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1 <tool id="get_flanks1" name="Get flanks" version="0.0.1">
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2 <description>returns flanking region/s for every gene</description>
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3 <requirements>
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4 <requirement type="package" version="0.7.1">bx-python</requirement>
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5 <requirement type="package" version="1.0.0">galaxy-ops</requirement>
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6 </requirements>
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7 <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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8 <inputs>
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9 <param format="interval" name="input" type="data" label="Select data"/>
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10 <param name="region" type="select" label="Region">
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11 <option value="whole" selected="true">Whole feature</option>
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12 <option value="start">Around Start</option>
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13 <option value="end">Around End</option>
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14 </param>
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15 <param name="direction" type="select" label="Location of the flanking region/s">
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16 <option value="Upstream">Upstream</option>
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17 <option value="Downstream">Downstream</option>
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18 <option value="Both">Both</option>
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19 </param>
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20 <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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21 <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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22
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23
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24 </inputs>
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25 <outputs>
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26 <data format="interval" name="out_file1" metadata_source="input"/>
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27 </outputs>
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28 <tests>
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29 <test>
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30 <param name="input" value="flanks_inp.bed"/>
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31 <param name="offset" value="-500"/>
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32 <param name="size" value="1000"/>
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33 <param name="direction" value="Both"/>
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34 <param name="region" value="whole"/>
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35 <output name="out_file1" file="flanks_out1.bed"/>
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36 </test>
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37 <test>
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38 <param name="input" value="flanks_inp.bed"/>
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39 <param name="offset" value="200"/>
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40 <param name="size" value="1000"/>
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41 <param name="direction" value="Downstream"/>
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42 <param name="region" value="start" />
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43 <output name="out_file1" file="flanks_out2.bed"/>
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44 </test>
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45 </tests>
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46 <help>
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47
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48 This tool finds the upstream and/or downstream flanking region(s) of all the selected regions in the input file.
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49
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50 **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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51
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52 -----
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53
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54
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55 **Example 1**
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56
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57 - For the following dataset::
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58
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59 chr22 1000 7000 NM_174568 0 +
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60
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61 - running get flanks with Region: Around start, Offset: -200, Flank-length: 300 and Location: Upstream will return **(Red: Dataset positive strand; Blue: Flanks output)**::
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62
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63 chr22 500 800 NM_174568 0 +
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64
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65 .. image:: ${static_path}/operation_icons/flanks_ex1.gif
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66
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67 **Example 2**
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68
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69 - For the following dataset::
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70
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71 chr22 1000 7000 NM_028946 0 -
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72
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73 - running get flanks with Region: Whole, Offset: 200, Flank-length: 300 and Location: Downstream will return **(Orange: Dataset negative strand; Magenta: Flanks output)**::
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74
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75 chr22 500 800 NM_028946 0 -
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76
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77 .. image:: ${static_path}/operation_icons/flanks_ex2.gif
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78
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79 </help>
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80
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81
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82 </tool>
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