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1 <tool id="get_flanks1" name="Get flanks">
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2 <description>returns flanking region/s for every gene</description>
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3 <command interpreter="python">get_flanks.py $input $out_file1 $size $direction $region -o $offset -l ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol}</command>
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4 <inputs>
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5 <param format="interval" name="input" type="data" label="Select data"/>
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6 <param name="region" type="select" label="Region">
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7 <option value="whole" selected="true">Whole feature</option>
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8 <option value="start">Around Start</option>
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9 <option value="end">Around End</option>
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10 </param>
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11 <param name="direction" type="select" label="Location of the flanking region/s">
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12 <option value="Upstream">Upstream</option>
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13 <option value="Downstream">Downstream</option>
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14 <option value="Both">Both</option>
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15 </param>
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16 <param name="offset" size="10" type="integer" value="0" label="Offset" help="Use positive values to offset co-ordinates in the direction of transcription and negative values to offset in the opposite direction."/>
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17 <param name="size" size="10" type="integer" value="50" label="Length of the flanking region(s)" help="Use non-negative value for length"/>
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18
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19
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20 </inputs>
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21 <outputs>
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22 <data format="interval" name="out_file1" metadata_source="input"/>
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23 </outputs>
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24 <tests>
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25 <test>
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26 <param name="input" value="flanks_inp.bed"/>
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27 <param name="offset" value="-500"/>
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28 <param name="size" value="1000"/>
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29 <param name="direction" value="Both"/>
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30 <param name="region" value="whole"/>
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31 <output name="out_file1" file="flanks_out1.bed"/>
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32 </test>
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33 <test>
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34 <param name="input" value="flanks_inp.bed"/>
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35 <param name="offset" value="200"/>
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36 <param name="size" value="1000"/>
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37 <param name="direction" value="Downstream"/>
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38 <param name="region" value="start" />
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39 <output name="out_file1" file="flanks_out2.bed"/>
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40 </test>
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41 </tests>
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42 <help>
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43
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44 This tool finds the upstream and/or downstream flanking region(s) of all the selected regions in the input file.
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45
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46 **Note:** Every line should contain at least 3 columns: Chromosome number, Start and Stop co-ordinates. If any of these columns is missing or if start and stop co-ordinates are not numerical, the tool may encounter exceptions and such lines are skipped as invalid. The number of invalid skipped lines is documented in the resulting history item as a "Data issue".
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47
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48 -----
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49
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50
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51 **Example 1**
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52
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53 - For the following query::
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54
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55 chr22 1000 7000 NM_174568 0 +
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56
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57 - running get flanks with Region: Around start, Offset: -200, Flank-length: 300 and Location: Upstream will return **(Red: Query positive strand; Blue: Flanks output)**::
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58
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59 chr22 500 800 NM_174568 0 +
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60
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61 .. image:: ./static/operation_icons/flanks_ex1.gif
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62
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63 **Example 2**
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64
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65 - For the following query::
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66
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67 chr22 1000 7000 NM_028946 0 -
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68
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69 - running get flanks with Region: Whole, Offset: 200, Flank-length: 300 and Location: Downstream will return **(Orange: Query negative strand; Magenta: Flanks output)**::
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70
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71 chr22 500 800 NM_028946 0 -
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72
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73 .. image:: ./static/operation_icons/flanks_ex2.gif
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74
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75 </help>
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76
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77
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78 </tool> |
