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1 <tool id="winSplitter" name="Make windows">
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2 <description></description>
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3 <command interpreter="python">windowSplitter.py $input $size $out_file1 ${wintype.choice} ${wintype.offset} -l ${input.metadata.chromCol},${input.metadata.startCol},${input.metadata.endCol},${input.metadata.strandCol}</command>
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4 <inputs>
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5 <!--<param label="Genome" name="dbkey" type="genomebuild"/>-->
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6 <param format="interval" name="input" type="data" label="Select data"/>
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7 <param name="size" size="10" type="integer" value="500" label="Window size"/>
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8 <conditional name="wintype">
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9 <param name="choice" type="select" label="Make sliding windows?">
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10 <option value="0" selected="true">No</option>
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11 <option value="1">Yes</option>
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12 </param>
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13 <when value="0">
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14 <param name="offset" type="hidden" value="0" />
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15 </when>
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16 <when value="1">
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17 <param name="offset" size="10" type="integer" value="10" label="Offset size"/>
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18 </when>
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19 </conditional>
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20 </inputs>
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21 <outputs>
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22 <data format="interval" name="out_file1" metadata_source="input"/>
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23 </outputs>
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24 <tests>
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25 <test>
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26 <param name="input" value="4.bed"/>
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27 <param name="size" value="5000"/>
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28 <param name="choice" value="1"/>
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29 <param name="offset" value="4000"/>
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30 <output name="out_file1" file="4_windows.bed"/>
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31 </test>
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32 </tests>
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33 <help>
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34
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35 .. class:: infomark
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36
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37 **What it does**
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38
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39 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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40
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41 -----
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42
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43 .. class:: warningmark
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44
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45 **Note**
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46
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47 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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48
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49 -----
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50
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51 .. class:: infomark
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52
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53 **About formats**
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54
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55 **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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56
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57 The first three BED fields (required) are::
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58
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59 1. chrom - The name of the chromosome (e.g. chr1, chrY_random).
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60 2. chromStart - The starting position in the chromosome. (The first base in a chromosome is numbered 0.)
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61 3. chromEnd - The ending position in the chromosome, plus 1 (i.e., a half-open interval).
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62
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63 The additional BED fields (optional) are::
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64
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65 4. name - The name of the BED line.
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66 5. score - A score between 0 and 1000.
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67 6. strand - Defines the strand - either '+' or '-'.
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68 7. thickStart - The starting position where the feature is drawn thickly at the Genome Browser.
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69 8. thickEnd - The ending position where the feature is drawn thickly at the Genome Browser.
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70 9. reserved - This should always be set to zero.
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71 10. blockCount - The number of blocks (exons) in the BED line.
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72 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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73 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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74 13. expCount - The number of experiments.
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75 14. expIds - A comma-separated list of experiment ids. The number of items in this list should correspond to expCount.
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76 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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77
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78 -----
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79
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80 **Example**
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81
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82 - For the following dataset::
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83
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84 chr22 1000 4700 NM_174568 0 +
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85
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86 - running this tool with **Window size as 1000**, will return::
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87
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88 chr22 1000 2000 NM_174568 0 +
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89 chr22 2000 3000 NM_174568 0 +
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90 chr22 3000 4000 NM_174568 0 +
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91
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92 - running this tool to make **Sliding windows** of **size 1000** and **offset 500**, will return::
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93
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94 chr22 1000 2000 NM_174568 0 +
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95 chr22 1500 2500 NM_174568 0 +
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96 chr22 2000 3000 NM_174568 0 +
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97 chr22 2500 3500 NM_174568 0 +
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98 chr22 3000 4000 NM_174568 0 +
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99 chr22 3500 4500 NM_174568 0 +
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100
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101 </help>
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102
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103
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104 </tool> |
