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comparison fastx_renamer.xml @ 0:4ed1114bfe88 draft

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author devteam
date Tue, 20 Aug 2013 10:50:39 -0400
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1 <tool id="cshl_fastx_renamer" name="Rename sequences" version="0.0.11" >
2 <description></description>
3 <requirements>
4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
5 </requirements>
6 <command>zcat -f $input | fastx_renamer -n $TYPE -o $output -v
7 #if $input.ext == "fastqsanger":
8 -Q 33
9 #end if
10 </command>
11
12 <inputs>
13 <param format="fastqsolexa,fasta,fastqsanger" name="input" type="data" label="FASTQ/A Library to rename" />
14
15 <param name="TYPE" type="select" label="Rename sequence identifiers to">
16 <option value="SEQ">Nucleotides sequence</option>
17 <option value="COUNT">Numeric Counter</option>
18 </param>
19 </inputs>
20
21 <outputs>
22 <data format="input" name="output" metadata_source="input" />
23 </outputs>
24
25 <help>
26
27 **What it does**
28
29 This tool renames the sequence identifiers in a FASTQ/A file.
30
31 .. class:: infomark
32
33 Use this tool at the beginning of your workflow, as a way to keep the original sequence (before trimming, clipping, barcode-removal, etc).
34
35 --------
36
37 **Example**
38
39 The following Solexa-FASTQ file::
40
41 @CSHL_4_FC042GAMMII_2_1_517_596
42 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
43 +CSHL_4_FC042GAMMII_2_1_517_596
44 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
45
46 Renamed to **nucleotides sequence**::
47
48 @GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
49 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
50 +GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
51 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
52
53 Renamed to **numeric counter**::
54
55 @1
56 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
57 +1
58 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
59
60 ------
61
62 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
63
64 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
65 </help>
66 <!-- FASTQ-to-FASTA is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
67 </tool>