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