Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/FindOutlierRegions.xml @ 17:ace7855c1017 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Add back tool_data_table_conf.xml.sample since apparently it's still needed.
author timpalpant
date Sat, 09 Jun 2012 16:10:42 -0400
parents 3e477c7e0e73
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
15
3e477c7e0e73 Update normalization tools to allow normalizing by chromosome (Z-scorer, scale, etc.) Add new tool to convert any interval file to Bed format. Miscellaneous bug fixes.
timpalpant
parents: 13
diff changeset
1 <tool id="WigFindOutliers" name="Find outlier regions" version="1.1.0">
12
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>
13
eb53be9a09f4 Uploaded
timpalpant
parents: 12
diff changeset
3 <command interpreter="sh">galaxyToolRunner.sh ngs.FindOutlierRegions -i $input -w $window -t $threshold $below -o $output</command>
12
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)" />
13
eb53be9a09f4 Uploaded
timpalpant
parents: 12
diff changeset
8 <param name="below" type="boolean" checked="false" truevalue="-b" falsevalue="" label="Search for outliers below the threshold" />
12
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
9 </inputs>
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
10 <outputs>
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
11 <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
12 </outputs>
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
13
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
14 <help>
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
15
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
16 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
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
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
20 .. class:: infomark
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
21
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
22 **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
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
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
26 **Syntax**
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
27
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
28 - **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
29 - **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
30 - **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
31
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
32 </help>
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
33 </tool>