Mercurial > repos > xuebing > bed_to_bigwig
comparison bed_to_bigwig.xml @ 0:abb55c0cfe38
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| author | xuebing |
|---|---|
| date | Sat, 31 Mar 2012 14:03:46 -0400 |
| parents | |
| children | c5bf1ec88e4e |
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| -1:000000000000 | 0:abb55c0cfe38 |
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| 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> |