comparison fastq_to_fasta.xml @ 0:04614cf6ed39 draft

Uploaded tool tarball.
author devteam
date Wed, 25 Sep 2013 11:04:26 -0400
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1 <tool id="cshl_fastq_to_fasta" name="FASTQ to FASTA">
2 <description>converter</description>
3 <requirements>
4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
5 </requirements>
6 <command>gunzip -cf $input | fastq_to_fasta $SKIPN $RENAMESEQ -o $output -v
7 #if $input.ext == "fastqsanger":
8 -Q 33
9 #end if
10 </command>
11
12 <inputs>
13 <param format="fastqsanger,fastqsolexa,fastqillumina" name="input" type="data" label="FASTQ Library to convert" />
14
15 <param name="SKIPN" type="select" label="Discard sequences with unknown (N) bases ">
16 <option value="">yes</option>
17 <option value="-n">no</option>
18 </param>
19
20 <param name="RENAMESEQ" type="select" label="Rename sequence names in output file (reduces file size)">
21 <option value="-r">yes</option>
22 <option value="">no</option>
23 </param>
24
25 </inputs>
26
27 <tests>
28 <test>
29 <!-- FASTQ-To-FASTA, keep N, don't rename -->
30 <param name="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" />
31 <param name="SKIPN" value=""/>
32 <param name="RENAMESEQ" value=""/>
33 <output name="output" file="fastq_to_fasta1a.out" />
34 </test>
35 <test>
36 <!-- FASTQ-To-FASTA, discard N, rename -->
37 <param name="input" value="fastq_to_fasta1.fastq" ftype="fastqsolexa" />
38 <param name="SKIPN" value="no"/>
39 <param name="RENAMESEQ" value="yes"/>
40 <output name="output" file="fastq_to_fasta1b.out" />
41 </test>
42 </tests>
43
44 <outputs>
45 <data format="fasta" name="output" metadata_source="input" />
46 </outputs>
47
48 <help>
49
50 **What it does**
51
52 This tool converts data from Solexa format to FASTA format (scroll down for format description).
53
54 --------
55
56 **Example**
57
58 The following data in Solexa-FASTQ format::
59
60 @CSHL_4_FC042GAMMII_2_1_517_596
61 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
62 +CSHL_4_FC042GAMMII_2_1_517_596
63 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
64
65 Will be converted to FASTA (with 'rename sequence names' = NO)::
66
67 >CSHL_4_FC042GAMMII_2_1_517_596
68 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
69
70 Will be converted to FASTA (with 'rename sequence names' = YES)::
71
72 >1
73 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
74
75 ------
76
77 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
78
79 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
80 </help>
81 <!-- FASTQ-to-FASTA is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
82 </tool>