Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/GreedyCaller.xml @ 25:b43c420a6135 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Incorporate fix: https://github.com/timpalpant/java-genomics-toolkit/commit/9a6c61b7c6b8d85a1cd3f595eed657a537b85dc9
author timpalpant
date Sat, 09 Feb 2019 14:02:24 -0500
parents 9d56b5b85740
children
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="CallNukes" name="Call Nucleosomes" version="1.1.0">
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
2 <description>in an MNase experiment</description>
25
b43c420a6135 Incorporate fix: https://github.com/timpalpant/java-genomics-toolkit/commit/9a6c61b7c6b8d85a1cd3f595eed657a537b85dc9
timpalpant
parents: 20
diff changeset
3 <command interpreter="bash">galaxyToolRunner.sh nucleosomes.GreedyCaller -d $dyads -s $smoothed -n $N -o $output</command>
20
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="dyads" type="data" format="bigwig,wig" label="Dyad counts" />
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
6 <param name="smoothed" type="data" format="bigwig,wig" label="Smoothed dyad counts" />
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
7 <param name="N" type="integer" value="147" optional="true" label="Assumed nucleosome size" />
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
8 </inputs>
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
9 <outputs>
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
10 <data name="output" format="tabular" />
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
11 </outputs>
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
12
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
13 <help>
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
14
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
15 Stereotypic nucleosome positions are identified from dyad density maps using an approach similar to the previously reported greedy algorithm in GeneTrack_ (Albert, et al. 2008). Nucleosome calls are identified at peak maxima (p) in the smoothed dyad density map, and then excluded in the surrounding window [p–N, p+N], where N is the assumed nucleosome size in base pairs. This process is continued until all possible sterically hindered nucleosome positions are identified.
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
16
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
17 .. _GeneTrack: http://atlas.bx.psu.edu/genetrack/docs/genetrack.html
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
18
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
19 .. class:: warningmark
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 This tool requires dyad counts and smoothed dyad counts in Wig or BigWig format. Smoothed dyad counts can be generated from dyad counts using the WigMath -> Gaussian smooth tool.
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
22
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
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
25 **Syntax**
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
26
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
27 - **Dyad counts** is the relative number of nucleosomes positioned at each base pair.
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
28 - **Smoothed dyad counts** should correspond to a smoothed version of the **Dyad counts**
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
29 - **Assumed nucleosome size** is the window size used while identifying maxima to restrict overlapping calls.
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
30
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
31 -----
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
32
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
33 **Output**
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
34
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
35 The output format has 10 columns defined as follows
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
36
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
37 - 1. **Chromosome:** the chromosome of this nucleosome call
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
38 - 2. **Start:** the lower coordinate of the call window, equal to the dyad position - N/2
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
39 - 3. **Stop:** the higher coordinate of the call window, equal to the dyad position + N/2
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
40 - 4. **Length:** the window size (N) of the nucleosome call, equal to the value specified when the tool was run
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
41 - 5. **Length standard deviation:** the standard deviation of the nucleosome call length (equal to 0 because it is not currently calculated)
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
42 - 6. **Dyad:** the location of the peak maximum (p) in the smoothed dyad density data
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
43 - 7. **Dyad standard deviation:** the standard deviation of dyad density around the dyad mean in the dyad counts data
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
44 - 8. **Conditional position:** the probability that a nucleosome is at this exact dyad location as opposed to anywhere else in the nucleosome call window [p-N/2, p+N/2]
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
45 - 9. **Dyad mean:** the mean of the dyad counts in the window [p-N/2, p+N/2]
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
46 - 10. **Occupancy:** the sum of the dyad counts in the window [p-N/2, p+N/2]
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
47
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
48 </help>
9d56b5b85740 Reuploaded to see if tools get loaded correctly this time.
timpalpant
parents:
diff changeset
49 </tool>