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comparison fastx_toolkit-0.0.6/galaxy/tools/fastx_toolkit/fastx_trimmer.xml @ 3:997f5136985f draft default tip

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author xilinxu
date Thu, 14 Aug 2014 04:52:17 -0400
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1 <tool id="cshl_fastx_trimmer" name="Trim">
2 <description>sequences</description>
3 <command>zcat -f '$input' | fastx_trimmer -v -f $first -l $last -o $output</command>
4
5 <inputs>
6 <param format="fasta,fastqsolexa" name="input" type="data" label="Library to clip" />
7
8 <param name="first" size="4" type="integer" value="1">
9 <label>First base to keep</label>
10 </param>
11
12 <param name="last" size="4" type="integer" value="21">
13 <label>Last base to keep</label>
14 </param>
15 </inputs>
16
17 <tests>
18 <test>
19 <!-- Trim a FASTA file - remove first four bases (e.g. a barcode) -->
20 <param name="input" value="fastx_trimmer1.fasta" />
21 <param name="first" value="5"/>
22 <param name="last" value="36"/>
23 <output name="output" file="fastx_trimmer1.out" />
24 </test>
25 <test>
26 <!-- Trim a FASTQ file - remove last 9 bases (e.g. keep only miRNA length sequences) -->
27 <param name="input" value="fastx_trimmer2.fastq" />
28 <param name="first" value="1"/>
29 <param name="last" value="27"/>
30 <output name="output" file="fastx_trimmer2.out" />
31 </test>
32 </tests>
33
34 <outputs>
35 <data format="input" name="output" metadata_source="input" />
36 </outputs>
37 <help>
38 **What it does**
39
40 This tool trims (cut bases from) sequences in a FASTA/Q file.
41
42 --------
43
44 **Example**
45
46 Input Fasta file (with 36 bases in each sequences)::
47
48 >1-1
49 TATGGTCAGAAACCATATGCAGAGCCTGTAGGCACC
50 >2-1
51 CAGCGAGGCTTTAATGCCATTTGGCTGTAGGCACCA
52
53
54 Trimming with First=1 and Last=21, we get a FASTA file with 21 bases in each sequences (starting from the first base)::
55
56 >1-1
57 TATGGTCAGAAACCATATGCA
58 >2-1
59 CAGCGAGGCTTTAATGCCATT
60
61 Trimming with First=6 and Last=10, will generate a FASTA file with 5 bases (bases 6,7,8,9,10) in each sequences::
62
63 >1-1
64 TCAGA
65 >2-1
66 AGGCT
67
68 </help>
69 </tool>
70 <!-- FASTX-Trimmer is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->