is_of_type('fastqillumina', 'fastqillumina.gz'): 87 #if $readtype.input_paired1.is_of_type('fastqillumina', 'fastqillumina.gz'):
90 -t illumina 88 -t illumina
91 #else if $readtype.input_paired1.is_of_type('fastqsolexa', 'fastqsolexa.gz'): 89 #else if $readtype.input_paired1.is_of_type('fastqsolexa', 'fastqsolexa.gz'):
92 -t solexa 90 -t solexa
93 #else: 91 #else:
94 -t sanger 92 -t sanger
95 #end if 93 #end if
96 #else if str($readtype.single_or_paired) == "pe_collection": 94 #else if str($readtype.single_or_paired) == "pe_collection":
97 pe -f ${read1} -r ${read2} -o '${output_paired_coll.forward}' -p '${output_paired_coll.reverse}' -s '${output_paired_coll_single}' 95 pe -f ${read1} -r ${read2} -o '${output_paired_coll.forward}' -p '${output_paired_coll.reverse}' -s '${output_paired_coll_single}'
98 96
99 #if $readtype.input_paired.forward.is_of_type('fastqillumina', 'fastqillumina.gz'): 97 #if $readtype.input_paired.forward.is_of_type('fastqillumina', 'fastqillumina.gz'):
100 -t illumina 98 -t illumina
101 #else if $readtype.input_paired.forward.is_of_type('fastqsolexa', 'fastqsolexa.gz'): 99 #else if $readtype.input_paired.forward.is_of_type('fastqsolexa', 'fastqsolexa.gz'):
102 -t solexa 100 -t solexa
103 #else: 101 #else:
104 -t sanger 102 -t sanger
105 #end if 103 #end if
106 #end if 104 #end if
107 105
108 $compressed 106 $compressed
109 107
110 #if str($qual_threshold) != "": 108 #if str($qual_threshold) != "":
111 -q $qual_threshold 109 -q $qual_threshold
112 #end if 110 #end if
113 111
114 #if str($length_threshold) != "": 112 #if str($length_threshold) != "":
115 -l $length_threshold 113 -l $length_threshold
116 #end if 114 #end if
117 115
118 #if $no_five_prime: 116 #if $no_five_prime:
119 -x 117 -x
120 #end if 118 #end if
121 119
122 #if $trunc_n: 120 #if $trunc_n:
123 -n 121 -n
124 #end if 122 #end if
125 ]]> 123 ]]></command>
126 </command>
127 124
128 <inputs> 125 <inputs>
129 <conditional name="readtype"> 126 <conditional name="readtype">
130 <param name="single_or_paired" type="select" label="Single-end or paired-end reads?" help="Note: Sickle will infer the quality type of the file from its datatype. I.e., if the datatype is fastqsanger, then the quality type is sanger. The default is fastqsanger."> 127 <param name="single_or_paired" type="select" label="Single-end or paired-end reads?" help="Note: Sickle will infer the quality type of the file from its datatype. I.e., if the datatype is fastqsanger, then the quality type is sanger. The default is fastqsanger.">
131 <option value="se" selected="true">Single-end</option> 128 <option value="se" selected="true">Single-end</option>
348 345
349 ----- 346 -----
350 347
351 Copyright: Nikhil Joshi 348 Copyright: Nikhil Joshi
352 349
353 http://bioinformatics.ucdavis.edu
354
355 http://github.com/najoshi/sickle 350 http://github.com/najoshi/sickle
356 </help> 351 </help>
357 <citations> 352 <citations>
358 <citation type="bibtex"> 353 <citation type="bibtex">
359 @unpublished{sickle_link, 354 @unpublished{sickle_link,