|
0
|
1 <tool id="annotateBed" name="annotateBed">
|
|
|
2
|
|
3
|
3 <description>Annotate BED files with overlapping BED files</description>
|
|
0
|
4
|
|
2
|
5 <command>
|
|
|
6 bedtools annotate
|
|
|
7 $countflag
|
|
|
8 -i '$inputRegion'
|
|
|
9 -names
|
|
|
10 #for $s in enumerate($annotateColumn)
|
|
|
11 ${s.colname}
|
|
0
|
12 #end for
|
|
2
|
13 -files
|
|
|
14 #for $s in enumerate($annotateColumn)
|
|
|
15 ${s.colfile}
|
|
|
16 #end for
|
|
|
17 > '$output'
|
|
0
|
18 </command>
|
|
|
19
|
|
|
20 <inputs>
|
|
|
21
|
|
|
22 <param name="countflag" type="boolean" label="Use count to annotate" truevalue="-count" falsevalue="" />
|
|
|
23 <param format="bed" name="inputRegion" type="data" label="The region to be annotated" />
|
|
|
24 <repeat name="annotateColumn" title="Column">
|
|
|
25 <param name="colname" type="text" label="Column name" />
|
|
|
26 <param name="colfile" type="data" format="bed" label="BED file to annotate for the column" />
|
|
|
27 </repeat>
|
|
|
28
|
|
|
29 </inputs>
|
|
|
30 <outputs>
|
|
4
|
31 <data format="bed" name="output" metadata_source="inputRegion" label="${inputRegion.name} annotated" />
|
|
0
|
32 </outputs>
|
|
|
33
|
|
|
34 <help>
|
|
|
35
|
|
|
36 .. class:: infomark
|
|
|
37
|
|
|
38 IMPORTANT INFORMATION
|
|
|
39
|
|
|
40 ----
|
|
|
41
|
|
|
42 WRITE HELP HERE
|
|
|
43
|
|
|
44 </help>
|
|
|
45
|
|
|
46 </tool> |
