Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/Phasogram.xml @ 21:51b28ce6ef7e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Improve file type autodetection
author timpalpant
date Mon, 18 Jun 2012 14:50:31 -0400
parents 9d56b5b85740
children b43c420a6135
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
20
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
1 <tool id="Phasogram" name="Make phasogram" version="1.0.0">
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
2 <description>of dyads</description>
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
3 <command interpreter="sh">galaxyToolRunner.sh nucleosomes.Phasogram -i $input -m $max -o $output</command>
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
4 <inputs>
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
5 <param name="input" type="data" format="bigwig,wig" label="Dyads (Big)Wig file" />
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
6 <param name="max" type="integer" value="1000" label="Maximum phase shift (bp)" />
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
7 </inputs>
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
8 <outputs>
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
9 <data name="output" format="tabular" />
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
10 </outputs>
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
11
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
12 <help>
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
13
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
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).
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
15
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
16 .. class:: infomark
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
17
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
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.
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
19
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
20 -----
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
21
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
22 **Citation**
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
23
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
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
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
25
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
26 </help>
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
27 </tool>