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1 <tool id="bedtools_multiintersectbed" name="Intersect multiple sorted BED files" version="@WRAPPER_VERSION@.0">
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2 <description></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>
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1
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9 <![CDATA[
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10 bedtools multiinter
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11 $header
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1
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12 $cluster
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13 -filler "${filler}"
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14 #if $zero.value == True:
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15 -empty
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1
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16 -g $genome
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0
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17 #end if
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18
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1
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19 #if str($tag.tag_select) == "tag":
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20 #set files = '" "'.join( [ str( $file ) for $file in $tag.inputs ] )
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21 -i "${files}"
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22 #else:
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23 -i
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24 #for $file in $tag.beds:
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25 "${file.input}"
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26 #end for
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27 -names
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28 #for $file in $tag.beds:
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29 "{$file.custom_name}"
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30 #end for
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0
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31 #end if
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32
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1
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33 > '$output'
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34 ]]>
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35 </command>
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36 <inputs>
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1
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37 <conditional name="tag">
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38 <param name="tag_select" type="select" label="Sample name">
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39 <option value="tag" selected="true">Use input's tag</option>
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1
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40 <option value="custom">Enter custom name per file</option>
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0
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41 </param>
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42 <when value="tag">
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1
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43 <param name="inputs" format="bed" type="data" multiple="True" label="BED files" />
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0
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44 </when>
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45 <when value="custom">
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46 <repeat name="beds" title="Add BED files" min="2" >
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47 <param name="input" format="bed" type="data" multiple="True" label="BED file" />
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48 <param name="custom_name" type="text" area="false" label="Custom sample name"/>
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49 </repeat>
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0
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50 </when>
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51 </conditional>
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1
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52 <expand macro="genome" />
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53 <param name="cluster" type="boolean" checked="false" truevalue="-cluster" falsevalue=""
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54 label="Invoke Ryan Layers's clustering algorithm"
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55 help="(-cluster)" />
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56 <param name="zero" type="boolean" checked="true"
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57 label="Report regions that are not covered by any of the files"
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58 help="If set, regions that are not overlapped by any file will also be reported. Requires a valid organism key for all input datasets" />
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59 <param name="filler" type="text" value="N/A"
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60 label="Text to use for no-coverage value"
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61 help="Can be 0.0, N/A, - or any other value. (-filler)" />
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62 <expand macro="print_header" />
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0
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63
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64 </inputs>
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65 <outputs>
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66 <data format="bed" name="output" />
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0
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67 </outputs>
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1
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68 <tests>
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69 <test>
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70 <param name="tag_select" value="tag"/>
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71 <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" />
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72 <param name="zero" value="False"/>
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73 <output name="output" file="multiIntersectBed_result1.bed" ftype="bed" />
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74 </test>
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75 <test>
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76 <param name="tag_select" value="tag"/>
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77 <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" />
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78 <param name="header" value="True"/>
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79 <param name="zero" value="False"/>
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80 <output name="output" file="multiIntersectBed_result2.bed" lines_diff="2" ftype="bed" />
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81 </test>
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82 <test>
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83 <param name="tag_select" value="tag"/>
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84 <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" />
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85 <param name="zero" value="True"/>
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86 <param name="genome" value="multiIntersectBed1.len"/>
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87 <output name="output" file="multiIntersectBed_result3.bed" ftype="bed" />
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88 </test>
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89 </tests>
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90 <help>
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91 <![CDATA[
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92 **What it does**
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93
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94 This tool identifies common intervals among multiple, sorted BED files. Intervals can be common among 0 to N of the N input BED files.
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0
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95
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96
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97 .. class:: warningmark
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98
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99 This tool requires that each BED file is reference-sorted (chrom, then start).
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100
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101
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102 .. class:: infomark
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103
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104 The output file will contain five fixed columns, plus additional columns for each BED file:
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105
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106 * 1. Chromosome name (or 'genome' for whole-genome coverage).
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107 * 2. The zero-based start position of the interval.
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108 * 3. The one-based end position of the interval.
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109 * 4. The number of input files that had at least one feature overlapping this interval.
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110 * 5. A list of input files or labels that had at least one feature overlapping this interval.
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111 * 6. For each input file, an indication (1 = Yes, 0 = No) of whether or not the file had at least one feature overlapping this interval.
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112
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113 ------
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114
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115 **Example input**::
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116
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117 # a.bed
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118 chr1 6 12bed
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0
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119 chr1 10 20
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120 chr1 22 27
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121 chr1 24 30
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122
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123 # b.bed
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124 chr1 12 32
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125 chr1 14 30
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126
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127 # c.bed
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128 chr1 8 15
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129 chr1 10 14
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130 chr1 32 34
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131
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132
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133 ------
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134
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135 **Example without a header and without reporting intervals with zero coverage**::
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136
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137
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138 chr1 6 8 1 1 1 0 0
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139 chr1 8 12 2 1,3 1 0 1
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140 chr1 12 15 3 1,2,3 1 1 1
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141 chr1 15 20 2 1,2 1 1 0
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142 chr1 20 22 1 2 0 1 0
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143 chr1 22 30 2 1,2 1 1 0
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144 chr1 30 32 1 2 0 1 0
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145 chr1 32 34 1 3 0 0 1
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146
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147
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148 **Example adding a header line**::
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149
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150
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151 chrom start end num list a.bed b.bed c.bed
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152 chr1 6 8 1 1 1 0 0
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153 chr1 8 12 2 1,3 1 0 1
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154 chr1 12 15 3 1,2,3 1 1 1
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155 chr1 15 20 2 1,2 1 1 0
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156 chr1 20 22 1 2 0 1 0
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157 chr1 22 30 2 1,2 1 1 0
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158 chr1 30 32 1 2 0 1 0
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159 chr1 32 34 1 3 0 0 1
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160
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161
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162 **Example adding a header line and custom file labels**::
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163
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164
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165 chrom start end num list joe bob sue
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166 chr1 6 8 1 joe 1 0 0
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167 chr1 8 12 2 joe,sue 1 0 1
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168 chr1 12 15 3 joe,bob,sue 1 1 1
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169 chr1 15 20 2 joe,bob 1 1 0
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170 chr1 20 22 1 bob 0 1 0
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171 chr1 22 30 2 joe,bob 1 1 0
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172 chr1 30 32 1 bob 0 1 0
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173 chr1 32 34 1 sue 0 0 1
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174
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175
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176 @REFERENCES@
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177 ]]>
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178 </help>
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179 <expand macro="citations" />
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180 </tool>
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