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comparison tools/fastx_toolkit/fastx_trimmer.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_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) -->