Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/BaseAlignCounts.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
12
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 9
diff changeset
1 <tool id="BaseAlignCounts" name="Calculate coverage" version="1.0.0">
4
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
2 <description>of sequencing reads</description>
5
604c98e58034 Uploaded
timpalpant
parents: 4
diff changeset
3 <command interpreter="sh">galaxyToolRunner.sh ngs.BaseAlignCounts -i $input -a ${chromInfo} -x $X -o $output</command>
4
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
4 <inputs>
7
4fc118372ae7 Uploaded new version with fixes and broader support for interval files
timpalpant
parents: 6
diff changeset
5 <param name="input" type="data" format="sam,bam,bed,bedgraph" label="Sequencing reads" />
13
eb53be9a09f4 Uploaded
timpalpant
parents: 12
diff changeset
6 <param name="X" type="integer" value="-1" label="In silico extension (-1 for fragment length)" />
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" />
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
10 </outputs>
13
eb53be9a09f4 Uploaded
timpalpant
parents: 12
diff changeset
11 <tests>
eb53be9a09f4 Uploaded
timpalpant
parents: 12
diff changeset
12 </tests>
4
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
13 <help>
12
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 9
diff changeset
14
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 9
diff changeset
15 This tool produces a new Wig file with the number of reads/intervals overlapping each base pair. Reads can be artificially extended to match known fragment lengths. If you wish to count the number of reads starting at each base pair, set the read extension to 1. If you wish to count the number of intervals overlapping each base pair, set the extension to -1.
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 9
diff changeset
16
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 9
diff changeset
17 -----
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 9
diff changeset
18
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 9
diff changeset
19 .. class:: warningmark
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 9
diff changeset
20
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 9
diff changeset
21 This tool requires sequencing reads in SAM, BAM, Bed, or BedGraph format. If you are artificially extending reads, ensure that the strand is set correctly in SAM, BAM, and Bed files.
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 9
diff changeset
22
13
eb53be9a09f4 Uploaded
timpalpant
parents: 12
diff changeset
23 .. class:: warningmark
eb53be9a09f4 Uploaded
timpalpant
parents: 12
diff changeset
24
eb53be9a09f4 Uploaded
timpalpant
parents: 12
diff changeset
25 Paired-end reads are considered to be the entire fragment (the distance from the 5' end of mate 1 to the 5' end of mate 2) if the extension is set to -1.
eb53be9a09f4 Uploaded
timpalpant
parents: 12
diff changeset
26
12
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 9
diff changeset
27 .. class:: infomark
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 9
diff changeset
28
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 9
diff changeset
29 If you would like to convert valued interval data (e.g. BedGraph files from microarrays) to Wig format, use the Converters -> Interval to Wig converter.
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 9
diff changeset
30
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 9
diff changeset
31 .. class:: infomark
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 9
diff changeset
32
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 9
diff changeset
33 **TIP:** If you are going to be using reads in SAM format for multiple analyses, it is often more efficient to first convert it into BAM format using NGS: SAM Tools -> SAM-to-BAM.
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 9
diff changeset
34
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 9
diff changeset
35 -----
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 9
diff changeset
36
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 9
diff changeset
37 **Syntax**
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 9
diff changeset
38
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 9
diff changeset
39 - **Sequencing reads** are mapped reads from a high-throughput sequencing experiment.
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 9
diff changeset
40 - **In silico extension:** Reads will be artificially extended from their 5' end to be this length.
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 9
diff changeset
41
4
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
42 </help>
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
43 </tool>