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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
author devteam
date Wed, 03 Jun 2020 09:45:06 -0400
parents 592089499ae7
children
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d8515fe22ac8 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/windowsplitter commit 6960b37b09831a1b83f18775677b83a3cc5c2cd0"
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1 <tool id="winSplitter" name="Make windows" version="1.0.1">
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2 <description></description>
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3 <requirements>
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4 <requirement type="package" version="0.8.8">bx-python</requirement>
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5 </requirements>
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6 <command>
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7 python $__tool_directory__/windowSplitter.py
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8 $input
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9 $size
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10 $out_file1
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11 ${wintype.choice}
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12 ${wintype.offset}
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13 -l ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol}
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14 </command>
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15 <inputs>
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16 <!--<param label="Genome" name="dbkey" type="genomebuild"/>-->
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17 <param format="interval" name="input" type="data" label="Select data"/>
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18 <param name="size" type="integer" value="500" label="Window size"/>
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19 <conditional name="wintype">
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20 <param name="choice" type="select" label="Make sliding windows?">
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21 <option value="0" selected="true">No</option>
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22 <option value="1">Yes</option>
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23 </param>
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24 <when value="0">
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25 <param name="offset" type="hidden" value="0" />
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26 </when>
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27 <when value="1">
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28 <param name="offset" type="integer" value="10" label="Offset size"/>
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29 </when>
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30 </conditional>
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31 </inputs>
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32 <outputs>
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33 <data format="interval" name="out_file1" 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="4.bed"/>
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38 <param name="size" value="5000"/>
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39 <param name="choice" value="1"/>
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40 <param name="offset" value="4000"/>
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41 <output name="out_file1" file="4_windows.bed"/>
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42 </test>
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43 </tests>
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44 <help>
0
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45
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46 .. class:: infomark
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47
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48 **What it does**
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49
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50 This tool splits the intervals in the input file into smaller intervals based on the specified window-size and window type.
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51
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52 -----
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53
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54 .. class:: warningmark
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55
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56 **Note**
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57
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58 The positions at the end of the input interval which do not fit into the last window or a new window of required size, will be omitted from the output.
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59
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60 -----
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61
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62 .. class:: infomark
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63
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64 **About formats**
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65
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66 **BED format** Browser Extensible Data format was designed at UCSC for displaying data tracks in the Genome Browser. It has three required fields and several additional optional ones:
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67
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68 The first three BED fields (required) are::
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69
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70 1. chrom - The name of the chromosome (e.g. chr1, chrY_random).
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71 2. chromStart - The starting position in the chromosome. (The first base in a chromosome is numbered 0.)
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72 3. chromEnd - The ending position in the chromosome, plus 1 (i.e., a half-open interval).
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73
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74 The additional BED fields (optional) are::
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75
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76 4. name - The name of the BED line.
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77 5. score - A score between 0 and 1000.
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78 6. strand - Defines the strand - either '+' or '-'.
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79 7. thickStart - The starting position where the feature is drawn thickly at the Genome Browser.
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80 8. thickEnd - The ending position where the feature is drawn thickly at the Genome Browser.
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81 9. reserved - This should always be set to zero.
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82 10. blockCount - The number of blocks (exons) in the BED line.
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83 11. blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.
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84 12. blockStarts - A comma-separated list of block starts. All of the blockStart positions should be calculated relative to chromStart. The number of items in this list should correspond to blockCount.
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85 13. expCount - The number of experiments.
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86 14. expIds - A comma-separated list of experiment ids. The number of items in this list should correspond to expCount.
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87 15. expScores - A comma-separated list of experiment scores. All of the expScores should be relative to expIds. The number of items in this list should correspond to expCount.
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88
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89 -----
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90
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91 **Example**
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92
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93 - For the following dataset::
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94
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95 chr22 1000 4700 NM_174568 0 +
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96
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97 - running this tool with **Window size as 1000**, will return::
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98
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99 chr22 1000 2000 NM_174568 0 +
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100 chr22 2000 3000 NM_174568 0 +
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101 chr22 3000 4000 NM_174568 0 +
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102
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103 - running this tool to make **Sliding windows** of **size 1000** and **offset 500**, will return::
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104
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105 chr22 1000 2000 NM_174568 0 +
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106 chr22 1500 2500 NM_174568 0 +
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107 chr22 2000 3000 NM_174568 0 +
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108 chr22 2500 3500 NM_174568 0 +
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109 chr22 3000 4000 NM_174568 0 +
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110 chr22 3500 4500 NM_174568 0 +
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111
3
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112 </help>
0
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113 </tool>