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comparison fastx_toolkit-0.0.6/galaxy/tools/fastx_toolkit/fastq_to_fasta.xml @ 3:997f5136985f draft default tip

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author xilinxu
date Thu, 14 Aug 2014 04:52:17 -0400
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1 <tool id="cshl_fastq_to_fasta" name="FASTQ to FASTA">
2 <description>converter</description>
3 <command>gunzip -cf $input | fastq_to_fasta $SKIPN $RENAMESEQ -o $output -v </command>
4
5 <inputs>
6 <param format="fastqsolexa" name="input" type="data" label="FASTQ Library to convert" />
7
8 <param name="SKIPN" type="select" label="Discard sequences with unknown (N) bases ">
9 <option value="">yes</option>
10 <option value="-n">no</option>
11 </param>
12
13 <param name="RENAMESEQ" type="select" label="Rename sequence names in output file (reduces file size)">
14 <option value="-r">yes</option>
15 <option value="">no</option>
16 </param>
17
18 </inputs>
19
20 <tests>
21 <test>
22 <!-- FASTQ-To-FASTA, keep N, don't rename -->
23 <param name="input" value="fastq_to_fasta1.fastq" />
24 <param name="SKIPN" value=""/>
25 <param name="RENAMESEQ" value=""/>
26 <output name="output" file="fastq_to_fasta1a.out" />
27 </test>
28 <test>
29 <!-- FASTQ-To-FASTA, discard N, rename -->
30 <param name="input" value="fastq_to_fasta1.fastq" />
31 <param name="SKIPN" value="no"/>
32 <param name="RENAMESEQ" value="yes"/>
33 <output name="output" file="fastq_to_fasta1b.out" />
34 </test>
35 </tests>
36
37 <outputs>
38 <data format="fasta" name="output" metadata_source="input" />
39 </outputs>
40
41 <help>
42
43 **What it does**
44
45 This tool converts data from Solexa format to FASTA format (scroll down for format description).
46
47 --------
48
49 **Example**
50
51 The following data in Solexa-FASTQ format::
52
53 @CSHL_4_FC042GAMMII_2_1_517_596
54 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
55 +CSHL_4_FC042GAMMII_2_1_517_596
56 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
57
58 Will be converted to FASTA (with 'rename sequence names' = NO)::
59
60 >CSHL_4_FC042GAMMII_2_1_517_596
61 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
62
63 Will be converted to FASTA (with 'rename sequence names' = YES)::
64
65 >1
66 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
67
68 </help>
69 </tool>
70 <!-- FASTQ-to-FASTA is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->