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comparison makebigwig.xml @ 11:b7f1d9f8f3bc

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author xuebing
date Sat, 10 Mar 2012 07:59:27 -0500
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10:1558594a3c2e 11:b7f1d9f8f3bc
1 <tool id="makebigwig" name="make bigwig">
2 <description>from BED or BAM</description>
3 <command interpreter="sh"> makebigwig.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>