[2] | 1 | <tool id="gops_complement_1" name="Complement"> |
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| 2 | <description>intervals of a query</description> |
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| 3 | <command interpreter="python">gops_complement.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -l ${chromInfo} $allchroms</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>Complement regions of</label> |
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| 7 | </param> |
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| 8 | <param name="allchroms" type="boolean" truevalue="--all" falsevalue="" label="Genome-wide complement"> |
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| 9 | </param> |
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| 10 | </inputs> |
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| 11 | <outputs> |
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| 12 | <data format="input" name="output" metadata_source="input1" /> |
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| 13 | </outputs> |
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| 14 | <code file="operation_filter.py"/> |
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| 15 | <tests> |
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| 16 | <test> |
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| 17 | <param name="input1" value="1.bed" /> |
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| 18 | <param name="allchroms" value="true" /> |
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| 19 | <output name="output" file="gops_complement_out.bed" /> |
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| 20 | </test> |
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| 21 | <test> |
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| 22 | <param name="input1" value="2_mod.bed" ftype="interval"/> |
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| 23 | <param name="allchroms" value="true" /> |
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| 24 | <output name="output" file="gops_complement_out_diffCols.dat" /> |
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| 25 | </test> |
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| 26 | <test> |
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| 27 | <param name="input1" value="gops_bigint.interval" /> |
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| 28 | <param name="allchroms" value="true" /> |
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| 29 | <output name="output" file="gops_complement_out2.bed" /> |
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| 30 | </test> |
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| 31 | </tests> |
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| 32 | <help> |
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| 33 | |
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| 34 | .. class:: infomark |
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| 35 | |
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| 36 | **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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| 37 | |
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| 38 | This operation complements the regions of a set of intervals. Regions are returned that represent the empty space in the input interval. |
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| 39 | |
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| 40 | ----- |
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| 41 | |
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| 42 | **Screencasts!** |
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| 43 | |
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| 44 | See Galaxy Interval Operation Screencasts_ (right click to open this link in another window). |
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| 45 | |
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| 46 | .. _Screencasts: http://bitbucket.org/galaxy/galaxy-central/wiki/GopsDesc |
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| 47 | |
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| 48 | ----- |
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| 49 | |
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| 50 | **Syntax** |
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| 51 | |
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| 52 | - **Genome-wide complement** will complement all chromosomes of the genome. Leaving this option unchecked will only complement chromosomes present in the query. |
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| 53 | |
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| 54 | ----- |
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| 55 | |
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| 56 | **Example** |
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| 57 | |
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| 58 | .. image:: ../static/operation_icons/gops_complement.gif |
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| 59 | |
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| 60 | </help> |
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| 61 | </tool> |
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