root/galaxy-central/tools/fastx_toolkit/fastx_trimmer.xml

リビジョン 2, 2.0 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
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</command>
5
6        <inputs>
7                <param format="fasta,fastqsanger" name="input" type="data" label="Library to clip" />
8
9                <param name="first" size="4" type="integer" value="1">
10                        <label>First base to keep</label>
11                </param>
12
13                <param name="last" size="4" type="integer" value="21">
14                        <label>Last base to keep</label>
15                </param>
16        </inputs>
17
18        <tests>
19                <test>
20                        <!-- Trim a FASTA file - remove first four bases (e.g. a barcode) -->
21                        <param name="input" value="fastx_trimmer1.fasta" />
22                        <param name="first" value="5"/>
23                        <param name="last" value="36"/>
24                        <output name="output" file="fastx_trimmer1.out" />
25                </test>
26                <test>
27                        <!-- Trim a FASTQ file - remove last 9 bases (e.g. keep only miRNA length sequences) -->
28                        <param name="input" value="fastx_trimmer2.fastq" />
29                        <param name="first" value="1"/>
30                        <param name="last" value="27"/>
31                        <output name="output" file="fastx_trimmer2.out" />
32                </test>
33        </tests>
34
35        <outputs>
36                <data format="input" name="output" metadata_source="input" />
37        </outputs>
38        <help>
39**What it does**
40
41This tool trims (cut bases from) sequences in a FASTA/Q file.
42 
43--------
44
45**Example**
46
47Input Fasta file (with 36 bases in each sequences)::
48
49    >1-1
50    TATGGTCAGAAACCATATGCAGAGCCTGTAGGCACC
51    >2-1
52    CAGCGAGGCTTTAATGCCATTTGGCTGTAGGCACCA
53   
54
55Trimming with First=1 and Last=21, we get a FASTA file with 21 bases in each sequences (starting from the first base)::
56
57    >1-1
58    TATGGTCAGAAACCATATGCA
59    >2-1
60    CAGCGAGGCTTTAATGCCATT
61
62Trimming with First=6 and Last=10, will generate a FASTA file with 5 bases (bases 6,7,8,9,10) in each sequences::
63
64    >1-1
65    TCAGA
66    >2-1
67    AGGCT
68   
69    ------
70
71This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
72
73 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
74   
75</help>
76</tool>
77<!-- FASTX-Trimmer is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->
Note: リポジトリブラウザについてのヘルプは TracBrowser を参照してください。