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1 <tool id="bedtools_multiintersectbed" name="Identify common intervals among multiple BED files." version="0.1.0">
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2 <description></description>
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11
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3
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4 <requirements>
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5 <requirement type="binary">multiIntersectBed</requirement>
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6 </requirements>
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7
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10
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8 <command>multiIntersectBed
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9 $header
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10 #if $zero.value == True:
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11 -empty
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12 -g ${chromInfo}
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13 #end if
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14
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15 -i '$input1'
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16 '$input2'
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17 #for $q in $beds
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18 '${q.input}'
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19 #end for
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20
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21 -names
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22 #if $name1.choice == "tag":
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23 '${input1.name}'
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24 #else
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25 '${name1.custom_name}'
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26 #end if
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27
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28 #if $name2.choice == "tag":
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29 '${input2.name}'
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30 #else
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31 '${name2.custom_name}'
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32 #end if
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33
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34 #for $q in $beds
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35 #if $q.name.choice == "tag":
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36 '${q.input.name}'
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37 #else
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38 '${q.input.custom_name}'
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39 #end if
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40 #end for
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41 > '$output'
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42 </command>
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43
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44 <inputs>
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45 <!-- Make it easy for the user, first two input files are always shown -->
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46 <!-- INPUT 1 -->
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47 <param name="input1" format="bed" type="data" label="First sorted BED file" />
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48
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49 <conditional name="name1">
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50 <param name="choice" type="select" label="Sample name">
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51 <option value="tag" selected="true">Use input's tag</option>
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52 <option value="custom">Enter custom table name</option>
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53 </param>
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54 <when value="tag">
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55 </when>
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56 <when value="custom">
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57 <param name="custom_name" type="text" area="false" label="Custom sample name"/>
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58 </when>
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59 </conditional>
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60
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61 <!-- INPUT 2 -->
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62 <param name="input2" format="bed" type="data" label="Second sorted BED file" />
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63
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64 <conditional name="name2">
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65 <param name="choice" type="select" label="Sample name">
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66 <option value="tag" selected="true">Use input's tag</option>
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67 <option value="custom">Enter custom table name</option>
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68 </param>
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69 <when value="tag">
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70 </when>
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71 <when value="custom">
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72 <param name="custom_name" type="text" area="false" label="Custom sample name"/>
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73 </when>
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74 </conditional>
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75
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76 <!-- Additional files, if the user needs more -->
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77 <repeat name="beds" title="Add'l sorted BED files" >
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78 <param name="input" format="bed" type="data" label="BED file" />
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79
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80 <conditional name="name">
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81 <param name="choice" type="select" label="Sample name">
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82 <option value="tag" selected="true">Use input's tag</option>
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83 <option value="custom">Enter custom table name</option>
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84 </param>
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85 <when value="tag">
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86 </when>
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87 <when value="custom">
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88 <param name="custom_name" type="text" area="false" label="Custom sample name"/>
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89 </when>
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90 </conditional>
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91 </repeat>
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92
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93 <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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94
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95 <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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96
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97 </inputs>
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98
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99 <outputs>
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100 <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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101 </outputs>
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102 <help>
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103
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104 **What it does**
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105
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106 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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107
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108
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109 .. image:: http://people.virginia.edu/~arq5x/files/bedtools-galaxy/mbi.png
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110
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111
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112 .. class:: warningmark
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113
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114 This tool requires that each BED file is reference-sorted (chrom, then start).
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115
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116 .. class:: warningmark
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117
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118 This tool requires that `bedtools`__ has been installed on your system.
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119
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120 .. class:: infomark
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121
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122 The output file will contain five fixed columns, plus additional columns for each BED file:
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123
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124 * 1. Chromosome name (or 'genome' for whole-genome coverage).
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125 * 2. The zero-based start position of the interval.
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126 * 3. The one-based end position of the interval.
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127 * 4. The number of input files that had at least one feature overlapping this interval.
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128 * 5. A list of input files or labels that had at least one feature overlapping this interval.
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129 * 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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130
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131 ------
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132
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133 **Example input**::
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134
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135 # a.bed
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136 chr1 6 12
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137 chr1 10 20
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138 chr1 22 27
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139 chr1 24 30
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140
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141 # b.bed
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142 chr1 12 32
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143 chr1 14 30
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144
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145 # c.bed
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146 chr1 8 15
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147 chr1 10 14
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148 chr1 32 34
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149
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150
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151 ------
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152
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153 **Example without a header and without reporting intervals with zero coverage**::
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154
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155
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156 chr1 6 8 1 1 1 0 0
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157 chr1 8 12 2 1,3 1 0 1
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158 chr1 12 15 3 1,2,3 1 1 1
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159 chr1 15 20 2 1,2 1 1 0
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160 chr1 20 22 1 2 0 1 0
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161 chr1 22 30 2 1,2 1 1 0
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162 chr1 30 32 1 2 0 1 0
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163 chr1 32 34 1 3 0 0 1
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164
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165
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166 **Example adding a header line**::
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167
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168
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169 chrom start end num list a.bed b.bed c.bed
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170 chr1 6 8 1 1 1 0 0
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171 chr1 8 12 2 1,3 1 0 1
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172 chr1 12 15 3 1,2,3 1 1 1
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173 chr1 15 20 2 1,2 1 1 0
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174 chr1 20 22 1 2 0 1 0
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175 chr1 22 30 2 1,2 1 1 0
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176 chr1 30 32 1 2 0 1 0
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177 chr1 32 34 1 3 0 0 1
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178
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179
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180 **Example adding a header line and custom file labels**::
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181
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182
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183 chrom start end num list joe bob sue
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184 chr1 6 8 1 joe 1 0 0
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185 chr1 8 12 2 joe,sue 1 0 1
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186 chr1 12 15 3 joe,bob,sue 1 1 1
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187 chr1 15 20 2 joe,bob 1 1 0
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188 chr1 20 22 1 bob 0 1 0
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189 chr1 22 30 2 joe,bob 1 1 0
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190 chr1 30 32 1 bob 0 1 0
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191 chr1 32 34 1 sue 0 0 1
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192
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193
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194 -----
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195
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196
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197 This tool is part of the `bedtools package`__ from the `Quinlan laboratory`__. If you use this tool, please cite `Quinlan AR, and Hall I.M. BEDTools: A flexible framework for comparing genomic features. Bioinformatics, 2010, 26, 6.`__
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198
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199 .. __: http://code.google.com/p/bedtools/
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200 .. __: http://code.google.com/p/bedtools/
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201 .. __: http://cphg.virginia.edu/quinlan/
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202 .. __: http://bioinformatics.oxfordjournals.org/content/26/6/841.short
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203
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204
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205
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206
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207 </help>
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208 </tool>
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