| Next changeset 1:ccd3fd69df1a (2012-03-31) |
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Commit message:
Uploaded |
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added:
bed_to_bigwig.xml |
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| diff -r 000000000000 -r abb55c0cfe38 bed_to_bigwig.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bed_to_bigwig.xml Sat Mar 31 14:03:46 2012 -0400 |
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| @@ -0,0 +1,37 @@ +<tool id="bed_to_bigwig" name="bed_to_bigwig"> + <description>make bigwig from BED or BAM</description> + <command interpreter="sh"> bed_to_bigwig.sh $input $outfile + #if $inputa_format.bedorbam == "bed": + bed + #else: + bam + #end if + $sorted $genome none $split >$log 2> $log </command> + <inputs> + <conditional name="inputa_format"> + <param name="bedorbam" type="select" label="Select input format" > + <option value="bed" selected="true">BED</option> + <option value="bam"> BAM</option> + </param> + <when value="bed"> + <param name="input" type="data" format="bed" label="Input file"/> + </when> + <when value="bam"> + <param name="input" type="data" format="bam" label="Input file"/> + </when> + </conditional> + <param name="genome" type="select" label="Select genome"> + <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/mouse.mm9.genome" selected="true">mm9</option> + <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/mouse.mm8.genome">mm8</option> + <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/human.hg18.genome">hg18</option> + <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/human.hg19.genome">hg19</option> + </param> + <param name="sorted" label="Check if the input is sorted" type="boolean" truevalue="sorted" falsevalue="none" checked="False"/> + <param name="split" label="Split junctions" help="Treat 'split' BAM or BED12 entries as distinct BED intervals." type="boolean" truevalue="-split" falsevalue="" checked="False"/> + </inputs> + <outputs> + <data format="txt" name="log" label="makebigwig LOG" /> + <data format="bigwig" name="outfile" /> + + </outputs> +</tool> |