[2] | 1 | <tool id="gops_basecoverage_1" name="Base Coverage"> |
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| 2 | <description>of all intervals</description> |
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| 3 | <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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| 4 | <inputs> |
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| 5 | <param format="interval" name="input1" type="data"> |
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| 6 | <label>Compute coverage for</label> |
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| 7 | </param> |
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| 8 | </inputs> |
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| 9 | <outputs> |
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| 10 | <data format="txt" name="output" /> |
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| 11 | </outputs> |
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| 12 | <code file="operation_filter.py"/> |
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| 13 | <tests> |
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| 14 | <test> |
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| 15 | <param name="input1" value="1.bed" /> |
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| 16 | <output name="output" file="gops_basecoverage_out.txt" /> |
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| 17 | </test> |
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| 18 | <test> |
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| 19 | <param name="input1" value="gops_bigint.interval" /> |
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| 20 | <output name="output" file="gops_basecoverage_out2.txt" /> |
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| 21 | </test> |
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| 22 | </tests> |
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| 23 | <help> |
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| 24 | |
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| 25 | .. class:: infomark |
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| 26 | |
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| 27 | **TIP:** If your query does not appear in the pulldown menu, it means that it is not in interval format. Use "edit attributes" to set chromosome, start, end, and strand columns. |
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| 28 | |
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| 29 | 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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| 30 | |
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| 31 | ----- |
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| 32 | |
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| 33 | **Screencasts!** |
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| 34 | |
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| 35 | See Galaxy Interval Operation Screencasts_ (right click to open this link in another window). |
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| 36 | |
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| 37 | .. _Screencasts: http://bitbucket.org/galaxy/galaxy-central/wiki/GopsDesc |
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| 38 | |
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| 39 | |
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| 40 | </help> |
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| 41 | </tool> |
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