|
0
|
1 <tool id="cshl_fastx_renamer" name="Rename sequences" version="0.0.11" >
|
|
|
2 <description></description>
|
|
|
3 <command>
|
|
|
4 cat '$input' |
|
|
|
5 fastx_renamer
|
|
|
6 #if $input.ext == "fastqsanger":
|
|
|
7 -Q 33
|
|
|
8 #elif $input.ext == "fastq":
|
|
|
9 -Q 64
|
|
|
10 #end if
|
|
|
11 -n $TYPE -o '$output' -v
|
|
|
12 </command>
|
|
|
13 <inputs>
|
|
|
14 <param format="fastq,fastqsanger,fasta" name="input" type="data" label="FASTQ/A Library to rename" />
|
|
|
15
|
|
|
16 <param name="TYPE" type="select" label="Rename sequence identifiers to">
|
|
|
17 <option value="SEQ">Nucleotides sequence</option>
|
|
|
18 <option value="COUNT">Numeric Counter</option>
|
|
|
19 </param>
|
|
|
20 </inputs>
|
|
|
21 <tests>
|
|
|
22 <test>
|
|
|
23 <param name="input" value="fastx_renamer1.fastq" ftype="fastq"/>
|
|
|
24 <param name="TYPE" value="SEQ" />
|
|
|
25 <output name="output" file="fastx_renamer1.out" />
|
|
|
26 </test>
|
|
|
27 </tests>
|
|
|
28
|
|
|
29 <outputs>
|
|
|
30 <data format="input" name="output" metadata_source="input" />
|
|
|
31 </outputs>
|
|
|
32
|
|
|
33 <help>
|
|
|
34
|
|
|
35 **What it does**
|
|
|
36
|
|
|
37 This tool renames the sequence identifiers in a FASTQ/A file.
|
|
|
38
|
|
|
39 .. class:: infomark
|
|
|
40
|
|
|
41 Use this tool at the beginning of your workflow, as a way to keep the original sequence (before trimming, clipping, barcode-removal, etc).
|
|
|
42
|
|
|
43 --------
|
|
|
44
|
|
|
45 **Example**
|
|
|
46
|
|
|
47 The following Solexa-FASTQ file::
|
|
|
48
|
|
|
49 @CSHL_4_FC042GAMMII_2_1_517_596
|
|
|
50 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
|
|
|
51 +CSHL_4_FC042GAMMII_2_1_517_596
|
|
|
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 Renamed to **nucleotides sequence**::
|
|
|
55
|
|
|
56 @GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
|
|
|
57 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
|
|
|
58 +GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
|
|
|
59 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
|
|
|
60
|
|
|
61 Renamed to **numeric counter**::
|
|
|
62
|
|
|
63 @1
|
|
|
64 GGTCAATGATGAGTTGGCACTGTAGGCACCATCAAT
|
|
|
65 +1
|
|
|
66 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
|
|
|
67
|
|
|
68 ------
|
|
|
69
|
|
|
70 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
|
|
|
71
|
|
|
72 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
|
|
|
73 </help>
|
|
|
74 </tool>
|
|
|
75 <!-- FASTX-renamer is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
|
