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comparison fastx_trimmer.xml @ 0:78a7d28f2a15 draft

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author idot
date Wed, 10 Jul 2013 06:13:48 -0400
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1 <tool id="cshl_fastx_trimmer" name="Trim sequences">
2 <description>to fixed length</description>
3 <command>
4 cat '$input' |
5 fastx_trimmer
6 #if $input.ext == "fastqsanger":
7 -Q 33
8 #elif $input.ext == "fastq":
9 -Q 64
10 #end if
11 -v -f $first -l $last -o '$output'
12 </command>
13 <inputs>
14 <param format="fasta,fastq,fastqsanger" name="input" type="data" label="Library to clip" />
15
16 <param name="first" size="4" type="integer" value="1">
17 <label>First base to keep</label>
18 </param>
19
20 <param name="last" size="4" type="integer" value="21">
21 <label>Last base to keep</label>
22 </param>
23 </inputs>
24
25 <tests>
26 <test>
27 <!-- Trim a FASTA file - remove first four bases (e.g. a barcode) -->
28 <param name="input" value="fastx_trimmer1.fasta" />
29 <param name="first" value="5"/>
30 <param name="last" value="36"/>
31 <output name="output" file="fastx_trimmer1.out" />
32 </test>
33 <test>
34 <!-- Trim a FASTQ file - remove last 9 bases (e.g. keep only miRNA length sequences) -->
35 <param name="input" value="fastx_trimmer2.fastq" />
36 <param name="first" value="1"/>
37 <param name="last" value="27"/>
38 <output name="output" file="fastx_trimmer2.out" />
39 </test>
40 </tests>
41
42 <outputs>
43 <data format="input" name="output" metadata_source="input"
44 />
45 </outputs>
46 <help>
47 **What it does**
48
49 This tool trims (cut nucleotides from) sequences in a FASTA/Q file.
50
51 --------
52
53 **Example**
54
55 Input Fasta file (with 36 bases in each sequences)::
56
57 >1-1
58 TATGGTCAGAAACCATATGCAGAGCCTGTAGGCACC
59 >2-1
60 CAGCGAGGCTTTAATGCCATTTGGCTGTAGGCACCA
61
62
63 Trimming with First=1 and Last=21, we get a FASTA file with 21 bases in each sequences (starting from the first base)::
64
65 >1-1
66 TATGGTCAGAAACCATATGCA
67 >2-1
68 CAGCGAGGCTTTAATGCCATT
69
70 Trimming with First=6 and Last=10, will generate a FASTA file with 5 bases (bases 6,7,8,9,10) in each sequences::
71
72 >1-1
73 TCAGA
74 >2-1
75 AGGCT
76
77 ------
78
79 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
80
81 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
82
83 </help>
84 </tool>
85 <!-- FASTX-Trimmer is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->