Mercurial > repos > timpalpant > java_genomics_toolkit

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
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: 12
diff changeset
1 <tool id="PredictFAIRE" name="Predict FAIRE signal" 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>from nucleosome occupancy</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 nucleosomes.PredictFAIRESignal -i $input -s $sonication -c $crosslinking -x $extend -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="Nucleosome occupancy 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 format="tabular" name="sonication" type="data" label="Sonication fragment length distribution" />
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="crosslinking" type="float" value="1.0" label="Crosslinking coefficient" />
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: 12
diff changeset
8 <param name="extend" type="integer" value="250" label="In silico read extension (-1 for paired-end mode)" />
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="wig" 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 attempts to predict FAIRE signal from nucleosome occupancy by calculating the probability that a random sonicated fragment is occupied anywhere by a nucleosome.
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 **Syntax**
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 - **Nucleosome occupancy data** should be fragment coverage data from an MNase-seq experiment
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
23 - **Sonication fragment length distribution:** The relative proportion of each size of fragment produced by sonication
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
24 - **Crosslinking coefficient** is the efficiency of crosslinking (what fraction of the time is a nucleosome crosslinked)
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
25 - **In silico read extension** is the length that single-end reads should be extended to match FAIRE-seq data
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 -----
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
28
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
29 Sonication fragment distribution must be provided in the following tabular format ::
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 length proportion
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
32
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
33 So for example ::
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
34
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
35 1 0.1
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
36 2 0.2
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
37 3 0.3
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
38 4 0.2
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
39 5 0.2
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
40
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
41 </help>
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
diff changeset
42 </tool>