Mercurial > repos > timpalpant > java_genomics_toolkit
annotate galaxy-conf/MapDyads.xml @ 10:d063d22f4e80
Uploaded
| author | timpalpant |
|---|---|
| date | Sat, 17 Mar 2012 08:11:55 -0400 |
| parents | 9266d807ca85 |
| children | b1952a90d4bf |
| 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
changeset
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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> | |
| 29 .. class:: warningmark | |
| 30 | |
| 9 | 31 This tool requires sequencing reads in SAM, BAM, Bed format. |
| 4 | 32 |
| 33 .. class:: warningmark | |
| 34 | |
| 35 For paired-end MNase data, read centers are approximated by using the center of the read. For single-end data, the estimated mononucleosome fragment length must be specified, which will be used to offset reads from the + and - strands. | |
| 36 </help> | |
| 37 </tool> |