Mercurial > repos > timpalpant > java_genomics_toolkit
annotate galaxy-conf/RollingReadLength.xml @ 15:3e477c7e0e73 draft
Update normalization tools to allow normalizing by chromosome (Z-scorer, scale, etc.) Add new tool to convert any interval file to Bed format. Miscellaneous bug fixes.
author | timpalpant |
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date | Sat, 09 Jun 2012 16:03:59 -0400 |
parents | 81d5b81fb3c2 |
children |
rev | line source |
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15
3e477c7e0e73
Update normalization tools to allow normalizing by chromosome (Z-scorer, scale, etc.) Add new tool to convert any interval file to Bed format. Miscellaneous bug fixes.
timpalpant
parents:
12
diff
changeset
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1 <tool id="RollingReadLength" name="Compute mean fragment length" version="1.1.0"> |
12
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
diff
changeset
|
2 <description>over each locus</description> |
4 | 3 <command interpreter="sh">galaxyToolRunner.sh ngs.RollingReadLength -i $input -a ${chromInfo} -o $output</command> |
4 <inputs> | |
7
4fc118372ae7
Uploaded new version with fixes and broader support for interval files
timpalpant
parents:
4
diff
changeset
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5 <param format="sam,bam,bed,bedgraph" name="input" type="data" label="Mapped reads" /> |
4 | 6 </inputs> |
7 <outputs> | |
8 <data format="wig" 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:
11
diff
changeset
|
12 |
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
diff
changeset
|
13 This tool will compute the mean length of all fragments overlapping a given locus, and can be used to identify sites with exceptionally long or short reads. |
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
diff
changeset
|
14 |
4 | 15 .. class:: warningmark |
16 | |
12
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
diff
changeset
|
17 This tool requires paired-end SAM, BAM, Bed, or BedGraph formatted data. Using single-end data will result in a constant read length. |
81d5b81fb3c2
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents:
11
diff
changeset
|
18 |
4 | 19 </help> |
20 </tool> |