java_genomics_toolkit: galaxy-conf/BaseAlignCounts.xml annotate

annotate galaxy-conf/BaseAlignCounts.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
date	Sat, 09 Jun 2012 16:03:59 -0400
parents	eb53be9a09f4
children

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: 13 diff changeset	1 <tool id="BaseAlignCounts" name="Calculate coverage" version="2.0.0">
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>

Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/BaseAlignCounts.xml @ 15:3e477c7e0e73 draft