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4
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1 <tool id="BaseAlignCounts" name="Map coverage" version="1.0.0">
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2 <description>of sequencing reads</description>
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5
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3 <command interpreter="sh">galaxyToolRunner.sh ngs.BaseAlignCounts -i $input -a ${chromInfo} -x $X -o $output</command>
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4
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4 <inputs>
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5 <param name="input" type="data" format="bam,sam,bed,bedgraph" label="Sequencing reads" />
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6 <param name="X" type="integer" value="0" label="In silico extension (leave 0 for read length)" />
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7 </inputs>
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8 <outputs>
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9 <data name="output" format="wig" />
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10 </outputs>
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11
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12 <help>
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13 .. class:: warningmark
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14
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15 This tool requires sequencing reads in SAM/BAM/Bed/BedGraph format.
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16 </help>
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17 </tool>
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