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

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 eb53be9a09f4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
1 <tool id="Phasogram" name="Make phasogram" version="1.0.0">
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
2 <description>of dyads</description>
5
604c98e58034 Uploaded
timpalpant
parents: 4
diff changeset
3 <command interpreter="sh">galaxyToolRunner.sh nucleosomes.Phasogram -i $input -m $max -o $output</command>
4
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
4 <inputs>
7
4fc118372ae7 Uploaded new version with fixes and broader support for interval files
timpalpant
parents: 5
diff changeset
5 <param name="input" type="data" format="bigwig,wig" label="Dyads (Big)Wig file" />
4
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
6 <param name="max" type="integer" value="1000" label="Maximum phase shift (bp)" />
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
7 </inputs>
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
8 <outputs>
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
9 <data name="output" format="tabular" />
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
10 </outputs>
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
11
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
12 <help>
12
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 7
diff changeset
13
13
eb53be9a09f4 Uploaded
timpalpant
parents: 12
diff changeset
14 This tool calculates the phase distribution of sequencing data. It can be used to identify genome-wide periodicities. Phase counts are aggregated for each base pair across the genome. This is equivalent to summing the autocovariance of a sliding window across the genome. The tool is a reimplementation of the algorithm described in (Valouev et al. 2011).
12
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 7
diff changeset
15
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 7
diff changeset
16 .. class:: infomark
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 7
diff changeset
17
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 7
diff changeset
18 **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: 7
diff changeset
19
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 7
diff changeset
20 -----
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 7
diff changeset
21
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 7
diff changeset
22 **Citation**
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 7
diff changeset
23
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 7
diff changeset
24 Valouev A, Johnson SM, Boyd SD, Smith CL, Fire AZ and Sidow A (2011) Determinants of nucleosome organization in primary human cells. Nature 474: 516–520
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 7
diff changeset
25
4
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
26 </help>
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
27 </tool>