annotate galaxy-conf/MapDyads.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 81d5b81fb3c2
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="MapDyads" name="Map dyads" version="1.1.0">
4
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
2 <description>from sequencing reads</description>
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
3 <command interpreter="sh">
5
604c98e58034 Uploaded
timpalpant
parents: 4
diff changeset
4 galaxyToolRunner.sh nucleosomes.MapDyads -i $input -a ${chromInfo} -o $output
4
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
5 #if $type.read == 'single'
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
6 -s $type.size
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
7 #end if
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
8 </command>
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
9 <inputs>
7
4fc118372ae7 Uploaded new version with fixes and broader support for interval files
timpalpant
parents: 5
diff changeset
10 <param name="input" type="data" format="sam,bam,bed,bedGraph" label="Sequencing reads" />
4
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
11 <conditional name="type">
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
12 <param name="read" type="select" label="Type of reads">
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
13 <option value="paired" selected="true">Paired-End</option>
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
14 <option value="single">Single-End</option>
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
15 </param>
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
16 <when value="single">
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
17 <param name="size" type="integer" value="147" label="Estimated mononucleosome length (used to offset +/- strands)" />
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
18 </when>
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
19 <when value="paired">
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
20 <!-- No values here -->
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
21 </when>
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
22 </conditional>
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
23 </inputs>
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
24 <outputs>
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
25 <data name="output" format="wig" />
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
26 </outputs>
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
27
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
28 <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
29
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 11
diff changeset
30 This tool produces a Wig file with the number of dyads at each base pair. For paired-end MNase data, dyads are approximated using the center of the fragment. For Bed/BedGraph formatted input, this means the center of the interval; for SAM/BAM formatted input, this means the middle between the 5' end of mate 1 and the 5' end of mate 2. For single-end data, the estimated mononucleosome fragment length (N) must be specified, which will be used to offset reads from the + and - strands by +/- N/2.
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 11
diff changeset
31
4
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
32 .. class:: warningmark
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
33
12
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 11
diff changeset
34 This tool requires sequencing reads in SAM, BAM, Bed, or BedGraph format.
4
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
35
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
36 .. class:: warningmark
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
37
12
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 11
diff changeset
38 Since BedGraph format does not contain strand information, all reads in BedGraph format are considered to be on the 5' strand.
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
timpalpant
parents: 11
diff changeset
39
4
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
40 </help>
4b32ed5d4a1b Uploaded
timpalpant
parents:
diff changeset
41 </tool>