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comparison fastx_trimmer.xml @ 0:9cb372481a71

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author devteam
date Wed, 25 Sep 2013 11:21:27 -0400
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1 <tool id="cshl_fastx_trimmer" version="1.0.0" name="Trim sequences">
2 <description></description>
3 <requirements>
4 <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
5 </requirements>
6 <command>zcat -f '$input' | fastx_trimmer -v -f $first -l $last -o $output
7 #if $input.ext == "fastqsanger":
8 -Q 33
9 #end if
10 </command>
11
12 <inputs>
13 <param format="fasta,fastqsolexa,fastqsanger" version="1.0.0" name="input" type="data" label="Library to clip" />
14
15 <param version="1.0.0" name="first" size="4" type="integer" value="1">
16 <label>First base to keep</label>
17 </param>
18
19 <param version="1.0.0" name="last" size="4" type="integer" value="21">
20 <label>Last base to keep</label>
21 </param>
22 </inputs>
23
24 <tests>
25 <test>
26 <!-- Trim a FASTA file - remove first four bases (e.g. a barcode) -->
27 <param version="1.0.0" name="input" value="fastx_trimmer1.fasta" />
28 <param version="1.0.0" name="first" value="5"/>
29 <param version="1.0.0" name="last" value="36"/>
30 <output version="1.0.0" name="output" file="fastx_trimmer1.out" />
31 </test>
32 <test>
33 <!-- Trim a FASTQ file - remove last 9 bases (e.g. keep only miRNA length sequences) -->
34 <param version="1.0.0" name="input" value="fastx_trimmer2.fastq" ftype="fastqsolexa"/>
35 <param version="1.0.0" name="first" value="1"/>
36 <param version="1.0.0" name="last" value="27"/>
37 <output version="1.0.0" name="output" file="fastx_trimmer2.out" />
38 </test>
39 </tests>
40
41 <outputs>
42 <data format="input" version="1.0.0" name="output" metadata_source="input" />
43 </outputs>
44 <help>
45 **What it does**
46
47 This tool trims (cut bases from) sequences in a FASTA/Q file.
48
49 --------
50
51 **Example**
52
53 Input Fasta file (with 36 bases in each sequences)::
54
55 >1-1
56 TATGGTCAGAAACCATATGCAGAGCCTGTAGGCACC
57 >2-1
58 CAGCGAGGCTTTAATGCCATTTGGCTGTAGGCACCA
59
60
61 Trimming with First=1 and Last=21, we get a FASTA file with 21 bases in each sequences (starting from the first base)::
62
63 >1-1
64 TATGGTCAGAAACCATATGCA
65 >2-1
66 CAGCGAGGCTTTAATGCCATT
67
68 Trimming with First=6 and Last=10, will generate a FASTA file with 5 bases (bases 6,7,8,9,10) in each sequences::
69
70 >1-1
71 TCAGA
72 >2-1
73 AGGCT
74
75 ------
76
77 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
78
79 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
80
81 </help>
82 <!-- FASTX-Trimmer is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
83 </tool>