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1 <tool id="rtg_coverage" name="Coverage">
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2 <description>coverage</description>
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3 <command interpreter="bash">galaxy-rtg-singleoutput-wrapper.sh $output $output.id $__new_file_path__ coverage.bed
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4 coverage -t ${template.extra_files_path}
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5 $input1
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6 #for $i in $inputs
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7 ${i.input}
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8 #end for
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9 -Z
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10 </command>
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11 <inputs>
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12 <param name="template" type="data" format="rtg_sdf" label="Reference SDF"/>
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13 <param name="input1" label="First SAM file" type="data" format="sam,samix" />
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14 <repeat name="inputs" title="Input SAM Files">
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15 <param name="input" label="Add file" type="data" format="sam,samix" />
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16 </repeat>
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17 </inputs>
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18 <outputs>
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19 <data name="output" format="bed"/>
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20 </outputs>
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21
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22 <help>
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23 This tool calculates coverage using rtg coverage
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24 </help>
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25
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26 </tool>
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