Mercurial > repos > hackdna > pathprint

annotate heatmap.xml @ 0:0cebe436a553 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Initial upload.
author hackdna
date Fri, 17 May 2013 14:29:33 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
1 <tool id="pathprint-heatmap" name="Generate a Heatmap">
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
2
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
3 <!--
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
4 <description>Generate a Heatmap</description>
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
5 -->
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
6
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
7 <command>heatmap.r $input $sdev $output</command>
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
8
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
9 <inputs>
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
10 <param name="input" type="data" label="Pathway Fingerprint" help="Submit a Pathway Fingerprint file from your history. Note that your file must contain multiple samples"/>
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
11 <param name="sdev" type="select" label="Standard deviation" help="Display only pathways with the selected standard deviation across samples">
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
12 <option value="0.9">0.9</option>
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
13 <option value="0.8">0.8</option>
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
14 <option value="0.7" selected="true">0.7 (default)</option>
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
15 <option value="0.6">0.6</option>
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
16 <option value="0.5">0.5</option>
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
17 </param>
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
18 </inputs>
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
19
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
20 <outputs>
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
21 <data format="pdf" name="output" label="Heatmap"/>
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
22 </outputs>
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
23
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
24 <stdio>
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
25 <exit_code range="1:" level="fatal" />
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
26 </stdio>
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
27
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
28 <help>
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
29 **What it does**
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
30
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
31 This tool creates a heatmap showing pathways with highest variability across samples (i.e. above the selected standard deviation threshold).
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
32
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
33 .. class:: infomark
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
34
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
35 You must have multiple samples in your PathPrint fingerprint file to generate a heatmap.
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
36
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
37 -----
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
38
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
39 **Input**: A PathPrint fingerprint file containing multiple samples from your History and a standard deviation cutoff.
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
40
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
41 Samples that are very similar to each other may not have any pathways meeting the standard deviation threhold, which will result in an error. If this occurs, try lowering the threshold.
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
42
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
43 If too many pathways are returned, labels will not be shown. Try increasing the standard deviation cutoff.
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
44
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
45 **Output**: PDF file showing a heatmap of the most variable pathway activities
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
46
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
47 -----
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
48
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
49 Feedback is welcome. Please send your questions, comments and suggestions to scde@hsci.harvard.edu.
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
50 </help>
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
51 </tool>
0cebe436a553 Initial upload.
hackdna
parents:
diff changeset
52