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1 <tool id="bedtools_mergebedgraph" name="Merge multiple BedGraph 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">unionBedGraphs</requirement>
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6 </requirements>
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7
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10
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8 <command>unionBedGraphs
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9 $header
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10 -filler '$filler'
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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 $bedgraphs
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19 '${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 $bedgraphs
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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="bedgraph" type="data" label="First BedGraph 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="bedgraph" type="data" label="Second BedGraph 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="bedgraphs" title="Add'l BedGraph files" >
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79 <param name="input" format="bedgraph" type="data" label="BedGraph 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 with zero coverage" help="If set, regions without any coverage will also be reported. Requires a valid organism key for all input datasets" />
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97
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98 <param name="filler" type="text" value="0" label="Text to use for no-coverage value" help="Can be 0.0, N/A, - or any other value." />
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99 </inputs>
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100
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101 <outputs>
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102 <data format="tabular" name="output" metadata_source="input1" label="Merged BedGraphs of ${input1.name}, ${input2.name} and so on." />
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103 </outputs>
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104 <help>
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105
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106 **What it does**
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107
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108 This tool merges multiple BedGraph files, allowing direct and fine-scale coverage comparisons among many samples/files. The BedGraph files need not represent the same intervals; the tool will identify both common and file-specific intervals. In addition, the BedGraph values need not be numeric: one can use any text as the BedGraph value and the tool will compare the values from multiple files.
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109
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110 .. image:: http://people.virginia.edu/~arq5x/files/bedtools-galaxy/ubg.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 BedGraph file is reference-sorted (chrom, then start) and contains non-overlapping intervals (within a given file).
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116
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117 .. class:: warningmark
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118
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119 This tool requires that `bedtools`__ has been installed on your system.
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120
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121 ------
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122
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123 **Example input**::
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124
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125 # 1.bedgraph
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126 chr1 1000 1500 10
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127 chr1 2000 2100 20
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128
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129 # 2.bedgraph
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130 chr1 900 1600 60
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131 chr1 1700 2050 50
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132
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133 # 3.bedgraph
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134 chr1 1980 2070 80
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135 chr1 2090 2100 20
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136
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137
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138 ------
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139
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140 **Examples using the Zero Coverage checkbox**
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141
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142 Output example (*without* checking "Report regions with zero coverage")::
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143
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144 chr1 900 1000 0 60 0
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145 chr1 1000 1500 10 60 0
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146 chr1 1500 1600 0 60 0
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147 chr1 1700 1980 0 50 0
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148 chr1 1980 2000 0 50 80
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149 chr1 2000 2050 20 50 80
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150 chr1 2050 2070 20 0 80
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151 chr1 2070 2090 20 0 0
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152 chr1 2090 2100 20 0 20
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153
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154
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155 Output example (*with* checking "Report regions with zero coverage"). The lines marked with (*) are not covered in any input file, but are still reported (The asterisk marking does not appear in the file).::
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156
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157 chr1 0 900 0 0 0 (*)
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158 chr1 900 1000 0 60 0
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159 chr1 1000 1500 10 60 0
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160 chr1 1500 1600 0 60 0
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161 chr1 1600 1700 0 0 0 (*)
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162 chr1 1700 1980 0 50 0
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163 chr1 1980 2000 0 50 80
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164 chr1 2000 2050 20 50 80
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165 chr1 2050 2070 20 0 80
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166 chr1 2070 2090 20 0 0
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167 chr1 2090 2100 20 0 20
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168 chr1 2100 247249719 0 0 0 (*)
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169
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170
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171 ------
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172
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173 **Examples adjusting the "Filler value" for no-covered intervals**
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174
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175 The default value is '0', but you can use any other value.
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176
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177 Output example with **filler = N/A**::
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178
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179 chr1 900 1000 N/A 60 N/A
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180 chr1 1000 1500 10 60 N/A
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181 chr1 1500 1600 N/A 60 N/A
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182 chr1 1600 1700 N/A N/A N/A
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183 chr1 1700 1980 N/A 50 N/A
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184 chr1 1980 2000 N/A 50 80
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185 chr1 2000 2050 20 50 80
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186 chr1 2050 2070 20 N/A 80
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187 chr1 2070 2090 20 N/A N/A
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188 chr1 2090 2100 20 N/A 20
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189
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190
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191 ------
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192
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193 **Examples using the "sample name" labels**::
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194
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195 chrom start end WT-1 WT-2 KO-1
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196 chr1 900 1000 N/A 60 N/A
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197 chr1 1000 1500 10 60 N/A
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198 chr1 1500 1600 N/A 60 N/A
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199 chr1 1600 1700 N/A N/A N/A
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200 chr1 1700 1980 N/A 50 N/A
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201 chr1 1980 2000 N/A 50 80
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202 chr1 2000 2050 20 50 80
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203 chr1 2050 2070 20 N/A 80
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204 chr1 2070 2090 20 N/A N/A
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205 chr1 2090 2100 20 N/A 20
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206
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207
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208 ------
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209
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210 **Non-numeric values**
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211
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212 The input BedGraph files can contain any kind of value in the fourth column, not necessarily a numeric value.
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213
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214 Input Example::
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215
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216 File-1 File-2
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217 chr1 200 300 Sample1 chr1 100 240 0.75
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218 chr1 400 450 Sample1 chr1 250 700 0.43
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219 chr1 530 600 Sample2
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220
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221 Output Example::
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222
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223 chr1 100 200 0 0.75
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224 chr1 200 240 Sample1 0.75
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225 chr1 240 250 Sample1 0
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226 chr1 250 300 Sample1 0.43
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227 chr1 300 400 0 0.43
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228 chr1 400 450 Sample1 0.43
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229 chr1 450 530 0 0.43
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230 chr1 530 600 Sample2 0.43
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231 chr1 600 700 0 0.43
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232
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233
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234 -----
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235
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236 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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237
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238 .. __: http://code.google.com/p/bedtools/
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239 .. __: http://code.google.com/p/bedtools/
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240 .. __: http://cphg.virginia.edu/quinlan/
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241 .. __: http://bioinformatics.oxfordjournals.org/content/26/6/841.short
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242
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243
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244
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245
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246 </help>
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247 </tool>
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