Mercurial > repos > timpalpant > java_genomics_toolkit
annotate galaxy-conf/MapDyads.xml @ 12:81d5b81fb3c2 draft
Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
| author | timpalpant |
|---|---|
| date | Wed, 25 Apr 2012 16:53:48 -0400 |
| parents | b1952a90d4bf |
| children | 3e477c7e0e73 |
| rev | line source |
|---|---|
| 4 | 1 <tool id="MapDyads" name="Map dyads" version="1.0.0"> |
| 2 <description>from sequencing reads</description> | |
| 3 <command interpreter="sh"> | |
| 5 | 4 galaxyToolRunner.sh nucleosomes.MapDyads -i $input -a ${chromInfo} -o $output |
| 4 | 5 #if $type.read == 'single' |
| 6 -s $type.size | |
| 7 #end if | |
| 8 </command> | |
| 9 <inputs> | |
|
7
4fc118372ae7
Uploaded new version with fixes and broader support for interval files
timpalpant
parents:
5
diff
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10 <param name="input" type="data" format="sam,bam,bed,bedGraph" label="Sequencing reads" /> |
| 4 | 11 <conditional name="type"> |
| 12 <param name="read" type="select" label="Type of reads"> | |
| 13 <option value="paired" selected="true">Paired-End</option> | |
| 14 <option value="single">Single-End</option> | |
| 15 </param> | |
| 16 <when value="single"> | |
| 17 <param name="size" type="integer" value="147" label="Estimated mononucleosome length (used to offset +/- strands)" /> | |
| 18 </when> | |
| 19 <when value="paired"> | |
| 20 <!-- No values here --> | |
| 21 </when> | |
| 22 </conditional> | |
| 23 </inputs> | |
| 24 <outputs> | |
| 25 <data name="output" format="wig" /> | |
| 26 </outputs> | |
| 27 | |
| 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 | 32 .. class:: warningmark |
| 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 | 35 |
| 36 .. class:: warningmark | |
| 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 | 40 </help> |
| 41 </tool> |