Mercurial > repos > iuc > resize_coordinate_window

annotate resize_coordinate_window.xml @ 2:541f300f322d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 174be06d7c7e7789df16ea5d5068f20b21257a2f
author iuc
date Mon, 14 Nov 2016 14:04:00 -0500
parents 0164d2edba9f
children 9ba78e8985dc
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1 <tool id="resize_coordinate_window" name="Resize coordinate window" version="1.0.1">
0
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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2 <description>of GFF data</description>
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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3 <command>
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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4 python $__tool_directory__/resize_coordinate_window.py
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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5 --input "$input"
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6 --start_coordinate $start_coordinate
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7 --subtract_from_start $subtract_from_start
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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8 --add_to_end $add_to_end
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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9 --extend_existing $extend_existing
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10 --chrom_len_file ${chromInfo}
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11 --region_boundaries $region_boundaries
0
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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12 --output "$output"
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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13 </command>
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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14 <inputs>
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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15 <param name="input" type="data" format="gff" label="Gff file" />
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16 <param name="start_coordinate" type="select" label="Start coordinate" help="Input data is 0-based or 1-based">
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17 <option value="0" selected="True">0</option>
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18 <option value="1">1</option>
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
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19 </param>
0
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20 <param name="subtract_from_start" type="integer" value="30" min="0" label="Distance to subtract from the start coordinate"/>
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21 <param name="add_to_end" type="integer" value="30" min="0" label="Distance to add to the end coordinate"/>
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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22 <param name="extend_existing" type="select" label="Resize window from" help="The midpoint is computed as (start + end) // 2">
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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23 <option value="midpoint" selected="True">the midpoint of the start and end coordinates</option>
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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24 <option value="existing">the start and end coordinates</option>
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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25 </param>
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26 <param name="region_boundaries" type="select" label="Handle chromosome boundaries by" help="Expanding the region may result in crossing chromosome start and end coordinate boundaries.">
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
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27 <option value="discard" selected="True">discarding the region</option>
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
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28 <option value="limit">keeping the region by limiting the expansion to not cross the start or end coordinate boundary</option>
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29 <option value="nothing">keeping the region by allowing the expansion to cross the start or end coordinate boundary</option>
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
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30 <option value="error">outputting an error</option>
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31 </param>
0
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32 </inputs>
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33 <outputs>
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34 <data name="output" format="gff" />
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35 </outputs>
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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36 <tests>
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37 <test>
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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38 <param name="input" value="input.gff" ftype="gff" />
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39 <param name="start_coordinate" value="1" />
0
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40 <param name="subtract_from_start" value="13" />
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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41 <param name="add_to_end" value="13" />
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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42 <param name="extend_existing" value="midpoint" />
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43 <param name="region_boundaries" value="error" />
0
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44 <output name="output" file="output.gff" ftype="gff" />
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45 </test>
1
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46 <test>
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47 <param name="input" value="input.gff" ftype="gff" />
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48 <param name="start_coordinate" value="0" />
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49 <param name="subtract_from_start" value="80" />
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50 <param name="add_to_end" value="80" />
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51 <param name="extend_existing" value="midpoint" />
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52 <param name="region_boundaries" value="discard" />
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53 <output name="output" file="output_discard.gff" ftype="gff" />
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54 </test>
0
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55 </tests>
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56 <help>
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57
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58 **What it does**
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59
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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60 Modifies the start and end coordinates of GFF data such that the new start and end position is based on a
1
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61 specified region size that is computed either from the existing start and end coordinates or centered on
0
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62 the midpoint between them.
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63
1
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64 Region expansion may result in the new start or end coordinates crossing the chromosome boundary. The
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
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65 chromosome start is set to 0 or 1 using the **Start coordinate** parameter. The end is retrieved from a
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66 file within the Galaxy environment that includes the length of chromosomes for all genome builds. If these
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
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67 files are missing, the end coordinate is set to 2147483647, which is the maximum value of a signed 32 bit
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68 integer. The **Handle chromosome boundaries by** parameter handles chromosome boundaries that are crossed
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69 by expanding the region using one of the following options.
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70
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71 * **discarding the region** - the region will be discarded and processing will continue with the next line in the dataset.
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72 * **keeping the region by limiting the expansion to not cross the start or end coordinate boundary** - expansion will be restricted to not cross the chromosome's start or end coordinates for the current region.
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73 * **keeping the region by allowing the expansion to cross the start or end coordinate boundary** - allow defined expansion, crossing the start boundary results in a negative start value.
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74 * **outputting an error** - Stop processing and display an error.
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75
0
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76 -----
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77
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78 **Example**
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79
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80 If the input dataset is::
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81
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82 chr1 genetrack . 17 37 918 + . stddev=5.96715849116
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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83 chr1 genetrack . 31 51 245 - . stddev=2.66582799529
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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84 chr1 genetrack . 40 60 2060 + . stddev=2.7859667372
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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85
1
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
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86 Setting start coordinate to 1 and resizing the coordinate window by 13 from the computed midpoint of the start and end coordinates produces::
0
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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87
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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88 chr1 genetrack . 14 40 918 + . stddev=5.96715849116
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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89 chr1 genetrack . 28 54 245 - . stddev=2.66582799529`
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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90 chr1 genetrack . 37 63 2060 + . stddev=2.7859667372
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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91
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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92 </help>
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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93 <citations>
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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94 <citation type="bibtex">
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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95 @unpublished{None,
1
0164d2edba9f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit 7aa2429d3f53a14be7e44dc6021ed3e11dc2f080
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96 author = {Greg Von Kuster},
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08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
iuc
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97 title = {None},
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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98 year = {None},
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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99 eprint = {None},
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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100 url = {http://www.huck.psu.edu/content/research/independent-centers-excellence/center-for-eukaryotic-gene-regulation}
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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101 }</citation>
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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102 </citations>
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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103 </tool>