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41 lines
1.4 KiB
XML
41 lines
1.4 KiB
XML
<tool id="gops_basecoverage_1" name="Base Coverage">
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<description>of all intervals</description>
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<command interpreter="python">gops_basecoverage.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol}</command>
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<inputs>
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<param format="interval" name="input1" type="data">
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<label>Compute coverage for</label>
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</param>
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</inputs>
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<outputs>
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<data format="txt" name="output" />
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</outputs>
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<code file="operation_filter.py"/>
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<tests>
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<test>
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<param name="input1" value="1.bed" />
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<output name="output" file="gops_basecoverage_out.txt" />
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</test>
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<test>
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<param name="input1" value="gops_bigint.interval" />
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<output name="output" file="gops_basecoverage_out2.txt" />
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</test>
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</tests>
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<help>
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.. class:: infomark
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**TIP:** If your query does not appear in the pulldown menu -> it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns
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This operation counts the total bases covered by a set of intervals. Bases that are covered by more than one interval are **not** counted more than once towards the total.
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-----
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**Screencasts!**
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See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).
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.. _Screencasts: http://www.bx.psu.edu/cgi-bin/trac.cgi/wiki/GopsDesc
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</help>
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</tool> |