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comparison fastq_to_fasta.xml @ 0:78a7d28f2a15 draft

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author idot
date Wed, 10 Jul 2013 06:13:48 -0400
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1 <tool id="cshl_fastq_to_fasta" name="FASTQ to FASTA">
2 <description>converter</description>
3 <command>
4 cat '$input' |
5 fastq_to_fasta
6 #if $input.ext == "fastqsanger":
7 -Q 33
8 #elif $input.ext == "fastq":
9 -Q 64
10 #end if
11 $SKIPN $RENAMESEQ -o '$output' -v
12 </command>
13 <inputs>
14 <param format="fastq,fastqsanger" name="input" type="data" label="FASTQ Library to convert" />
15
16 <param name="SKIPN" type="select" label="Discard sequences with unknown (N) bases ">
17 <option value="">yes</option>
18 <option value="-n">no</option>
19 </param>
20
21 <param name="RENAMESEQ" type="select" label="Rename sequence names in output file (reduces file size)">
22 <option value="-r">yes</option>
23 <option value="">no</option>
24 </param>
25
26 </inputs>
27
28 <tests>
29 <test>
30 <!-- FASTQ-To-FASTA, keep N, don't rename -->
31 <param name="input" value="fastq_to_fasta1.fastq" />
32 <param name="SKIPN" value=""/>
33 <param name="RENAMESEQ" value=""/>
34 <output name="output" file="fastq_to_fasta1a.out" />
35 </test>
36 <test>
37 <!-- FASTQ-To-FASTA, discard N, rename -->
38 <param name="input" value="fastq_to_fasta1.fastq" />
39 <param name="SKIPN" value="no"/>
40 <param name="RENAMESEQ" value="yes"/>
41 <output name="output" file="fastq_to_fasta1b.out" />
42 </test>
43 </tests>
44
45 <outputs>
46 <data format="fasta" name="output" metadata_source="input"
47 />
48 </outputs>
49
50 <help>
51
52 **What it does**
53
54 This tool converts data from Solexa format to FASTA format (scroll down for format description).
55
56 --------
57
58 **Example**
59
60 The following data in Solexa-FASTQ format::
61
62 @CSHL_4_FC042GAMMII_2_1_517_596
63 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
64 +CSHL_4_FC042GAMMII_2_1_517_596
65 40 40 40 40 40 40 40 40 40 40 38 40 40 40 40 40 14 40 40 40 40 40 36 40 13 14 24 24 9 24 9 40 10 10 15 40
66
67 Will be converted to FASTA (with 'rename sequence names' = NO)::
68
69 >CSHL_4_FC042GAMMII_2_1_517_596
70 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
71
72 Will be converted to FASTA (with 'rename sequence names' = YES)::
73
74 >1
75 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
76
77 ------
78
79 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
80
81 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
82 </help>
83 </tool>
84 <!-- FASTQ-to-FASTA is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->