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1 <macros>
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2 <xml name="requirements">
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3 <requirements>
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4 <requirement type="package" version="0.67.5">circos</requirement>
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5 <requirement type="package" version="0.20">circostools</requirement>
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6 <yield/>
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7 </requirements>
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8 </xml>
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9 <token name="@WRAPPER_VERSION@">0.67.5</token>
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10 <xml name="stdio">
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11 <stdio>
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12 <!-- Anything other than zero is an error -->
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13 <exit_code range="1:" />
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14 <exit_code range=":-1" />
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15 <!-- In case the return code has not been set propery check stderr too -->
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16 <regex match="Error:" />
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17 <regex match="Exception:" />
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18 </stdio>
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19 </xml>
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20
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21
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22
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23 <xml name="strand2">
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24 <param name="strand" type="select" label="Calculation based on strandedness?">
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25 <option value="" selected="True">Overlaps on either strand</option>
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26 <option value="-s">Only overlaps occurring on the **same** strand.</option>
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27 <option value="-S">Only overlaps occurring on the **opposite** strand.</option>
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28 </param>
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29 </xml>
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30 <xml name="seed">
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31 <conditional name="seed">
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32 <param name="seed_choose" type="select" label="Choose Seed?" help="(-seed)">
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33 <option value="False" selected="True">Random Shuffling</option>
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34 <option value="True">Choose fixed seed</option>
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35 </param>
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36 <when value="True">
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37 <param name="seed" type="integer" value="12345" label="Enter Seed" />
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38 </when>
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39 <when value="False" />
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40 </conditional>
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41 </xml>
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42 <xml name="split">
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43 <param name="split" type="boolean" checked="false" truevalue="-split" falsevalue=""
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44 label="Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage."
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45 help="If set, the coverage will be calculated based the spliced intervals only. For BAM files, this inspects the CIGAR N operation to infer the blocks for computing coverage. For BED12 files, this inspects the BlockCount, BlockStarts, and BlockEnds fields (i.e., columns 10,11,12). If this option is not set, coverage will be calculated based on the interval's START/END coordinates, and would include introns in the case of RNAseq data. (-split)" />
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46 </xml>
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47 <xml name="genome">
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48 <param format="tabular" name="genome" type="data" label="Genome file" />
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49 <!--TODO: make use of: ${chromInfo} -->
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50 </xml>
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51 <xml name="addition">
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52 <conditional name="addition">
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53 <param name="addition_select" type="select" label="Choose what you want to do">
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54 <option value="b" selected="True">Increase the BED/GFF/VCF entry by the same number base pairs in each direction.</option>
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55 <option value="lr">Increase by Start Coordinate and End Coordinate</option>
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56 </param>
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57 <when value="b">
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58 <param name="b" value="1" label="Number of base pairs" type="integer" />
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59 </when>
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60 <when value="lr">
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61 <param name="l" type="integer" value="0" label="The number of base pairs to subtract from the start coordinate" />
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62 <param name="r" type="integer" value="0" label="The number of base pairs to add to the end coordinate" />
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63 </when>
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64 </conditional>
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65 </xml>
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66 <xml name="print_header">
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67 <param name="header" type="boolean" checked="False" truevalue="-header" falsevalue=""
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68 label="Print the header from the A file prior to results" help="(-header)" />
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69 </xml>
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70 <!-- TODO this is currently not used, but we should make use of it -->
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71 <xml name="genome_validator">
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72 <validator type="unspecified_build" />
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73 <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." />
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74 </xml>
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75
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76 <!-- ToDo column_picker -->
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77 <xml name="choose_columns">
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78 <param name="cols" type="text" value=""
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79 label="Specify the column(s) (comma separated) that should be summarized"
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80 help="(-c)">
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81 <sanitizer invalid_char="">
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82 <valid initial="string.digits"><add value=","/></valid>
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83 </sanitizer>
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84 </param>
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85 </xml>
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86
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87 <xml name="choose_operations">
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88 <param name="operation" type="select" label="Specify the operation">
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89 <yield />
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90 </param>
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91 </xml>
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92
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93 <xml name="citations">
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94 <citations>
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95 <citation type="doi">10.1101/gr.092759.109</citation>
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96 <yield />
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97 </citations>
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98 </xml>
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99 </macros>
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