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