/tools/expression/eiplot.xml

 1<?xml version="1.0"?>
 2
 3<tool name="Draw a histogram/box plot" id="expindxplotId">
 4  <description>
 5    of Expression index for a given a list of Genes
 6  </description>
 7  <code file="eiplot_code.py"/>
 8  <command interpreter="python">
 9  eiplot.py  '$title' '$expression_index_file' '$opMode.sampleName' '$opMode.geneList1' '$opMode.refChoice' '$opMode.geneList2' '$logmeta'
10  </command>
11
12  <inputs>
13    <page>        
14        <param name="title" label="Title to label the new output file" type="text" size="80" value="Expression Index Plot" />
15        <param name="expression_index_file" type="data" format="txt" label="Expression index file" 
16         optional="false" size="120" help="Choose an expression index file from your current history"/>
17    </page>
18    <page>
19        <conditional name="opMode">
20
21       <param name="opMode" type="select" label="Operation Type">
22            <option value="basic" selected="true">Basic</option>
23            <option value="advanced">Advanced</option>
24        </param>
25
26        <when value="basic">
27            <param name="sampleName" type="select" label="Samples from the Expression Index File"
28            dynamic_options="getSampleNames(expression_index_file)"
29            help="Choose a sample from the expression index file">
30            </param>
31
32            <param name="geneList1" type="data" format="txt" label="Select a second gene list to compare"
33            optional="false" size="120" help="Choose a gene list file from your current history.Genes must be separated by new line."/>
34
35            <param name="refChoice" type="hidden" value="All"/>
36            <param name="geneList2" type="hidden" value=""/>
37
38        </when>
39        <when value="advanced">
40            <param name="sampleName" type="select" label="Samples from the Expression Index File"
41            dynamic_options="getSampleNames(expression_index_file)"
42            help="Choose a sample from the expression index file">
43            </param>
44
45            <param name="geneList1" type="data" format="txt" label="Select a second gene list to compare"
46            optional="false" size="120" help="Choose a gene list file from your current history.Genes must be separated by new line."/>
47
48            <param name="refChoice" type="select" display="radio" label="Select Genes">
49            <option value="All">All Genes in the expression index file</option>
50            <option value="Partial">Choose a partial gene list file</option>
51            </param>
52
53            <param name="geneList2" type="data" format="txt" label="Partial expression index genes"
54            optional="true" size="120" help="Choose a partial genes file from your current history. Genes must be separated by new line.  "/>
55
56        </when>
57
58    </conditional>
59
60
61       
62    </page>
63  </inputs>
64
65  <outputs>     
66    <data format='txt' name="logmeta"/>
67  </outputs>
68  <help>
69
70**Syntax**
71
72- **Title:**  Label for the output file
73- **Expression index file:** Select a Normalized Expression Index (.txt)  file from your history
74- **Samples from the Expression Index File:**   Select the sample column that will serve as reference
75- **Select a Gene List to compare:**  Choose from your history a gene symbol list to compare
76- **Select Genes:** You could select all other genes from the previously selected sample as "gene universe" to compare the expression or
77- **Select a second gene list to compare:** If you want to compare 2  gene list among each other, you should select a gene list 2
78
79-----
80
81**Summary**
82
83This tool allows you to visualize (box plot and histograms) the expression index distribution of:
84
85- One gene list when compared with the "gene universe" of all other genes for a particular sample or
86- Two gene lists to compare the expression distribution of one list with the other
87
88The output of this tool is a .pdf file containing 3 figures.
89
90- Box plot of the compared Expression Index
91- Expression distribution histogram of gene list 1
92- Expression distribution histogram of gene list 2 or gene universe
93
94  </help>
95</tool>