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annotate mapBed.xml @ 50:df28283b3778 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
author iuc
date Mon, 29 Apr 2019 05:54:22 -0400
parents 2f457890d8c8
children b06c53665eb6
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1 <tool id="bedtools_map" name="bedtools MapBed" version="@TOOL_VERSION@.2">
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2 <description>apply a function to a column for each overlapping interval</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="stdio" />
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8 <command><![CDATA[
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9 bedtools map
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10 -a '${inputA}'
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11 -b '${inputB}'
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12 $strand
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13 @C_AND_O_ARGUMENT@
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14 @OVERLAP@
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15 #if str($overlapB):
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16 -F $overlapB
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17 #end if
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18 $reciprocal
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19 $split
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20 $header
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21 @GENOME_FILE_MAPBED@
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22 > '${output}'
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23 ]]></command>
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24 <inputs>
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25 <param name="inputA" argument="-a" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="File A (BAM/@STD_BEDTOOLS_INPUT_LABEL@)" />
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26 <param name="inputB" argument="-b" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="File B (BAM/@STD_BEDTOOLS_INPUT_LABEL@)" />
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27 <expand macro="overlap" />
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28 <expand macro="overlap" name="overlapB" argument="-F" fracof="B"/>
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29 <param name="reciprocal" argument="-r" type="boolean" truevalue="-r" falsevalue="" checked="false"
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30 label="Require reciprocal overlap"
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31 help="If set, the overlap between the BAM alignment and the BED interval must affect the above fraction of both the alignment and the BED interval" />
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32 <expand macro="strand2" />
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33 <expand macro="c_and_o_argument">
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34 <param name="col" argument="-c" type="data_column" data_ref="inputB" label="Specify the column(s) from the B file to map onto intervals in A" help="Multiple columns can be specified in a comma-delimited list" />
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35 </expand>
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36 <expand macro="split" />
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37 <expand macro="print_header" />
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38 <conditional name="genome">
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39 <param name="genome_choose" argument="-g" type="select"
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40 label="Specify a genome file the defines the expected chromosome order in the input files." >
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41 <option value="" selected="true">No</option>
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42 <option value="-g">Yes</option>
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43 </param>
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44 <when value="-g">
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45 <expand macro="input_conditional_genome_file" />
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46 </when>
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47 <when value="" />
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48 </conditional>
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49 </inputs>
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50 <outputs>
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51 <data name="output" format_source="inputA" metadata_source="inputA" label="Mapping of ${inputB.name} into ${inputA.name}" />
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52 </outputs>
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53 <tests>
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54 <test>
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55 <param name="inputA" value="mapBed1.bed" ftype="bed" />
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56 <param name="inputB" value="mapBed2.bed" ftype="bed" />
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57 <repeat name="c_and_o_argument_repeat">
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58 <param name="col" value="5" />
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59 <param name="operation" value="mean" />
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60 </repeat>
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61 <output name="output" file="mapBed_result1.bed" ftype="bed" />
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62 </test>
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63 <test>
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64 <param name="inputA" value="mapBed1.bed" ftype="bed" />
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65 <param name="inputB" value="mapBed2.bed" ftype="bed" />
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66 <repeat name="c_and_o_argument_repeat">
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67 <param name="col" value="5" />
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68 <param name="operation" value="collapse" />
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69 </repeat>
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70 <output name="output" file="mapBed_result2.bed" ftype="bed" />
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71 </test>
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72 <test>
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73 <param name="inputA" value="mapBed1.bed" ftype="bed" />
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74 <param name="inputB" value="mapBed2.bed" ftype="bed" />
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75 <repeat name="c_and_o_argument_repeat">
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76 <param name="col" value="5" />
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77 <param name="operation" value="collapse" />
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78 </repeat>
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79 <param name="strand" value="-S" />
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80 <output name="output" file="mapBed_result3.bed" ftype="bed" />
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81 </test>
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82 <test>
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83 <param name="inputA" value="mapBed1.bed" ftype="bed" />
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84 <param name="inputB" value="mapBed2.bed" ftype="bed" />
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85 <repeat name="c_and_o_argument_repeat">
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86 <param name="col" value="5" />
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87 <param name="operation" value="collapse" />
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88 </repeat>
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89 <param name="strand" value="-s" />
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90 <output name="output" file="mapBed_result4.bed" ftype="bed" />
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91 </test>
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92 <test>
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93 <param name="inputA" value="mapBed3.bed" ftype="bed" />
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94 <param name="inputB" value="mapBed4.bed" ftype="bed" />
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95 <repeat name="c_and_o_argument_repeat">
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96 <param name="col" value="5" />
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97 <param name="operation" value="collapse" />
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98 </repeat>
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99 <param name="strand" value="-s" />
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100 <param name="genome_choose" value="-g" />
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101 <param name="genome_file_opts_selector" value="hist" />
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102 <param name="genome" value="mm9.len" ftype="bed" />
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103 <output name="output" file="mapBed_result5.bed" ftype="bed" />
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104 </test>
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105 </tests>
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106 <help><![CDATA[
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107 **What it does**
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108
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109 bedtools map allows one to map overlapping features in a B file onto features in an A file and apply statistics and/or summary operations on those features.
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110
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111 .. image:: $PATH_TO_IMAGES/map-glyph.png
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112
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113 .. class:: infomark
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115 bedtools map requires each input file to be sorted by genome coordinate. For BED files, this can be done with sort -k1,1 -k2,2n. Other sorting criteria are allowed if a genome file (-g) is provides that specifies the expected chromosome order.
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116
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117 .. class:: infomark
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118
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119 The map tool is substantially faster in versions 2.19.0 and later. The plot below demonstrates the increased speed when, for example, counting the number of exome alignments that align to each exon. The bedtools times are compared to the bedops bedmap utility as a point of reference.
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120
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121 @REFERENCES@
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122 ]]></help>
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123 <expand macro="citations" />
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124 </tool>