Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/RollingReadLength.xml @ 17:ace7855c1017 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Add back tool_data_table_conf.xml.sample since apparently it's still needed.
author timpalpant
date Sat, 09 Jun 2012 16:10:42 -0400
parents 3e477c7e0e73
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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
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
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
3 <command interpreter="sh">galaxyToolRunner.sh ngs.RollingReadLength -i $input -a ${chromInfo} -o $output</command>
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
4 <inputs>
7
4fc118372ae7 Uploaded new version with fixes and broader support for interval files
timpalpant
parents: 4
diff changeset
5 <param format="sam,bam,bed,bedgraph" name="input" type="data" label="Mapped reads" />
4
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
6 </inputs>
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
7 <outputs>
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
8 <data format="wig" name="output" />
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
9 </outputs>
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
10
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
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
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
15 .. class:: warningmark
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
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
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
19 </help>
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
20 </tool>