java_genomics_toolkit: galaxy-conf/IntervalStats.xml annotate

annotate galaxy-conf/IntervalStats.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	81d5b81fb3c2
children

rev	line source
12 81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools. timpalpant parents: 4 diff changeset	1 <tool id="IntervalStats" name="Compute mean/min/max of intervals" version="1.0.0">
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools. timpalpant parents: 4 diff changeset	2 <description>of data in a Wiggle file</description>
4 4b32ed5d4a1b Uploaded timpalpant parents: diff changeset	3 <command interpreter="sh">
12 81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools. timpalpant parents: 4 diff changeset	4 galaxyToolRunner.sh ngs.IntervalStats -l $windows -s $stat -o $output
4 4b32ed5d4a1b Uploaded timpalpant parents: diff changeset	5 #for $input in $inputs
4b32ed5d4a1b Uploaded timpalpant parents: diff changeset	6 ${input.file}
4b32ed5d4a1b Uploaded timpalpant parents: diff changeset	7 #end for
4b32ed5d4a1b Uploaded timpalpant parents: diff changeset	8 </command>
4b32ed5d4a1b Uploaded timpalpant parents: diff changeset	9 <inputs>
4b32ed5d4a1b Uploaded timpalpant parents: diff changeset	10 <repeat name="inputs" title="BigWig file">
4b32ed5d4a1b Uploaded timpalpant parents: diff changeset	11 <param name="file" type="data" format="bigwig,wig" />
4b32ed5d4a1b Uploaded timpalpant parents: diff changeset	12 </repeat>
4b32ed5d4a1b Uploaded timpalpant parents: diff changeset	13 <param format="bed,bedgraph,gff" name="windows" type="data" label="List of intervals" />
12 81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools. timpalpant parents: 4 diff changeset	14 <param name="stat" type="select" optional="true" label="For each interval, compute the">
4 4b32ed5d4a1b Uploaded timpalpant parents: diff changeset	15 <option value="mean">Mean</option>
12 81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools. timpalpant parents: 4 diff changeset	16 <!-- TODO <option value="median">Median</option> -->
4 4b32ed5d4a1b Uploaded timpalpant parents: diff changeset	17 <option value="max">Max</option>
4b32ed5d4a1b Uploaded timpalpant parents: diff changeset	18 <option value="min">Min</option>
12 81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools. timpalpant parents: 4 diff changeset	19 </param>
4 4b32ed5d4a1b Uploaded timpalpant parents: diff changeset	20 </inputs>
4b32ed5d4a1b Uploaded timpalpant parents: diff changeset	21 <outputs>
4b32ed5d4a1b Uploaded timpalpant parents: diff changeset	22 <data format="tabular" name="output" />
4b32ed5d4a1b Uploaded timpalpant parents: diff changeset	23 </outputs>
4b32ed5d4a1b Uploaded timpalpant parents: diff changeset	24
4b32ed5d4a1b Uploaded timpalpant parents: diff changeset	25 <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	26
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools. timpalpant parents: 4 diff changeset	27 This tool calculates the arithmetic mean, maximum, or minimum value for the Wig data in each interval. For each Wig file provided, an additional column is added to the output file in the order that they are added above.
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools. timpalpant parents: 4 diff changeset	28
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools. timpalpant parents: 4 diff changeset	29 .. 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	30
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools. timpalpant parents: 4 diff changeset	31 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	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 -----
4 4b32ed5d4a1b Uploaded timpalpant parents: diff changeset	34
12 81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools. timpalpant parents: 4 diff changeset	35 Example
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools. timpalpant parents: 4 diff changeset	36
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools. timpalpant parents: 4 diff changeset	37 Calculate the mean change in nucleosome occupancy for each gene in the yeast genome:
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools. timpalpant parents: 4 diff changeset	38
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools. timpalpant parents: 4 diff changeset	39 - 1. Create a "change in occupancy" dataset by subtracting the normalized occupancy Wig files from your two conditions using the WigMath -> Subtract tool.
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools. timpalpant parents: 4 diff changeset	40 - 2. Upload a list of intervals corresponding to the genes in the yeast genome, or pull the data from UCSC using Get Data -> UCSC Main.
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools. timpalpant parents: 4 diff changeset	41 - 3. Calculate the mean change in occupancy for each gene using this tool and the datasets from (1) and (2).
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools. timpalpant parents: 4 diff changeset	42
4 4b32ed5d4a1b Uploaded timpalpant parents: diff changeset	43 </help>
4b32ed5d4a1b Uploaded timpalpant parents: diff changeset	44 </tool>

Mercurial > repos > timpalpant > java_genomics_toolkit

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