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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
author devteam
date Thu, 22 Jun 2017 18:41:29 -0400
parents 4cd116158aef
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c3b1781c6fd1 Corrected version string.
devteam <devteam@galaxyproject.org>
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1 <tool id="get_flanks1" name="Get flanks" version="1.0.0">
4
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devteam
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2 <description>returns flanking region/s for every gene</description>
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3 <macros>
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devteam
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4 <import>macros.xml</import>
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devteam
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5 </macros>
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6 <expand macro="requirements" />
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devteam
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7 <command><![CDATA[
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8 python '$__tool_directory__/get_flanks.py'
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9 '$input'
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10 '$out_file1'
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11 $size
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12 $direction
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13 $region
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14 -o $offset
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15 -l ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol}
077f404ae1bb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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16 ]]></command>
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17 <inputs>
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18 <param name="input" type="data" format="interval" label="Select data"/>
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19 <param name="region" type="select" label="Region">
077f404ae1bb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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20 <option value="whole" selected="true">Whole feature</option>
077f404ae1bb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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21 <option value="start">Around Start</option>
077f404ae1bb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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22 <option value="end">Around End</option>
077f404ae1bb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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23 </param>
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24 <param name="direction" type="select" label="Location of the flanking region/s">
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25 <option value="Upstream">Upstream</option>
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26 <option value="Downstream">Downstream</option>
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27 <option value="Both">Both</option>
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28 </param>
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29 <param name="offset" 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."/>
077f404ae1bb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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30 <param name="size" type="integer" value="50" label="Length of the flanking region(s)" help="Use non-negative value for length"/>
077f404ae1bb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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31 </inputs>
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32 <outputs>
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33 <data name="out_file1" format_source="input" metadata_source="input"/>
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34 </outputs>
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35 <tests>
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36 <test>
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37 <param name="input" value="flanks_inp.bed"/>
077f404ae1bb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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38 <param name="offset" value="-500"/>
077f404ae1bb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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39 <param name="size" value="1000"/>
077f404ae1bb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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40 <param name="direction" value="Both"/>
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41 <param name="region" value="whole"/>
077f404ae1bb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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42 <output name="out_file1" file="flanks_out1.bed"/>
077f404ae1bb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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43 </test>
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44 <test>
077f404ae1bb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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45 <param name="input" value="flanks_inp.bed"/>
077f404ae1bb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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46 <param name="offset" value="200"/>
077f404ae1bb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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47 <param name="size" value="1000"/>
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48 <param name="direction" value="Downstream"/>
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49 <param name="region" value="start" />
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50 <output name="out_file1" file="flanks_out2.bed"/>
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51 </test>
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52 </tests>
077f404ae1bb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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53 <help><![CDATA[
077f404ae1bb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gops/get_flanks commit cae3e05d02e60f595bb8b6d77a84f030e9bd1689
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54 This tool finds the upstream and/or downstream flanking region(s) of all the selected regions in the input file.
0
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55
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56 **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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57
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58 -----
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59
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60 **Example 1**
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61
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62 - For the following dataset::
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63
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64 chr22 1000 7000 NM_174568 0 +
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65
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66 - 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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67
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68 chr22 500 800 NM_174568 0 +
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69
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70 .. image:: flanks_ex1.gif
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71
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72 **Example 2**
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73
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74 - For the following dataset::
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75
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76 chr22 1000 7000 NM_028946 0 -
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77
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78 - 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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79
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80 chr22 500 800 NM_028946 0 -
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81
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82 .. image:: flanks_ex2.gif
4
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83 ]]></help>
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84 </tool>