|
0
|
1 <tool id="bed_to_bigwig" name="bed_to_bigwig">
|
|
|
2 <description>make bigwig from BED or BAM</description>
|
|
|
3 <command interpreter="sh"> bed_to_bigwig.sh $input $outfile
|
|
|
4 #if $inputa_format.bedorbam == "bed":
|
|
|
5 bed
|
|
|
6 #else:
|
|
|
7 bam
|
|
|
8 #end if
|
|
|
9 $sorted $genome none $split >$log 2> $log </command>
|
|
|
10 <inputs>
|
|
|
11 <conditional name="inputa_format">
|
|
|
12 <param name="bedorbam" type="select" label="Select input format" >
|
|
|
13 <option value="bed" selected="true">BED</option>
|
|
|
14 <option value="bam"> BAM</option>
|
|
|
15 </param>
|
|
|
16 <when value="bed">
|
|
|
17 <param name="input" type="data" format="bed" label="Input file"/>
|
|
|
18 </when>
|
|
|
19 <when value="bam">
|
|
|
20 <param name="input" type="data" format="bam" label="Input file"/>
|
|
|
21 </when>
|
|
|
22 </conditional>
|
|
|
23 <param name="genome" type="select" label="Select genome">
|
|
|
24 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/mouse.mm9.genome" selected="true">mm9</option>
|
|
|
25 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/mouse.mm8.genome">mm8</option>
|
|
|
26 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/human.hg18.genome">hg18</option>
|
|
|
27 <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/human.hg19.genome">hg19</option>
|
|
|
28 </param>
|
|
|
29 <param name="sorted" label="Check if the input is sorted" type="boolean" truevalue="sorted" falsevalue="none" checked="False"/>
|
|
|
30 <param name="split" label="Split junctions" help="Treat 'split' BAM or BED12 entries as distinct BED intervals." type="boolean" truevalue="-split" falsevalue="" checked="False"/>
|
|
|
31 </inputs>
|
|
|
32 <outputs>
|
|
|
33 <data format="txt" name="log" label="makebigwig LOG" />
|
|
|
34 <data format="bigwig" name="outfile" />
|
|
|
35
|
|
|
36 </outputs>
|
|
|
37 </tool>
|
