Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/IntervalToWig.xml @ 13:eb53be9a09f4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author timpalpant
date Sat, 19 May 2012 10:36:45 -0400
parents 81d5b81fb3c2
children 3e477c7e0e73
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
1 <tool id="BedToWig" name="Interval to Wig" version="1.0.0">
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
2 <description>converter</description>
11
b1952a90d4bf Uploaded
timpalpant
parents: 4
diff changeset
3 <command interpreter="sh">galaxyToolRunner.sh converters.IntervalToWig -i $input $zero -a ${chromInfo} -o $output</command>
4
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
4 <inputs>
13
eb53be9a09f4 Uploaded
timpalpant
parents: 12
diff changeset
5 <param name="input" type="data" format="bed,bedgraph,gff" label="Input Bed/BedGraph/GFF file" />
11
b1952a90d4bf Uploaded
timpalpant
parents: 4
diff changeset
6 <param name="zero" type="boolean" checked="false" truevalue="-z" falsevalue="" label="Assume zero where there is no data (default is NaN)" />
4
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
7 </inputs>
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
8 <outputs>
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
9 <data name="output" format="wig" metadata_source="input" />
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
10 </outputs>
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
11
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
12 <help>
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
13
12
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 11
diff changeset
14 This tool converts data from an interval format, such as Bed, BedGraph or GFF, to Wig format. This can be used to convert data from microarrays to Wig format. The value of each interval is mapped into the Wig file. Intervals that overlap in the original file (multiple-valued base pairs) are averaged, and bases without data in the original interval file are set to NaN.
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 11
diff changeset
15
4
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
16 .. class:: warningmark
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
17
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
18 This tool requires Bed, BedGraph, or GFF formatted data. If you have tabular data that was not correctly autodetected, change the metadata by clicking on the pencil icon for the dataset.
12
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 11
diff changeset
19
4
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
20 </help>
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
21 </tool>