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60 lines
1.8 KiB
XML
60 lines
1.8 KiB
XML
<tool id="createInterval" name="Create single interval" version="1.0.0">
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<description>as a new dataset</description>
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<requirements>
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<requirement type="package" version="5.26">perl</requirement>
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</requirements>
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<command>
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perl '$__tool_directory__/CreateInterval.pl' '$chrom' $start $end '$name' $strand '$out_file1'
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</command>
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<inputs>
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<param name="chrom" type="text" value="chr7" label="Chromosome"/>
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<param name="start" type="integer" value="100" label="Start position"/>
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<param name="end" type="integer" value="1000" label="End position"/>
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<param name="name" type="text" value="myInterval" label="Name"/>
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<param name="strand" type="select" label="Strand" help="If your interval is strandless set strand to plus" >
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<option value="plus">plus</option>
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<option value="minus">minus</option>
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</param>
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</inputs>
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<outputs>
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<data name="out_file1" format="bed" />
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</outputs>
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<tests>
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<test>
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<param name="chrom" value="chr7"/>
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<param name="start" value="100"/>
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<param name="end" value="1000"/>
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<param name="name" value="myinterval"/>
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<param name="strand" value="plus"/>
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<output name="out_file1" file="eq-createinterval.dat"/>
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</test>
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</tests>
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<help>
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.. class:: warningmark
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**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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-----
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**What it does**
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This tool allows you to create a single genomic interval. The resulting history item will be in the BED format.
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-----
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**Example**
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Typing the following values in the form::
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Chromosome: chrX
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Start position: 151087187
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End position: 151370486
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Name: NM_000808
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Strand: minus
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will create a single interval::
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chrX 151087187 151370486 NM_000808 0 -
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</help>
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</tool>
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