Mercurial > repos > timpalpant > java_genomics_toolkit
annotate galaxy-conf/IntervalLengthDistribution.xml @ 12:81d5b81fb3c2 draft
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
author | timpalpant |
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date | Wed, 25 Apr 2012 16:53:48 -0400 |
parents | 4b32ed5d4a1b |
children | eb53be9a09f4 |
rev | line source |
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4 | 1 <tool id="IntervalLengthDistribution" name="Make histogram" version="1.0.0"> |
2 <description>of read lengths</description> | |
3 <command interpreter="sh">galaxyToolRunner.sh ngs.IntervalLengthDistribution -i $input -o $output</command> | |
4 <inputs> | |
5 <param name="input" type="data" format="sam,bam,bed,bedgraph,gff" label="Reads/Intervals" /> | |
6 </inputs> | |
7 <outputs> | |
8 <data format="tabular" name="output" /> | |
9 </outputs> | |
10 | |
11 <help> | |
12
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
4
diff
changeset
|
12 |
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
4
diff
changeset
|
13 This tool calculates the distribution of interval lengths from a list of intervals or reads in SAM, BAM, Bed, BedGraph, or GFF format. |
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
4
diff
changeset
|
14 |
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
4
diff
changeset
|
15 .. class:: warningmark |
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
4
diff
changeset
|
16 |
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
4
diff
changeset
|
17 For paired-end sequencing reads, the length is the length of the fragment (5' end of read 1 to 5' end of read 2) |
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
4
diff
changeset
|
18 |
4 | 19 </help> |
20 </tool> |