root/galaxy-central/tools/fastx_toolkit/fastq_to_fasta.xml

リビジョン 2, 2.2 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

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