diff histogram2.xml @ 0:9c0d844f4e48 draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/histogram2.xml	Mon Jul 28 11:30:12 2014 -0400
@@ -0,0 +1,77 @@
+<tool id="histogram_rpy" name="Histogram" version="1.0.3">
+  <description>of a numeric column</description>
+  <requirements>
+    <requirement type="package" version="1.0.3">rpy</requirement>
+    <requirement type="package" version="2.11.0">R</requirement>
+  </requirements>
+  <command interpreter="python">histogram.py $input $out_file1 $numerical_column "$title" "$xlab" $breaks $density $frequency</command>
+  <inputs>
+    <param name="input" type="data" format="tabular" label="Dataset" help="Dataset missing? See TIP below"/>
+    <param name="numerical_column" type="data_column" data_ref="input" numerical="True" label="Numerical column for x axis" />
+    <param name="breaks" type="integer" size="4" value="0" label="Number of breaks (bars)"/>
+    <param name="title" type="text" size="30" value="Histogram" label="Plot title"/>
+    <param name="xlab" type="text" size="30" value="V1" label="Label for x axis"/>
+    <param name="density" type="boolean" checked="yes" label="Include smoothed density"/>
+    <param name="frequency" type="boolean" checked="no" label="Plot as frequency (counts)"/>
+  </inputs>
+  <outputs>
+    <data format="pdf" name="out_file1" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input" value="histogram_in1.tabular" ftype="tabular"/>
+      <param name="numerical_column" value="2"/>
+      <param name="breaks" value="0"/>
+      <param name="title" value="Histogram"/>
+      <param name="xlab" value="V1"/>
+      <param name="density" value="true"/>
+      <param name="frequency" value="false"/>
+      <output name="out_file1" file="histogram_out1.pdf"/>
+    </test>
+  </tests>
+  <help>
+
+.. class:: infomark
+
+**TIP:** To remove comment lines that do not begin with a *#* character, use *Text Manipulation-&gt;Remove beginning*
+
+ .. class:: infomark
+
+**TIP:** If your data is not TAB delimited, use *Text Manipulation-&gt;Convert*
+
+-----
+
+**Syntax**
+
+This tool computes a histogram of the numerical values in a column of a dataset.
+
+- All invalid, blank and comment lines in the dataset are skipped.  The number of skipped lines is displayed in the resulting history item.
+- **Column for x axis** - only numerical columns are possible.
+- **Number of breaks(bars)** - breakpoints between histogram cells. Value of '0' will determine breaks automatically.
+- **Plot title** - the histogram title.
+- **Label for x axis** - the label of the x axis for the histogram.
+- **Include smoothed density** - if checked, the resulting graph will join the given corresponding points with line segments.
+
+-----
+
+**Example**
+
+- Input file::
+
+    1	68	4.1
+    2	71	4.6
+    3	62	3.8
+    4	75	4.4
+    5	58	3.2
+    6	60	3.1
+    7	67	3.8
+    8	68	4.1
+    9	71	4.3
+    10	69	3.7 
+
+- Create a histogram on column 2 of the above dataset. 
+
+.. image:: histogram2.png
+
+</help>
+</tool>