Mercurial > repos > timpalpant > java_genomics_toolkit
annotate galaxy-conf/NRLCalculator.xml @ 14:f58706d4d421 draft
Uploaded
author | timpalpant |
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date | Sat, 19 May 2012 10:40:16 -0400 |
parents | 81d5b81fb3c2 |
children |
rev | line source |
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4 | 1 <tool id="NRLCalculator" name="Compute the NRL" version="1.0.0"> |
2 <description>from nucleosome calls</description> | |
5 | 3 <command interpreter="sh">galaxyToolRunner.sh nucleosomes.NRLCalculator -i $input -l $windows -o $output</command> |
4 | 4 <inputs> |
5 <param format="tabular" name="input" type="data" label="Nucleosome calls" /> | |
6 <param format="bed,bedgraph,gff" name="windows" type="data" label="List of intervals/genes" /> | |
7 </inputs> | |
8 <outputs> | |
9 <data format="tabular" name="output" /> | |
10 </outputs> | |
11 | |
12 <help> | |
12
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
5
diff
changeset
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13 |
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
5
diff
changeset
|
14 This tool calculates the distance between adjacent nucleosome calls (dyads) emanating from the 5' end of an interval. For each interval, the distance is calculated from the +1 to +2 nucleosome, +2 to +3 nucleosome, etc. These distances are appended as additional columns for each interval. :: |
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
5
diff
changeset
|
15 |
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
5
diff
changeset
|
16 chr start stop id alignment strand +1-to-+2 +2-to-+3 ... |
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
5
diff
changeset
|
17 |
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
5
diff
changeset
|
18 Each interval will have a different number of columns based on the number of nucleosome calls that were in that interval. |
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
5
diff
changeset
|
19 |
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
5
diff
changeset
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20 ----- |
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
5
diff
changeset
|
21 |
4 | 22 .. class:: warningmark |
23 | |
12
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
5
diff
changeset
|
24 Because the distances are calculated from the 5' end of each gene, as you move into the gene body it becomes more likely that a nucleosome call will be skipped, resulting in an outlier distance (~320bp rather than ~165bp). In addition, nucleosome calls in fuzzy regions tend to be inaccurate, so the NRL distances will not be robust. |
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
5
diff
changeset
|
25 |
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
5
diff
changeset
|
26 .. class:: warningmark |
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
5
diff
changeset
|
27 |
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
5
diff
changeset
|
28 This tool requires a set of nucleosome calls as input in the format created by the Nucleosomes -> Call Nucleosomes tool. |
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
5
diff
changeset
|
29 |
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
5
diff
changeset
|
30 .. class:: warningmark |
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
5
diff
changeset
|
31 |
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
5
diff
changeset
|
32 Intervals must be provided in Bed, BedGraph, or GFF format. BedGraph intervals are always considered to be on the + strand. |
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
5
diff
changeset
|
33 |
4 | 34 </help> |
35 </tool> |