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1 <tool id="createInterval" name="Create single interval">
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2 <description>as a new dataset</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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