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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
author iuc
date Fri, 21 Feb 2025 21:38:34 +0000
parents 9f6bd4c9479f
children
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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="@TOOL_VERSION@">bedtools</requirement>
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5 <yield/>
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6 </requirements>
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7 </xml>
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8 <xml name="bio_tools">
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9 <xrefs>
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10 <xref type="bio.tools">bedtools</xref>
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11 </xrefs>
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12 </xml>
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13 <token name="@TOOL_VERSION@">2.31.1</token>
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14 <token name="@SAMTOOLS_VERSION@">1.9</token>
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15 <token name="@STD_BEDTOOLS_INPUTS@">bed,bedgraph,gff,vcf,encodepeak</token>
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16 <token name="@STD_BEDTOOLS_INPUT_LABEL@">BED/bedGraph/GFF/VCF/EncodePeak</token>
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17 <token name="@PROFILE@">20.05</token>
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18 <xml name="stdio">
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19 <stdio>
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20 <!-- Anything other than zero is an error -->
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21 <exit_code range="1:" />
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22 <exit_code range=":-1" />
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23 <!-- In case the return code has not been set propery check stderr too -->
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24 <regex match="Error:" />
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25 <regex match="Exception:" />
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26 </stdio>
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27 <version_command>bedtools --version</version_command>
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28 </xml>
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29 <xml name="reciprocal">
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30 <param name="reciprocal" argument="-r" type="select" label="Require that the fraction of overlap be reciprocal for A and B" help="In other words, if -f is 0.90 and -r is used, this requires that B overlap at least 90% of A and that A also overlaps at least 90% of B.">
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31 <option value="" selected="true">No</option>
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32 <option value="-r">Yes</option>
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33 </param>
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34 </xml>
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35 <xml name="fraction" token_name="" token_argument="" token_label="" token_help="" >
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36 <param name="@NAME@" argument="@ARGUMENT@" type="float" min="0" max="1" optional="true" label="@LABEL@" help="@HELP@" />
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37 </xml>
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38 <xml name="overlap" token_name="overlap" token_argument="-f" token_fracof="A">
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39 <expand macro="fraction" name="@NAME@" argument="@ARGUMENT@" label="Minimum overlap required as a fraction of @FRACOF@" help="Default is 1E-9, i.e. 1bp."/>
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40 </xml>
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41 <token name="@OVERLAP@"><![CDATA[
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42 #if str($overlap):
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43 -f $overlap
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44 #end if
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45 ]]></token>
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46 <xml name="strand2">
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47 <param name="strand" type="select" label="Calculation based on strandedness?">
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48 <option value="" selected="true">Overlaps on either strand</option>
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49 <option value="-s">Only overlaps occurring on the **same** strand.</option>
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50 <option value="-S">Only overlaps occurring on the **opposite** strand.</option>
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51 </param>
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52 </xml>
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53 <xml name="seed">
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54 <param argument="-seed" type="integer" value="" min="0" optional="true" label="Seed" help="For reproducible 'randomness'"/>
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55 </xml>
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56 <xml name="split">
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57 <param argument="-split" type="boolean" truevalue="-split" falsevalue="" checked="false"
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58 label="Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage."
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59 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." />
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60 </xml>
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61 <xml name="input_conditional_genome_file" token_optional="false" token_help="">
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62 <conditional name="genome_file_opts">
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63 <param name="genome_file_opts_selector" type="select" label="Genome file" help="@HELP@">
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64 <option value="loc" selected="true">Locally installed Genome file</option>
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65 <option value="hist">Genome file from your history</option>
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66 </param>
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67 <when value="loc">
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68 <param name="genome" type="select" optional="@OPTIONAL@" multiple="false" label="Genome file">
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69 <options from_data_table="__dbkeys__" />
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70 </param>
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71 </when>
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72 <when value="hist">
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73 <param name="genome" type="data" optional="@OPTIONAL@" format="tabular" label="Genome file" />
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74 </when>
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75 </conditional>
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76 </xml>
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77 <token name="@GENOME_FILE@">
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78 #if $genome_file_opts.genome
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79 -g
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80 #if $genome_file_opts.genome_file_opts_selector == "loc":
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81 '$genome_file_opts.genome.fields.len_path'
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82 #elif $genome_file_opts.genome_file_opts_selector == "hist":
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83 '$genome_file_opts.genome'
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84 #end if
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85 #end if
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86 </token>
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87 <token name="@GENOME_FILE_MAKEWINDOWS@">
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88 #if $type.type_select == "genome":
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89 #if $type.genome_file_opts.genome_file_opts_selector == "loc":
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90 -g '$type.genome_file_opts.genome.fields.len_path'
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91 #elif $type.genome_file_opts.genome_file_opts_selector == "hist":
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92 -g '$type.genome_file_opts.genome'
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93 #end if
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94 #end if
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95 </token>
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96 <token name="@GENOME_FILE_UNION@">
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97 #if $empty.empty_selector == "-empty":
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98 #if $empty.genome_file_opts.genome_file_opts_selector == "loc":
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99 -g '$empty.genome_file_opts.genome.fields.len_path'
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100 #elif $empty.genome_file_opts.genome_file_opts_selector == "hist":
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101 -g '$empty.genome_file_opts.genome'
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102 #end if
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103 #end if
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104 </token>
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105 <token name="@GENOME_FILE_COVERAGE@">
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106 #if $input_type.input_type_select == "bam":
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107 -ibam '$input_type.input'
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108 #else:
32
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109 -i '$input_type.input'
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110 #if $input_type.genome_file_opts.genome_file_opts_selector == "loc":
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111 -g '$input_type.genome_file_opts.genome.fields.len_path'
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112 #elif $input_type.genome_file_opts.genome_file_opts_selector == "hist":
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113 -g '$input_type.genome_file_opts.genome'
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114 #end if
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115 #end if
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116 </token>
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117 <xml name="closest_D_option">
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118 <param argument="-iu" type="boolean" truevalue="-iu" falsevalue="" checked="false"
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119 label="Ignore features in B that are upstream of features in A"
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120 help="This option requires -D and follows its orientation rules for determining what is 'upstream'" />
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121
50
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122 <param argument="-id" type="boolean" truevalue="-id" falsevalue="" checked="false"
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123 label="Ignore features in B that are downstream of features in A"
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124 help="This option requires -D and follows its orientation rules for determining what is 'downstream'" />
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125
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126 <param argument="-fu" type="boolean" truevalue="-fu" falsevalue="" checked="false"
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127 label="Choose first from features in B that are upstream of features in A"
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128 help="This option requires -D and follows its orientation rules for determining what is 'upstream'" />
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129
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130 <param argument="-fd" type="boolean" truevalue="-fd" falsevalue="" checked="false"
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131 label="Choose first from features in B that are downstream of features in A"
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132 help="This option requires -D and follows its orientation rules for determining what is 'downstream'" />
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133 </xml>
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134 <xml name="addition">
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135 <conditional name="addition">
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136 <param name="addition_select" type="select" label="Choose what you want to do">
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137 <option value="b" selected="true">Increase the @STD_BEDTOOLS_INPUT_LABEL@ entry by the same number base pairs in each direction.</option>
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138 <option value="lr">Increase by Start Coordinate and End Coordinate</option>
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139 </param>
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140 <when value="b">
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141 <param name="b" value="1" label="Number of base pairs" type="integer" />
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142 </when>
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143 <when value="lr">
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144 <param name="l" type="integer" value="0" label="The number of base pairs to subtract from the start coordinate" />
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145 <param name="r" type="integer" value="0" label="The number of base pairs to add to the end coordinate" />
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146 </when>
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147 </conditional>
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148 </xml>
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149 <xml name="print_header">
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150 <param argument="-header" type="boolean" truevalue="-header" falsevalue="" checked="false"
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151 label="Print the header from the A file prior to results" />
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152 </xml>
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153 <!-- TODO this is currently not used, but we should make use of it -->
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154 <xml name="genome_validator">
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155 <validator type="unspecified_build" />
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156 <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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157 </xml>
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158
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159 <!-- ToDo column_picker -->
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160 <xml name="choose_columns">
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161 <param name="cols" argument="-c" type="text" value=""
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162 label="Specify the column(s) that should be summarized"
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163 help="Comma separated">
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164 <sanitizer invalid_char="">
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165 <valid initial="string.digits"><add value=","/></valid>
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166 </sanitizer>
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167 </param>
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168 </xml>
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169
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170 <token name="@C_AND_O_ARGUMENT@">
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171 #set $col = list()
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172 #set $op = list()
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173 #for $item in $c_and_o_argument_repeat:
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174 #silent $col.append( str($item.col) )
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175 #silent $op.append( str($item.operation) )
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176 #end for
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177 #if $col:
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178 -c #echo ','.join($col)#
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179 -o #echo ','.join($op)#
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180 #end if
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181 </token>
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182
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183 <xml name="c_and_o_argument">
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184 <repeat name="c_and_o_argument_repeat" title="Applying operations to columns from merged intervals" min="0">
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185 <yield />
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186 <expand macro="choose_operations">
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187 <expand macro="math_options" />
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188 <expand macro="additional_math_options" />
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189 </expand>
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190 </repeat>
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191 </xml>
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192
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193 <xml name="choose_operations">
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194 <param name="operation" type="select" label="Specify the operation">
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195 <yield />
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196 </param>
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197 </xml>
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198
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199 <xml name="math_options">
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200 <option value="sum" selected="true">Sum - numeric only</option>
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201 <option value="min">Min - numeric only</option>
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202 <option value="max">Max - numeric only</option>
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203 <option value="absmin">AbsMin - numeric only</option>
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204 <option value="absmax">AbsMax - numeric only</option>
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205 <option value="mean">Mean - numeric only</option>
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206 <option value="median">Median - numeric only</option>
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207 <option value="mode">Mode - numeric only</option>
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208 <option value="antimode">Antimode - numeric only</option>
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209 <option value="stdev">Standard deviation - numeric only</option>
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210 <option value="sstdev">Sample standard deviation - numeric only</option>
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211 <option value="collapse">collapse (i.e., print a comma separated list) - numeric or text</option>
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212 </xml>
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213 <xml name="additional_math_options">
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214 <option value="count">Count - numeric or text</option>
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215 <option value="count_disctinct">Count Distinct - numeric or text</option>
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216 <option value="distinct">distinct (i.e., print a comma separated list) - numeric or text</option>
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217 <option value="distinct_sort_num">distinct sorted numerially (i.e., print a comma separated list) - numeric</option>
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218 <option value="distinct_sort_num_desc">distinct sorted numerially descending (i.e., print a comma separated list) - numeric</option>
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219 <option value="distinct_only">delimited list of only unique values - numeric or text</option>
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220 <option value="first">just the first value in the column - numeric or text</option>
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221 <option value="last">just the last value in the column - numeric or text</option>
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222 </xml>
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223 <xml name="sorted">
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224 <!-- -sorted -g -->
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225 <param argument="-sorted" type="boolean" truevalue="-sorted" falsevalue="" checked="false"
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226 label="For coordinate sorted input file the more efficient sweeping algorithm is enabled."/>
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227 </xml>
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228 <token name="@SORTED@">
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229 <![CDATA[
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230 $sorted
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231 #if str($sorted) != '':
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232 #if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate' and $reduce_or_iterate.inputB.is_of_type('bam'):
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233 -g <(samtools view -H $reduce_or_iterate.inputB | tr ':' '\t' | grep SN | cut -f 3,5)
b06c53665eb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
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234 #else if str($reduce_or_iterate.reduce_or_iterate_selector) == 'reduce' and str($reduce_or_iterate.inputB) != 'None' and $reduce_or_iterate.inputB[0].is_of_type('bam'):
b06c53665eb6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
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235 -g <(samtools view -H $reduce_or_iterate.inputB[0] | tr ':' '\t' | grep SN | cut -f 3,5)
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236 #end if
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237 #end if
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238 ]]>
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239 </token>
8
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240 <token name="@REFERENCES@">
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241 <![CDATA[
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242 ------
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243
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244 This tool is part of the `bedtools package`_ from the `Quinlan laboratory`_.
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245
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246 .. _bedtools package: https://github.com/arq5x/bedtools2
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f0aca67fdb71 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 391d2d41095edb2badf70924d3636238453ee377
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247 .. _Quinlan laboratory: http://quinlanlab.org
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248
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249
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250 **Citation**
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251
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252 If you use this tool in Galaxy, please cite:
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253
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254 Bjoern A. Gruening (2014), `Galaxy wrapper <https://github.com/bgruening/galaxytools>`_
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255 ]]>
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256 </token>
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257 <xml name="citations">
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258 <citations>
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259 <citation type="doi">10.1093/bioinformatics/btq033</citation>
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260 <yield />
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261 </citations>
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262 </xml>
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263 </macros>