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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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9 multiIntersectBed
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10 $header
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11 #if $zero.value == True:
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12 -empty
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13 -g ${chromInfo}
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14 #end if
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15
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16 -i '$input1'
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17 '$input2'
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18 #for $q in $beds
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19 '${q.input}'
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20 #end for
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21
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22 -names
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23 #if $name1.choice == "tag":
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24 '${input1.name}'
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25 #else
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26 '${name1.custom_name}'
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27 #end if
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28
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29 #if $name2.choice == "tag":
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30 '${input2.name}'
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31 #else
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32 '${name2.custom_name}'
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33 #end if
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34
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35 #for $q in $beds
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36 #if $q.name.choice == "tag":
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37 '${q.input.name}'
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38 #else
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39 '${q.input.custom_name}'
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40 #end if
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41 #end for
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42 > '$output'
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43 </command>
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44
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45 <inputs>
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46 <!-- Make it easy for the user, first two input files are always shown -->
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47 <!-- INPUT 1 -->
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48 <param name="input1" format="bed" type="data" label="First sorted BED file" />
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49
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50 <conditional name="name1">
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51 <param name="choice" type="select" label="Sample name">
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52 <option value="tag" selected="true">Use input's tag</option>
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53 <option value="custom">Enter custom table name</option>
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54 </param>
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55 <when value="tag">
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56 </when>
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57 <when value="custom">
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58 <param name="custom_name" type="text" area="false" label="Custom sample name"/>
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59 </when>
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60 </conditional>
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61
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62 <!-- INPUT 2 -->
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63 <param name="input2" format="bed" type="data" label="Second sorted BED file" />
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64
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65 <conditional name="name2">
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66 <param name="choice" type="select" label="Sample name">
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67 <option value="tag" selected="true">Use input's tag</option>
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68 <option value="custom">Enter custom table name</option>
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69 </param>
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70 <when value="tag">
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71 </when>
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72 <when value="custom">
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73 <param name="custom_name" type="text" area="false" label="Custom sample name"/>
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74 </when>
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75 </conditional>
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76
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77 <!-- Additional files, if the user needs more -->
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78 <repeat name="beds" title="Add'l sorted BED files" >
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79 <param name="input" format="bed" type="data" label="BED file" />
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80
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81 <conditional name="name">
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82 <param name="choice" type="select" label="Sample name">
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83 <option value="tag" selected="true">Use input's tag</option>
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84 <option value="custom">Enter custom table name</option>
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85 </param>
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86 <when value="tag">
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87 </when>
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88 <when value="custom">
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89 <param name="custom_name" type="text" area="false" label="Custom sample name"/>
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90 </when>
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91 </conditional>
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92 </repeat>
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93
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94 <param name="header" type="boolean" checked="true" truevalue="-header" falsevalue="" label="Print header line" help="The first line will include the name of each sample." />
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95
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96 <param name="zero" type="boolean" checked="true" label="Report regions that are not covered by any of the files" 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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97
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98 </inputs>
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99
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100 <outputs>
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101 <data format="tabular" name="output" metadata_source="input1" label="Common intervals identified from among ${input1.name}, ${input2.name} and so on." />
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102 </outputs>
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103 <help>
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104
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105 **What it does**
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106
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107 This tool identifies common intervals among multiple, sorted BED files. Intervals can be common among 0 to N of the N input BED files. The pictorial and raw data examples below illustrate the behavior of this tool more clearly.
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108
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109
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110 .. image:: http://people.virginia.edu/~arq5x/files/bedtools-galaxy/mbi.png
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111
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112
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113 .. class:: warningmark
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114
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115 This tool requires that each BED file is reference-sorted (chrom, then start).
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116
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117
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118 .. class:: infomark
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119
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120 The output file will contain five fixed columns, plus additional columns for each BED file:
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121
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122 * 1. Chromosome name (or 'genome' for whole-genome coverage).
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123 * 2. The zero-based start position of the interval.
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124 * 3. The one-based end position of the interval.
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125 * 4. The number of input files that had at least one feature overlapping this interval.
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126 * 5. A list of input files or labels that had at least one feature overlapping this interval.
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127 * 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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128
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129 ------
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130
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131 **Example input**::
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132
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133 # a.bed
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134 chr1 6 12
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135 chr1 10 20
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136 chr1 22 27
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137 chr1 24 30
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138
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139 # b.bed
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140 chr1 12 32
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141 chr1 14 30
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142
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143 # c.bed
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144 chr1 8 15
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145 chr1 10 14
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146 chr1 32 34
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147
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148
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149 ------
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150
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151 **Example without a header and without reporting intervals with zero coverage**::
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152
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153
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154 chr1 6 8 1 1 1 0 0
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155 chr1 8 12 2 1,3 1 0 1
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156 chr1 12 15 3 1,2,3 1 1 1
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157 chr1 15 20 2 1,2 1 1 0
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158 chr1 20 22 1 2 0 1 0
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159 chr1 22 30 2 1,2 1 1 0
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160 chr1 30 32 1 2 0 1 0
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161 chr1 32 34 1 3 0 0 1
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162
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163
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164 **Example adding a header line**::
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165
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166
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167 chrom start end num list a.bed b.bed c.bed
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168 chr1 6 8 1 1 1 0 0
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169 chr1 8 12 2 1,3 1 0 1
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170 chr1 12 15 3 1,2,3 1 1 1
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171 chr1 15 20 2 1,2 1 1 0
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172 chr1 20 22 1 2 0 1 0
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173 chr1 22 30 2 1,2 1 1 0
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174 chr1 30 32 1 2 0 1 0
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175 chr1 32 34 1 3 0 0 1
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176
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177
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178 **Example adding a header line and custom file labels**::
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179
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180
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181 chrom start end num list joe bob sue
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182 chr1 6 8 1 joe 1 0 0
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183 chr1 8 12 2 joe,sue 1 0 1
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184 chr1 12 15 3 joe,bob,sue 1 1 1
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185 chr1 15 20 2 joe,bob 1 1 0
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186 chr1 20 22 1 bob 0 1 0
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187 chr1 22 30 2 joe,bob 1 1 0
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188 chr1 30 32 1 bob 0 1 0
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189 chr1 32 34 1 sue 0 0 1
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190
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191
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192 @REFERENCES@
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193
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194 </help>
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195 </tool>
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