|
0
|
1 <tool id="cshl_fastx_trimmer" name="Trim sequences">
|
|
|
2 <description></description>
|
|
|
3 <requirements><requirement type="package">fastx_toolkit</requirement></requirements>
|
|
|
4 <command>zcat -f '$input' | fastx_trimmer -v -f $first -l $last -o $output
|
|
|
5 #if $input.ext == "fastqsanger":
|
|
|
6 -Q 33
|
|
|
7 #end if
|
|
|
8 </command>
|
|
|
9
|
|
|
10 <inputs>
|
|
|
11 <param format="fasta,fastqsolexa,fastqsanger" name="input" type="data" label="Library to clip" />
|
|
|
12
|
|
|
13 <param name="first" size="4" type="integer" value="1">
|
|
|
14 <label>First base to keep</label>
|
|
|
15 </param>
|
|
|
16
|
|
|
17 <param name="last" size="4" type="integer" value="21">
|
|
|
18 <label>Last base to keep</label>
|
|
|
19 </param>
|
|
|
20 </inputs>
|
|
|
21
|
|
|
22 <tests>
|
|
|
23 <test>
|
|
|
24 <!-- Trim a FASTA file - remove first four bases (e.g. a barcode) -->
|
|
|
25 <param name="input" value="fastx_trimmer1.fasta" />
|
|
|
26 <param name="first" value="5"/>
|
|
|
27 <param name="last" value="36"/>
|
|
|
28 <output name="output" file="fastx_trimmer1.out" />
|
|
|
29 </test>
|
|
|
30 <test>
|
|
|
31 <!-- Trim a FASTQ file - remove last 9 bases (e.g. keep only miRNA length sequences) -->
|
|
|
32 <param name="input" value="fastx_trimmer2.fastq" ftype="fastqsolexa"/>
|
|
|
33 <param name="first" value="1"/>
|
|
|
34 <param name="last" value="27"/>
|
|
|
35 <output name="output" file="fastx_trimmer2.out" />
|
|
|
36 </test>
|
|
|
37 </tests>
|
|
|
38
|
|
|
39 <outputs>
|
|
|
40 <data format="input" name="output" metadata_source="input" />
|
|
|
41 </outputs>
|
|
|
42 <help>
|
|
|
43 **What it does**
|
|
|
44
|
|
|
45 This tool trims (cut bases from) sequences in a FASTA/Q file.
|
|
|
46
|
|
|
47 --------
|
|
|
48
|
|
|
49 **Example**
|
|
|
50
|
|
|
51 Input Fasta file (with 36 bases in each sequences)::
|
|
|
52
|
|
|
53 >1-1
|
|
|
54 TATGGTCAGAAACCATATGCAGAGCCTGTAGGCACC
|
|
|
55 >2-1
|
|
|
56 CAGCGAGGCTTTAATGCCATTTGGCTGTAGGCACCA
|
|
|
57
|
|
|
58
|
|
|
59 Trimming with First=1 and Last=21, we get a FASTA file with 21 bases in each sequences (starting from the first base)::
|
|
|
60
|
|
|
61 >1-1
|
|
|
62 TATGGTCAGAAACCATATGCA
|
|
|
63 >2-1
|
|
|
64 CAGCGAGGCTTTAATGCCATT
|
|
|
65
|
|
|
66 Trimming with First=6 and Last=10, will generate a FASTA file with 5 bases (bases 6,7,8,9,10) in each sequences::
|
|
|
67
|
|
|
68 >1-1
|
|
|
69 TCAGA
|
|
|
70 >2-1
|
|
|
71 AGGCT
|
|
|
72
|
|
|
73 ------
|
|
|
74
|
|
|
75 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
|
|
|
76
|
|
|
77 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
|
|
|
78
|
|
|
79 </help>
|
|
|
80 </tool>
|
|
|
81 <!-- FASTX-Trimmer is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
|
