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1 <tool id="bedtools_genomecoveragebed" name="Genome Coverage" version="@WRAPPER_VERSION@.0">
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2 <description>in bedGraph or histogram format</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 <![CDATA[
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10 bedtools genomecov
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11 #if $input.ext == "bam"
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12 -ibam '$input'
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13 #else
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14 -i '$input'
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15 -g $genome
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16 #end if
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17
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18 $split
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19 $strand
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20
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21 #if str($report.report_select) == "bg":
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22 #if $zero_regions.value:
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23 $zero_regions
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24 #else:
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25 -bg
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26 #end if
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27
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28 #if str($scale):
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29 -scale $scale
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30 #end if
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31 #else:
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32 #if str($report.max):
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33 -max $report.max
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34 #end if
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35 #end if
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36 $d
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37 $dz
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38 $five
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39 $three
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40
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41 > '$output'
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42 ]]>
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43 </command>
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44 <inputs>
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45 <param format="bed,bam" name="input" type="data" label="The BAM or BED file from which coverage should be computed">
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46 <validator type="unspecified_build" />
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47 </param>
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48 <conditional name="report">
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49 <param name="report_select" type="select" label="Output type">
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50 <option value="bg" selected="true">BedGraph coverage file</option>
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51 <option value="hist">Data suiteable for Histogram</option>
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52 </param>
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53 <when value="bg">
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54 <param name="zero_regions" type="boolean" checked="False" truevalue="-bga" falsevalue=""
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55 label="Report regions with zero coverage" help="If set, regions without any coverage will also be reported. (-bga)" />
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56 <param name="scale" type="float" value="1.0"
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57 label="Scale the coverage by a constant factor"
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58 help="Each bedGraph coverage value is multiplied by this factor before being reported. Useful for normalizing coverage by, e.g., reads per million (RPM). (-scale)"/>
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59 </when>
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60 <when value="hist">
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61 <param name="max" type="integer" label="Specify max depth" value="0"
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62 help="Combine all positions with a depth >= max into a single bin in the histogram. (-max)"/>
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63 </when>
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64 </conditional>
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65 <expand macro="genome" />
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66 <expand macro="split" />
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67 <param name="strand" type="select" label="Calculate coverage based on" help="(-strand)">
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68 <option value="">both strands combined</option>
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69 <option value="-strand +">positive strand only</option>
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70 <option value="-strand -">negative strand only</option>
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71 </param>
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72
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73 <param name="d" type="boolean" checked="False" truevalue="-d" falsevalue=""
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74 label="Report the depth at each genome position with 1-based coordinates" help="(-d)" />
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75 <param name="dz" type="boolean" checked="False" truevalue="-dz" falsevalue=""
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76 label="Report the depth at each genome position with 0-based coordinatess" help="(-dz)" />
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77 <param name="five" type="boolean" checked="False" truevalue="-d" falsevalue=""
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78 label="Calculate coverage of 5’ positions" help="Instead of entire interval. (-5)" />
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79 <param name="three" type="boolean" checked="False" truevalue="-3" falsevalue=""
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80 label="Calculate coverage of 3’ positions" help="Instead of entire interval. (-3)" />
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81 </inputs>
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82 <outputs>
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83 <data format="bedgraph" name="output">
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84 <change_format>
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85 <when input="report.report_select" value="hist" format="tabular" />
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86 </change_format>
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87 </data>
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88 </outputs>
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89 <tests>
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90 <test>
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91 <param name="input" value="genomeCoverageBed1.bed" ftype="bed" />
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92 <param name="genome" value="genomeCoverageBed1.len" />
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93 <param name="report_select" value="hist" />
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94 <output name="output" file="genomeCoverageBed_result1.bed" ftype="tabular" />
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95 </test>
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96 </tests>
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97 <help>
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98 <![CDATA[
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99 **What it does**
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100
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101 This tool calculates the genome-wide coverage of intervals defined in a BAM or BED file and reports them in BedGraph format.
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102
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103 .. image:: $PATH_TO_IMAGES/genomecov-glyph.png
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104
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105 .. class:: warningmark
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106
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107 The input BED or BAM file must be sorted by chromosome name (but doesn't necessarily have to be sorted by start position).
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108
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109 -----
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110
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111 **Example 1**
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112
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113 Input (BED format)-
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114 Overlapping, un-sorted intervals::
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115
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116 chr1 140 176
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117 chr1 100 130
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118 chr1 120 147
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119
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120
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121 Output (BedGraph format)-
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122 Sorted, non-overlapping intervals, with coverage value on the 4th column::
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123
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124 chr1 100 120 1
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125 chr1 120 130 2
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126 chr1 130 140 1
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127 chr1 140 147 2
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128 chr1 147 176 1
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129
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130 -----
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131
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132 **Example 2 - with ZERO-Regions selected (assuming hg19)**
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133
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134 Input (BED format)-
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135 Overlapping, un-sorted intervals::
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136
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137 chr1 140 176
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138 chr1 100 130
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139 chr1 120 147
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140
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141
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142 BedGraph output will contain five columns:
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143
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144 * 1. Chromosome name (or 'genome' for whole-genome coverage)
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145 * 2. Coverage depth
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146 * 3. The number of bases on chromosome (or genome) with depth equal to column 2.
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147 * 4. The size of chromosome (or entire genome) in base pairs
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148 * 5. The fraction of bases on chromosome (or entire genome) with depth equal to column 2.
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149
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150 **Example Output**:
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151
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152 chr2L 0 1379895 23011544 0.0599653
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153 chr2L 1 837250 23011544 0.0363839
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154 chr2L 2 904442 23011544 0.0393038
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155 chr2L 3 913723 23011544 0.0397072
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156 chr2L 4 952166 23011544 0.0413778
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157 chr2L 5 967763 23011544 0.0420555
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158 chr2L 6 986331 23011544 0.0428624
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159 chr2L 7 998244 23011544 0.0433801
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160 chr2L 8 995791 23011544 0.0432735
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161 chr2L 9 996398 23011544 0.0432999
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162
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163
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164 @REFERENCES@
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165 ]]>
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166 </help>
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167 <expand macro="citations" />
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168 </tool>
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