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

リビジョン 2, 1.9 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="cshl_fastx_renamer" name="Rename sequences" version="0.0.11" >
2        <description></description>
3        <requirements><requirement type="package">fastx_toolkit</requirement></requirements>
4        <command>zcat -f $input | fastx_renamer -n $TYPE -o $output -v </command>
5
6        <inputs>
7                <param format="fastqsolexa,fasta,fastqsanger" name="input" type="data" label="FASTQ/A Library to rename" />
8
9                <param name="TYPE" type="select" label="Rename sequence identifiers to">
10                        <option value="SEQ">Nucleotides sequence</option>
11                        <option value="COUNT">Numeric Counter</option>
12                </param>
13        </inputs>
14
15        <outputs>
16                <data format="input" name="output" metadata_source="input" />
17        </outputs>
18
19<help>
20
21**What it does**
22
23This tool renames the sequence identifiers in a FASTQ/A file.
24
25.. class:: infomark
26
27Use this tool at the beginning of your workflow, as a way to keep the original sequence (before trimming, clipping, barcode-removal, etc).
28
29--------
30
31**Example**
32
33The following Solexa-FASTQ file::
34
35    @CSHL_4_FC042GAMMII_2_1_517_596
36    GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
37    +CSHL_4_FC042GAMMII_2_1_517_596
38    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
39 
40Renamed to **nucleotides sequence**::
41
42    @GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
43    GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
44    +GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
45    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
46
47Renamed to **numeric counter**::
48
49    @1
50    GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
51    +1
52    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
53
54------
55
56This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
57
58 .. __: http://hannonlab.cshl.edu/fastx_toolkit/   
59</help>
60</tool>
61<!-- FASTQ-to-FASTA is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
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