annotate histogram2.xml @ 0:6ff47de059a0 draft

Imported from capsule None
author devteam
date Mon, 28 Jul 2014 11:56:34 -0400
parents
children cdb9e89e2970
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
1 <tool id="histogram_rpy" name="Histogram" version="1.0.3">
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
2 <description>of a numeric column</description>
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
3 <requirements>
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
4 <requirement type="package" version="1.0.3">rpy</requirement>
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
5 <requirement type="package" version="2.11.0">R</requirement>
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
6 </requirements>
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
7 <command interpreter="python">histogram.py $input $out_file1 $numerical_column "$title" "$xlab" $breaks $density $frequency</command>
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
8 <inputs>
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
9 <param name="input" type="data" format="tabular" label="Dataset" help="Dataset missing? See TIP below"/>
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
10 <param name="numerical_column" type="data_column" data_ref="input" numerical="True" label="Numerical column for x axis" />
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
11 <param name="breaks" type="integer" size="4" value="0" label="Number of breaks (bars)"/>
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
12 <param name="title" type="text" size="30" value="Histogram" label="Plot title"/>
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
13 <param name="xlab" type="text" size="30" value="V1" label="Label for x axis"/>
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
14 <param name="density" type="boolean" checked="yes" label="Include smoothed density"/>
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
15 <param name="frequency" type="boolean" checked="no" label="Plot as frequency (counts)"/>
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
16 </inputs>
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
17 <outputs>
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
18 <data format="pdf" name="out_file1" />
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
19 </outputs>
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
20 <tests>
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
21 <test>
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
22 <param name="input" value="histogram_in1.tabular" ftype="tabular"/>
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
23 <param name="numerical_column" value="2"/>
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
24 <param name="breaks" value="0"/>
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
25 <param name="title" value="Histogram"/>
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
26 <param name="xlab" value="V1"/>
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
27 <param name="density" value="true"/>
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
28 <param name="frequency" value="false"/>
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
29 <output name="out_file1" file="histogram_out1.pdf"/>
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
30 </test>
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
31 </tests>
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
32 <help>
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
33
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
34 .. class:: infomark
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
35
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
36 **TIP:** To remove comment lines that do not begin with a *#* character, use *Text Manipulation-&gt;Remove beginning*
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
37
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
38 .. class:: infomark
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
39
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
40 **TIP:** If your data is not TAB delimited, use *Text Manipulation-&gt;Convert*
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
41
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
42 -----
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
43
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
44 **Syntax**
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
45
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
46 This tool computes a histogram of the numerical values in a column of a dataset.
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
47
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
48 - All invalid, blank and comment lines in the dataset are skipped. The number of skipped lines is displayed in the resulting history item.
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
49 - **Column for x axis** - only numerical columns are possible.
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
50 - **Number of breaks(bars)** - breakpoints between histogram cells. Value of '0' will determine breaks automatically.
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
51 - **Plot title** - the histogram title.
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
52 - **Label for x axis** - the label of the x axis for the histogram.
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
53 - **Include smoothed density** - if checked, the resulting graph will join the given corresponding points with line segments.
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
54
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
55 -----
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
56
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
57 **Example**
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
58
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
59 - Input file::
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
60
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
61 1 68 4.1
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
62 2 71 4.6
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
63 3 62 3.8
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
64 4 75 4.4
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
65 5 58 3.2
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
66 6 60 3.1
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
67 7 67 3.8
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
68 8 68 4.1
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
69 9 71 4.3
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
70 10 69 3.7
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
71
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
72 - Create a histogram on column 2 of the above dataset.
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
73
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
74 .. image:: histogram2.png
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
75
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
76 </help>
6ff47de059a0 Imported from capsule None
devteam
parents:
diff changeset
77 </tool>