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/tools/stats/gsummary.xml.groups

https://bitbucket.org/cistrome/cistrome-harvard/
Unknown | 62 lines | 40 code | 22 blank | 0 comment | 0 complexity | bed0fa5d00fe8333b02538e7cc254c00 MD5 | raw file
 1<tool id="Summary Statistics1" name="Summary Statistics">
 2  <description>of a column in a tab delimited file according to an expression</description>
 3  <command interpreter="python">gsummary.py $input $out_file1 "$cond" "$groups"</command>
 4  <inputs>
 5    <param name="cond" size="40" type="text" value="c5" label="expression"/>
 6    <param name="groups" size="40" type="text" value="none" label="group terms (c1,c4,etc.)"/>
 7    <param format="txt" name="input" type="data" label="summary statistics on"/>
 8
 9  </inputs>
10  <outputs>
11    <data format="txt" name="out_file1" />
12  </outputs>
13  <help>
14
15.. class:: warningmark
16
17This tool expects input datasets to consist of tab-delimited columns (blank or comment lines beginning with a # character are automatically skipped).
18
19.. class:: infomark
20
21**TIP:** If your data is not TAB delimited, use *Text Manipulation-&gt;Convert*
22
23.. class:: infomark
24
25**TIP:** Computing summary statistics may throw exceptions if the data value in every line of the columns being summarized is not numerical.  If a line is missing a value or contains a non-numerical value in the column being summarized, that line is skipped and the value is not included in the statistical computation.  The number of invalid skipped lines is documented in the resulting history item.
26
27**Syntax**
28
29This tool computes basic summary statistics on a given column, or on an expression containing those columns
30
31- Columns are referenced with **c** and a **number**. For example, **c1** refers to the first column of a tab-delimited file
32- To group the summary by the values in a column or columns, specify in the **group terms** box...
33    + **c1**  *group by the values in column 1*
34    + **c1,c4** *group by the values in column 1, then by the values in column 4*
35
36
37-----
38
39**Expression examples**
40
41- **log(c5)** calculates the summary statistics for the natural log of column 5
42- **(c5 + c6 + c7) / 3** calculates the summary statistics on the average of columns 5-7
43- **log(c5,10)** summary statistics of the base 10 log of column 5
44- **sqrt(c5+c9)** summary statistics of the square root of column 5 + column 9
45
46**Group examples**
47
48- **c1**  group by the values in column 1
49- **c1,c4** group by the values in column 1, then by the values in column 4
50
51-----
52
53.. class:: infomark
54
55**TIP:** Most functions (like *abs*) take only a single expression. *log* can take one or two parameters, like *log(expression,base)* 
56
57Currently, these R functions are supported: *abs, sign, sqrt, floor, ceiling, trunc, round, signif, exp, log, cos, sin, tan, acos, asin, atan, cosh, sinh, tanh, acosh, asinh, atanh, lgamma, gamma, gammaCody, digamma, trigamma, cumsum, cumprod, cummax, cummin*
58
59.. |INFO| image:: ./static/images/icon_info_sml.gif
60
61</help>
62</tool>