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comparison tools/fastx_toolkit/fastq_to_fasta.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 <tool id="cshl_fastq_to_fasta" name="FASTQ to FASTA">
2 <description>converter</description>
3 <requirements><requirement type="package">fastx_toolkit</requirement></requirements>
4 <command>gunzip -cf $input | fastq_to_fasta $SKIPN $RENAMESEQ -o $output -v
5 #if $input.ext == "fastqsanger":
6 -Q 33
7 #end if
8 </command>
9
10 <inputs>
11 <param format="fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="FASTQ Library to convert" />
12
13 <param name="SKIPN" type="select" label="Discard sequences with unknown (N) bases ">
14 <option value="">yes</option>
15 <option value="-n">no</option>
16 </param>
17
18 <param name="RENAMESEQ" type="select" label="Rename sequence names in output file (reduces file size)">
19 <option value="-r">yes</option>
20 <option value="">no</option>
21 </param>
22
23 </inputs>
24
25 <tests>
26 <test>
27 <!-- FASTQ-To-FASTA, keep N, don't rename -->
28 <param name="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" />
29 <param name="SKIPN" value=""/>
30 <param name="RENAMESEQ" value=""/>
31 <output name="output" file="fastq_to_fasta1a.out" />
32 </test>
33 <test>
34 <!-- FASTQ-To-FASTA, discard N, rename -->
35 <param name="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" />
36 <param name="SKIPN" value="no"/>
37 <param name="RENAMESEQ" value="yes"/>
38 <output name="output" file="fastq_to_fasta1b.out" />
39 </test>
40 </tests>
41
42 <outputs>
43 <data format="fasta" name="output" metadata_source="input" />
44 </outputs>
45
46 <help>
47
48 **What it does**
49
50 This tool converts data from Solexa format to FASTA format (scroll down for format description).
51
52 --------
53
54 **Example**
55
56 The following data in Solexa-FASTQ format::
57
58 @CSHL_4_FC042GAMMII_2_1_517_596
59 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
60 +CSHL_4_FC042GAMMII_2_1_517_596
61 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
62
63 Will be converted to FASTA (with 'rename sequence names' = NO)::
64
65 >CSHL_4_FC042GAMMII_2_1_517_596
66 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
67
68 Will be converted to FASTA (with 'rename sequence names' = YES)::
69
70 >1
71 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
72
73 ------
74
75 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
76
77 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
78 </help>
79 </tool>
80 <!-- FASTQ-to-FASTA is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->