[2] | 1 | <tool id="createInterval" name="Create single interval"> |
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| 2 | <description>as a new query</description> |
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| 3 | <command interpreter="perl">CreateInterval.pl $chrom $start $end "$name" $strand $out_file1</command> |
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| 4 | <inputs> |
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| 5 | <param name="chrom" size="20" type="text" value="chr7" label="Chromosome"/> |
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| 6 | <param name="start" size="20" type="integer" value="100" label="Start position"/> |
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| 7 | <param name="end" size="20" type="integer" value="1000" label="End position"/> |
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| 8 | <param name="name" size="20" type="text" value="myInterval" label="Name"/> |
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| 9 | <param name="strand" type="select" label="Strand" help="If your interval is strandless set strand to plus" > |
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| 10 | <option value="plus">plus</option> |
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| 11 | <option value="minus">minus</option> |
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| 12 | </param> |
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| 13 | </inputs> |
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| 14 | <outputs> |
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| 15 | <data format="bed" name="out_file1" /> |
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| 16 | </outputs> |
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| 17 | <tests> |
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| 18 | <test> |
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| 19 | <param name="chrom" value="chr7"/> |
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| 20 | <param name="start" value="100"/> |
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| 21 | <param name="end" value="1000"/> |
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| 22 | <param name="name" value="myinterval"/> |
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| 23 | <param name="strand" value="plus"/> |
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| 24 | <output name="out_file1" file="eq-createinterval.dat"/> |
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| 25 | </test> |
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| 26 | </tests> |
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| 27 | <help> |
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| 28 | |
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| 29 | .. class:: warningmark |
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| 30 | |
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| 31 | **TIP**. Once your interval appears in history, you must tell Galaxy which genome it belongs to by clicking pencil icon or the "?" link in the history item. |
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| 32 | |
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| 33 | ----- |
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| 34 | |
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| 35 | **What it does** |
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| 36 | |
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| 37 | This tool allows you to create a single genomic interval. The resulting history item will be in the BED format. |
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| 38 | |
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| 39 | ----- |
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| 40 | |
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| 41 | **Example** |
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| 42 | |
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| 43 | Typing the following values in the form:: |
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| 44 | |
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| 45 | Chromosome: chrX |
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| 46 | Start position: 151087187 |
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| 47 | End position: 151370486 |
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| 48 | Name: NM_000808 |
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| 49 | Strand: minus |
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| 50 | |
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| 51 | will create a single interval:: |
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| 52 | |
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| 53 | chrX 151087187 151370486 NM_000808 0 - |
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| 54 | |
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| 55 | </help> |
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| 56 | </tool> |
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