| Previous changeset 1:2cc30e606803 (2012-03-31) Next changeset 3:4cab9f01eb6f (2012-03-31) |
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added:
bedclean.xml |
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| diff -r 2cc30e606803 -r 3ef31e76adf3 bedclean.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bedclean.xml Sat Mar 31 13:01:25 2012 -0400 |
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| @@ -0,0 +1,33 @@ +<tool id="bedclean" name="clean interval"> + <description>remove off-chromosome lines</description> + <command interpreter="python">bedclean.py $input $genome $output > $log </command> + <inputs> + <param name="input" type="data" format="interval" label="Original interval file"/> + <param name="genome" type="select" label="Select genome"> + <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/mouse.mm9.genome" selected="true">mm9</option> + <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/mouse.mm8.genome">mm8</option> + <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/human.hg18.genome">hg18</option> + <option value="/Users/xuebing/galaxy-dist/tool-data/genome/chrsize/human.hg19.genome">hg19</option> + </param> + </inputs> + <outputs> + <data format="input" name="output" label="${tool.name} on ${on_string} (interval)"/> + <data format="txt" name="log" label="${tool.name} on ${on_string} (log)"/> + </outputs> + <help> + +**Description** + +remove lines that are + +1. comment or track name lines + +2. on chr*_random + +3. or have negative coordinates + +4. or the end is larger than chromosome size + + + </help> +</tool> |