[2] | 1 | <tool id="gops_merge_1" name="Merge"> |
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| 2 | <description>the overlapping intervals of a query</description> |
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| 3 | <command interpreter="python">gops_merge.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} $returntype</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>Merge overlaping regions of</label> |
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| 7 | </param> |
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| 8 | <param name="returntype" type="boolean" truevalue="-3" falsevalue=""> |
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| 9 | <label>Output 3 column bed</label> |
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| 10 | </param> |
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| 11 | </inputs> |
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| 12 | <outputs> |
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| 13 | <data format="input" name="output" metadata_source="input1" /> |
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| 14 | </outputs> |
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| 15 | <code file="operation_filter.py"> |
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| 16 | <hook exec_after_process="exec_after_merge" /> |
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| 17 | </code> |
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| 18 | <tests> |
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| 19 | <test> |
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| 20 | <param name="input1" value="1.bed" /> |
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| 21 | <output name="output" file="gops-merge.dat" /> |
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| 22 | <param name="returntype" value="true" /> |
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| 23 | </test> |
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| 24 | <test> |
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| 25 | <param name="input1" value="2_mod.bed" ftype="interval"/> |
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| 26 | <output name="output" file="gops_merge_diffCols.dat" /> |
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| 27 | <param name="returntype" value="true" /> |
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| 28 | </test> |
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| 29 | <test> |
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| 30 | <param name="input1" value="gops_bigint.interval" /> |
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| 31 | <output name="output" file="gops_merge_out2.bed" /> |
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| 32 | <param name="returntype" value="true" /> |
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| 33 | </test> |
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| 34 | </tests> |
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| 35 | <help> |
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| 36 | |
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| 37 | .. class:: infomark |
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| 38 | |
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| 39 | **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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| 40 | |
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| 41 | ----- |
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| 42 | |
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| 43 | **Screencasts!** |
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| 44 | |
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| 45 | See Galaxy Interval Operation Screencasts_ (right click to open this link in another window). |
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| 46 | |
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| 47 | .. _Screencasts: http://bitbucket.org/galaxy/galaxy-central/wiki/GopsDesc |
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| 48 | |
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| 49 | ----- |
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| 50 | |
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| 51 | This operation merges all overlapping intervals into single intervals. |
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| 52 | |
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| 53 | **Example** |
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| 54 | |
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| 55 | .. image:: ../static/operation_icons/gops_merge.gif |
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| 56 | |
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| 57 | </help> |
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| 58 | </tool> |
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