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

リビジョン 2, 1.7 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="cshl_fastx_nucleotides_distribution" name="Draw nucleotides distribution chart">
2        <description></description>
3        <requirements><requirement type="package">fastx_toolkit</requirement></requirements>
4        <command>fastx_nucleotide_distribution_graph.sh -t '$input.name' -i $input -o $output</command>
5       
6        <inputs>
7                <param format="txt" name="input" type="data" label="Statistics Text File" help="output of 'FASTX Statistics' tool" />
8        </inputs>
9       
10        <outputs>
11                <data format="png" name="output" metadata_source="input" />
12        </outputs>
13<help>
14
15**What it does**
16
17Creates a stacked-histogram graph for the nucleotide distribution in the Solexa library.
18
19.. class:: infomark
20
21**TIP:** Use the **FASTQ Statistics** tool to generate the report file needed for this tool.
22
23-----
24
25**Output Examples**
26
27The following chart clearly shows the barcode used at the 5'-end of the library: **GATCT**
28
29.. image:: ./static/fastx_icons/fastq_nucleotides_distribution_1.png
30 
31In the following chart, one can almost 'read' the most abundant sequence by looking at the dominant values: **TGATA TCGTA TTGAT GACTG AA...**
32
33.. image:: ./static/fastx_icons/fastq_nucleotides_distribution_2.png
34
35The following chart shows a growing number of unknown (N) nucleotides towards later cycles (which might indicate a sequencing problem):
36
37.. image:: ./static/fastx_icons/fastq_nucleotides_distribution_3.png
38
39But most of the time, the chart will look rather random:
40
41.. image:: ./static/fastx_icons/fastq_nucleotides_distribution_4.png
42
43------
44
45This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
46
47 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
48
49</help>
50</tool>
51<!-- FASTQ-Nucleotides-Distribution 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。