Mercurial > repos > devteam > get_flanks
annotate get_flanks.xml @ 2:0eae46dcc35c
Added tool images.
| author | devteam <devteam@galaxyproject.org> |
|---|---|
| date | Mon, 14 Apr 2014 09:17:59 -0400 |
| parents | 1f2b0650b1db |
| children | 2fdec558c935 |
| rev | line source |
|---|---|
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1f2b0650b1db
Corrected version string.
devteam <devteam@galaxyproject.org>
parents:
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changeset
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1 <tool id="get_flanks1" name="Get flanks" version="1.0.0"> |
| 0 | 2 <description>returns flanking region/s for every gene</description> |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.7.1">bx-python</requirement> | |
| 5 <requirement type="package" version="1.0.0">galaxy-ops</requirement> | |
| 6 </requirements> | |
| 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> | |
| 8 <inputs> | |
| 9 <param format="interval" name="input" type="data" label="Select data"/> | |
| 10 <param name="region" type="select" label="Region"> | |
| 11 <option value="whole" selected="true">Whole feature</option> | |
| 12 <option value="start">Around Start</option> | |
| 13 <option value="end">Around End</option> | |
| 14 </param> | |
| 15 <param name="direction" type="select" label="Location of the flanking region/s"> | |
| 16 <option value="Upstream">Upstream</option> | |
| 17 <option value="Downstream">Downstream</option> | |
| 18 <option value="Both">Both</option> | |
| 19 </param> | |
| 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."/> | |
| 21 <param name="size" size="10" type="integer" value="50" label="Length of the flanking region(s)" help="Use non-negative value for length"/> | |
| 22 | |
| 23 | |
| 24 </inputs> | |
| 25 <outputs> | |
| 26 <data format="interval" name="out_file1" metadata_source="input"/> | |
| 27 </outputs> | |
| 28 <tests> | |
| 29 <test> | |
| 30 <param name="input" value="flanks_inp.bed"/> | |
| 31 <param name="offset" value="-500"/> | |
| 32 <param name="size" value="1000"/> | |
| 33 <param name="direction" value="Both"/> | |
| 34 <param name="region" value="whole"/> | |
| 35 <output name="out_file1" file="flanks_out1.bed"/> | |
| 36 </test> | |
| 37 <test> | |
| 38 <param name="input" value="flanks_inp.bed"/> | |
| 39 <param name="offset" value="200"/> | |
| 40 <param name="size" value="1000"/> | |
| 41 <param name="direction" value="Downstream"/> | |
| 42 <param name="region" value="start" /> | |
| 43 <output name="out_file1" file="flanks_out2.bed"/> | |
| 44 </test> | |
| 45 </tests> | |
| 46 <help> | |
| 47 | |
| 48 This tool finds the upstream and/or downstream flanking region(s) of all the selected regions in the input file. | |
| 49 | |
| 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". | |
| 51 | |
| 52 ----- | |
| 53 | |
| 54 | |
| 55 **Example 1** | |
| 56 | |
| 57 - For the following dataset:: | |
| 58 | |
| 59 chr22 1000 7000 NM_174568 0 + | |
| 60 | |
| 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)**:: | |
| 62 | |
| 63 chr22 500 800 NM_174568 0 + | |
| 64 | |
| 2 | 65 .. image:: flanks_ex1.gif |
| 0 | 66 |
| 67 **Example 2** | |
| 68 | |
| 69 - For the following dataset:: | |
| 70 | |
| 71 chr22 1000 7000 NM_028946 0 - | |
| 72 | |
| 73 - running get flanks with Region: Whole, Offset: 200, Flank-length: 300 and Location: Downstream will return **(Orange: Dataset negative strand; Magenta: Flanks output)**:: | |
| 74 | |
| 75 chr22 500 800 NM_028946 0 - | |
| 76 | |
| 2 | 77 .. image:: flanks_ex2.gif |
| 0 | 78 |
| 79 </help> | |
| 80 | |
| 81 | |
| 82 </tool> |