annotate galaxy-conf/FindOutlierRegions.xml @ 12:81d5b81fb3c2 draft

Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
author timpalpant
date Wed, 25 Apr 2012 16:53:48 -0400
parents
children eb53be9a09f4
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
12
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
1 <tool id="WigFindOutliers" name="Find outlier regions" version="1.0.0">
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
2 <description>such as CNVs</description>
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
3 <command interpreter="sh">galaxyToolRunner.sh ngs.FindOutlierRegions -i $input -w $window -t $threshold -o $output</command>
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
4 <inputs>
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
5 <param format="bigwig,wig" name="input" type="data" label="Input data" />
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
6 <param name="window" type="integer" value="150" label="Window size" />
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
7 <param name="threshold" type="float" value="3" label="Threshold (fold times the mean)" />
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
8 </inputs>
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
9 <outputs>
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
10 <data format="bed" name="output" metadata_source="input" />
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
11 </outputs>
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
12
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
13 <help>
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
14
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
15 This tool identifies regions of the genome that may be repetitive elements or CNVs by scanning for windows that have an exceptionally high mean relative to the genome-wide mean.
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
16
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
17 -----
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
18
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
19 .. class:: infomark
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
20
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
21 **TIP:** If your dataset does not appear in the pulldown menu, it means that it is not in Wig or BigWig format. Use "edit attributes" to set the correct format if it was not detected correctly.
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
22
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
23 -----
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
24
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
25 **Syntax**
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
26
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
27 - **Input data** is Wig or BigWig formatted data from a high-throughput sequencing experiment.
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
28 - **Window size** is the size of the moving average to use.
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
29 - **Threshold** is the fold times the genome-wide mean that a window's mean must be in order to be considered an outlier region.
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
30
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
31 </help>
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
32 </tool>