java_genomics_toolkit: galaxy-conf/IntervalAverager.xml annotate

annotate galaxy-conf/IntervalAverager.xml @ 15:3e477c7e0e73 draft

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.

author	timpalpant
date	Sat, 09 Jun 2012 16:03:59 -0400
parents	eb53be9a09f4
children

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="IntervalAverager" name="Average intervals" version="2.1.0">
4 4b32ed5d4a1b Uploaded timpalpant parents: diff changeset	2 <description>that have been aligned</description>
13 eb53be9a09f4 Uploaded timpalpant parents: 12 diff changeset	3 <command interpreter="sh">
eb53be9a09f4 Uploaded timpalpant parents: 12 diff changeset	4 galaxyToolRunner.sh visualization.IntervalAverager -l $loci -o $output $file1
eb53be9a09f4 Uploaded timpalpant parents: 12 diff changeset	5 #for $input in $inputs
eb53be9a09f4 Uploaded timpalpant parents: 12 diff changeset	6 ${input.file}
eb53be9a09f4 Uploaded timpalpant parents: 12 diff changeset	7 #end for
eb53be9a09f4 Uploaded timpalpant parents: 12 diff changeset	8 </command>
4 4b32ed5d4a1b Uploaded timpalpant parents: diff changeset	9 <inputs>
13 eb53be9a09f4 Uploaded timpalpant parents: 12 diff changeset	10 <param name="file1" label="Sequencing data" type="data" format="bigwig,wig" />
eb53be9a09f4 Uploaded timpalpant parents: 12 diff changeset	11 <repeat name="inputs" title="Additional sequencing data">
eb53be9a09f4 Uploaded timpalpant parents: 12 diff changeset	12 <param name="file" type="data" format="bigwig,wig" />
eb53be9a09f4 Uploaded timpalpant parents: 12 diff changeset	13 </repeat>
4 4b32ed5d4a1b Uploaded timpalpant parents: diff changeset	14 <param format="bed" name="loci" type="data" label="List of intervals (with alignment points)" />
4b32ed5d4a1b Uploaded timpalpant parents: diff changeset	15 </inputs>
4b32ed5d4a1b Uploaded timpalpant parents: diff changeset	16 <outputs>
4b32ed5d4a1b Uploaded timpalpant parents: diff changeset	17 <data format="tabular" name="output" />
4b32ed5d4a1b Uploaded timpalpant parents: diff changeset	18 </outputs>
4b32ed5d4a1b Uploaded timpalpant parents: diff changeset	19
4b32ed5d4a1b Uploaded timpalpant parents: diff changeset	20 <help>
12 81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools. timpalpant parents: 4 diff changeset	21
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools. timpalpant parents: 4 diff changeset	22 This tool calculates the average signal for a set of aligned intervals. Intervals are lined up on their alignment point (column 5 in the Bed file), flipped if on the - strand, and averaged. The output is equivalent to aligning the data in a matrix and then taking the columnwise average of the matrix.
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools. timpalpant parents: 4 diff changeset	23
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools. timpalpant parents: 4 diff changeset	24 Intervals with alignment points must be provided in the following extended Bed format ::
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools. timpalpant parents: 4 diff changeset	25
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools. timpalpant parents: 4 diff changeset	26 chr low high id alignment strand
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools. timpalpant parents: 4 diff changeset	27
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools. timpalpant parents: 4 diff changeset	28 .. class:: infomark
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools. timpalpant parents: 4 diff changeset	29
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools. timpalpant parents: 4 diff changeset	30 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: 4 diff changeset	31
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools. timpalpant parents: 4 diff changeset	32 -----
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools. timpalpant parents: 4 diff changeset	33
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools. timpalpant parents: 4 diff changeset	34 Syntax
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools. timpalpant parents: 4 diff changeset	35
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools. timpalpant parents: 4 diff changeset	36 - Sequencing data is the genomic data used to create the average
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools. timpalpant parents: 4 diff changeset	37 - List of intervals is a list of intervals in Bed format with alignment points
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools. timpalpant parents: 4 diff changeset	38
4 4b32ed5d4a1b Uploaded timpalpant parents: diff changeset	39 </help>
4b32ed5d4a1b Uploaded timpalpant parents: diff changeset	40 </tool>

Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/IntervalAverager.xml @ 15:3e477c7e0e73 draft