annotate fastq_quality_boxplot.xml @ 0:78a7d28f2a15 draft

Uploaded
author idot
date Wed, 10 Jul 2013 06:13:48 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
1 <tool id="cshl_fastq_quality_boxplot" name="Draw quality score boxplot">
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
2 <description></description>
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
3
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
4 <command>fastq_quality_boxplot_graph.sh -t '$input.name' -i $input -o '$output'</command>
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
5
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
6 <inputs>
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
7 <param format="txt" name="input" type="data" label="Statistics report file" help="output of 'FASTQ Statistics' tool" />
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
8 </inputs>
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
9
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
10 <outputs>
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
11 <data format="png" name="output" metadata_source="input"
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
12 />
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
13 </outputs>
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
14 <help>
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
15
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
16 **What it does**
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
17
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
18 Creates a boxplot graph for the quality scores in the library.
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
19
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
20 .. class:: infomark
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
21
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
22 **TIP:** Use the **FASTQ Statistics** tool to generate the report file needed for this tool.
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
23
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
24 -----
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
25
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
26 **Output Examples**
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
27
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
28 * Black horizontal lines are medians
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
29 * Rectangular red boxes show the Inter-quartile Range (IQR) (top value is Q3, bottom value is Q1)
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
30 * Whiskers show outlier at max. 1.5*IQR
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
31
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
32
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
33 An excellent quality library (median quality is 40 for almost all 36 cycles):
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
34
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
35 .. image:: ../static/fastx_icons/fastq_quality_boxplot_1.png
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
36
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
37
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
38 A relatively good quality library (median quality degrades towards later cycles):
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
39
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
40 .. image:: ../static/fastx_icons/fastq_quality_boxplot_2.png
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
41
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
42 A low quality library (median drops quickly):
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
43
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
44 .. image:: ../static/fastx_icons/fastq_quality_boxplot_3.png
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
45
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
46 ------
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
47
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
48 This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
49
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
50 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
51
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
52 </help>
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
53 </tool>
78a7d28f2a15 Uploaded
idot
parents:
diff changeset
54 <!-- FASTQ-Quality-Boxplot is part of the FASTX-toolkit, by A.Gordon (gordon@cshl.edu) -->