Mercurial > repos > iuc > resize_coordinate_window

annotate resize_coordinate_window.xml @ 4:4eb3cc1f8466 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit d357611d8d49631f0eb7c5e022e80cb4c9483308"
author iuc
date Wed, 11 Dec 2019 18:06:42 -0500
parents 9ba78e8985dc
children
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4eb3cc1f8466 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit d357611d8d49631f0eb7c5e022e80cb4c9483308"
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1 <tool id="resize_coordinate_window" name="Resize coordinate window" version="1.0.2">
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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>
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4eb3cc1f8466 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit d357611d8d49631f0eb7c5e022e80cb4c9483308"
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3 <requirements>
4eb3cc1f8466 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit d357611d8d49631f0eb7c5e022e80cb4c9483308"
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4 <requirement type="package" version="3.8.0">python</requirement>
4eb3cc1f8466 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit d357611d8d49631f0eb7c5e022e80cb4c9483308"
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5 </requirements>
3
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6 <command detect_errors="exit_code"><![CDATA[
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7 python '$__tool_directory__/resize_coordinate_window.py'
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8 --input '$input'
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9 --start_coordinate $start_coordinate
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10 --subtract_from_start $subtract_from_start
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11 --add_to_end $add_to_end
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12 --extend_existing $extend_existing
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13 --chrom_len_file '${chromInfo}'
9ba78e8985dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit ad3846c086321d9bd604e974fd21323347b73470
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14 --region_boundaries $region_boundaries
9ba78e8985dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit ad3846c086321d9bd604e974fd21323347b73470
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15 --output '$output'
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16 ]]></command>
0
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17 <inputs>
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18 <param name="input" type="data" format="gff" label="Gff file" />
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19 <param name="start_coordinate" type="select" label="Start coordinate" help="Input data is 0-based or 1-based">
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20 <option value="0" selected="True">0</option>
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21 <option value="1">1</option>
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22 </param>
0
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23 <param name="subtract_from_start" type="integer" value="30" min="0" label="Distance to subtract from the start coordinate"/>
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24 <param name="add_to_end" type="integer" value="30" min="0" label="Distance to add to the end coordinate"/>
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25 <param name="extend_existing" type="select" label="Resize window from" help="The midpoint is computed as (start + end) // 2">
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26 <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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27 <option value="existing">the start and end coordinates</option>
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28 </param>
1
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29 <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.">
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30 <option value="discard" selected="True">discarding the region</option>
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31 <option value="limit">keeping the region by limiting the expansion to not cross the start or end coordinate boundary</option>
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32 <option value="nothing">keeping the region by allowing the expansion to cross the start or end coordinate boundary</option>
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33 <option value="error">outputting an error</option>
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34 </param>
0
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35 </inputs>
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36 <outputs>
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37 <data name="output" format="gff" />
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38 </outputs>
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39 <tests>
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40 <test>
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41 <param name="input" value="input.gff" ftype="gff" />
1
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42 <param name="start_coordinate" value="1" />
0
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43 <param name="subtract_from_start" value="13" />
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44 <param name="add_to_end" value="13" />
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45 <param name="extend_existing" value="midpoint" />
1
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46 <param name="region_boundaries" value="error" />
0
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47 <output name="output" file="output.gff" ftype="gff" />
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48 </test>
1
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49 <test>
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50 <param name="input" value="input.gff" ftype="gff" />
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51 <param name="start_coordinate" value="0" />
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52 <param name="subtract_from_start" value="80" />
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53 <param name="add_to_end" value="80" />
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54 <param name="extend_existing" value="midpoint" />
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55 <param name="region_boundaries" value="discard" />
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56 <output name="output" file="output_discard.gff" ftype="gff" />
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57 </test>
0
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58 </tests>
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59 <help>
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60
08b6255afde7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/resize_coordinate_window commit b'67cff25a50ba173b0468819204d0999496f68ea9'
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61 **What it does**
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62
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63 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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64 specified region size that is computed either from the existing start and end coordinates or centered on
0
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65 the midpoint between them.
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66
1
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67 Region expansion may result in the new start or end coordinates crossing the chromosome boundary. The
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68 chromosome start is set to 0 or 1 using the **Start coordinate** parameter. The end is retrieved from a
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69 file within the Galaxy environment that includes the length of chromosomes for all genome builds. If these
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70 files are missing, the end coordinate is set to 2147483647, which is the maximum value of a signed 32 bit
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71 integer. The **Handle chromosome boundaries by** parameter handles chromosome boundaries that are crossed
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72 by expanding the region using one of the following options.
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73
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74 * **discarding the region** - the region will be discarded and processing will continue with the next line in the dataset.
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75 * **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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76 * **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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77 * **outputting an error** - Stop processing and display an error.
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78
0
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79 -----
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80
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81 **Example**
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82
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83 If the input dataset is::
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84
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 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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86 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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87 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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88
1
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89 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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90
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 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'
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92 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'
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93 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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94
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95 </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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96 <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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97 <citation type="bibtex">
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98 @unpublished{None,
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99 author = {Greg Von Kuster},
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100 title = {None},
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101 year = {None},
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102 eprint = {None},
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103 url = {http://www.huck.psu.edu/content/research/independent-centers-excellence/center-for-eukaryotic-gene-regulation}
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104 }</citation>
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105 </citations>
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106 </tool>