root/galaxy-central/tools/solid_tools/solid_qual_stats.xml

リビジョン 2, 2.3 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central
行番号 
1<tool id="solid_qual_stats" name="Compute quality statistics" version="1.0.0">
2    <description>for SOLiD data</description>
3    <command interpreter="python">solid_qual_stats.py $input $output1</command>
4
5    <inputs>
6        <param format="qualsolid" name="input" type="data" label="SOLiD qual file" help="If your dataset doesn't show up in the menu, click the pencil icon next to your dataset and set the datatype to 'qualsolid'" />
7    </inputs>
8    <outputs>
9        <data format="txt" name="output1" metadata_source="input" />
10    </outputs>
11    <tests>
12        <test>
13            <param name="input" value="qualscores.qualsolid" />
14            <output name="output1" file="qualsolid.stats" />
15        </test>
16    </tests>
17
18<help>
19
20**What it does**
21
22Creates quality statistics report for the given SOLiD quality score file.
23
24.. class:: infomark
25
26**TIP:** This statistics report can be used as input for **Quality Boxplot for SOLiD data** tool.
27
28-----
29
30**The output file will contain the following fields:**
31
32* column    = column number (position on the read)
33* count   = number of bases found in this column.
34* min     = Lowest quality score value found in this column.
35* max     = Highest quality score value found in this column.
36* sum     = Sum of quality score values for this column.
37* mean    = Mean quality score value for this column.
38* Q1    = 1st quartile quality score.
39* med   = Median quality score.
40* Q3    = 3rd quartile quality score.
41* IQR   = Inter-Quartile range (Q3-Q1).
42* lW    = 'Left-Whisker' value (for boxplotting).
43* rW    = 'Right-Whisker' value (for boxplotting).
44
45
46
47
48
49**Output Example**::
50
51    column  count   min max sum mean    Q1  med Q3  IQR lW  rW
52    1   6362991 2  32  250734117   20.41   5  9  28  23   2  31
53    2   6362991 2  32  250531036   21.37  10  26 30  20   5  31
54    3   6362991 2  34  248722469   19.09  10  26 30  20   5  31
55    4   6362991 2  34  247654797   18.92  10  26 30  20   5  31
56    .
57    .   
58    32  6362991 2  31  143436943   16.54   3  10  25  22  2  31
59    33  6362991 2  32  114269843   16.96   3  10  25  22  2  31
60    34  6362991 2  29  140638447   12.10   3  10  25  22  2  29
61    35  6362991 2  29  138910532   11.83   3  10  25  22  2  29
62   
63------
64
65This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
66
67 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
68</help>
69</tool>
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