changeset 5:635c4cfd83ee draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scatterplot.xml	Wed Jan 15 04:33:21 2014 -0500
@@ -0,0 +1,71 @@
+<tool id="scatterplot_rpy" name="Scatterplot">
+  <description>of two numeric columns</description>
+  <command interpreter="python">scatterplot.py $input $out_file1 $col1 $col2 "$title" "$xlab" "$ylab"</command>
+  <inputs>
+    <param name="input" type="data" format="tabular" label="Dataset" help="Dataset missing? See TIP below"/>
+    <param name="col1" type="data_column" data_ref="input" numerical="True" label="Numerical column for x axis" />
+    <param name="col2" type="data_column" data_ref="input" numerical="True" label="Numerical column for y axis" />
+    <param name="title" size="30" type="text" value="Scatterplot" label="Plot title"/>
+    <param name="xlab" size="30" type="text" value="V1" label="Label for x axis"/>
+    <param name="ylab" size="30" type="text" value="V2" label="Label for y axis"/>
+  </inputs>
+  <outputs>
+    <data format="pdf" name="out_file1" />
+  </outputs>
+  <requirements>
+    <requirement type="python-module">rpy</requirement>
+  </requirements>
+  <!-- TODO: uncomment the following test when we have tools.update_state() working for 
+       multiple dependents with the same dependency.
+  <tests>
+    <test>
+      <param name="input" value="scatterplot_in1.tabular" ftype="tabular"/>
+      <param name="col1" value="2"/>
+      <param name="col2" value="3"/>
+      <param name="title" value="Scatterplot"/>
+      <param name="xlab" value="V1"/>
+      <param name="ylab" value="V2"/>
+      <output name="out_file1" file="scatterplot_out1.pdf" />
+    </test>
+  </tests>
+  -->
+  <help>
+
+.. class:: infomark
+
+**TIP:** If your data is not TAB delimited, use *Text Manipulation-&gt;Convert*
+
+-----
+
+**Syntax**
+
+This tool creates a simple scatter plot between two variables containing numeric values of a selected dataset. 
+
+- All invalid, blank and comment lines in the dataset are skipped.  The number of skipped lines is displayed in the resulting history item.
+
+- **Plot title** The scatterplot title
+- **Label for x axis** and **Label for y axis** The labels for x and y axis of the scatterplot.
+
+-----
+
+**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 simple scatterplot between the variables in column 2 and column 3 of the above dataset.
+
+.. image:: ${static_path}/images/scatterplot.png
+
+</help>
+</tool>
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