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1 <tool id="bedtools_genomecoveragebed" name="BedTools Genome Coverage" version="@TOOL_VERSION@" profile="@PROFILE@">
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2 <description>Compute Read Coverage Over An Entire Genome</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="bio_tools" />
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7 <expand macro="requirements" />
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8 <expand macro="stdio" />
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9 <command><![CDATA[
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10 bedtools genomecov
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11 @GENOME_FILE_COVERAGE@
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12
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13 $split
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14 $strand
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15
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16 #if str($report.report_select) == "bg":
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17 #if $report.zero_regions:
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18 $report.zero_regions
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19 #else:
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20 -bg
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21 #end if
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22
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23 #if str($report.scale):
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24 -scale $report.scale
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25 #end if
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26 #else:
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27 #if str($report.max):
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28 -max $report.max
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29 #end if
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30 #end if
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31 $d
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32 $dz
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33 $five
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34 $three
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14
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35 | sort -k1,1 -k2,2n > '$output'
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13
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36 ]]>
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14
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37 </command>
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3
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38 <inputs>
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39 <conditional name="input_type">
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40 <param name="input_type_select" type="select" label="Input type">
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41 <option value="bed">@STD_BEDTOOLS_INPUT_LABEL@</option>
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42 <option value="bam" selected='true'>BAM</option>
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43 </param>
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44 <when value="bed">
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45 <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
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46 <expand macro="input_conditional_genome_file" />
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47 </when>
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48 <when value="bam">
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49 <param name="input" argument="-ibam" type="data" format="bam" label="BAM file" />
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50 </when>
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51 </conditional>
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52 <conditional name="report">
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53 <param name="report_select" type="select" label="Output type">
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54 <option value="bg" selected="true">BedGraph coverage file</option>
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55 <option value="hist">Data suiteable for Histogram</option>
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56 </param>
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57 <when value="bg">
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58 <param name="zero_regions" argument="-bga" type="boolean" truevalue="-bga" falsevalue="" checked="false"
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59 label="Report regions with zero coverage" help="If set, regions without any coverage will also be reported" />
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60 <param argument="-scale" type="float" value="1.0"
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61 label="Scale the coverage by a constant factor"
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62 help="Each bedGraph coverage value is multiplied by this factor before being reported. Useful for normalizing coverage by, e.g., reads per million (RPM)." />
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63 </when>
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64 <when value="hist">
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65 <param argument="-max" type="integer" value="0" label="Specify max depth"
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66 help="Combine all positions with a depth >= max into a single bin in the histogram" />
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67 </when>
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68 </conditional>
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69 <expand macro="split" />
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70 <param argument="-strand" type="select" label="Calculate coverage based on">
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71 <option value="">both strands combined</option>
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72 <option value="-strand +">positive strand only</option>
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73 <option value="-strand -">negative strand only</option>
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74 </param>
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75
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76 <param argument="-d" type="boolean" truevalue="-d" falsevalue="" checked="false"
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77 label="Report the depth at each genome position with 1-based coordinates" />
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78 <param argument="-dz" type="boolean" truevalue="-dz" falsevalue="" checked="false"
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79 label="Report the depth at each genome position with 0-based coordinatess" />
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80 <param name="five" argument="-5" type="boolean" truevalue="-5" falsevalue="" checked="false"
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81 label="Calculate coverage of 5’ positions" help="Instead of entire interval" />
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82 <param name="three" argument="-3" type="boolean" truevalue="-3" falsevalue="" checked="false"
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83 label="Calculate coverage of 3’ positions" help="Instead of entire interval" />
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84 </inputs>
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85 <outputs>
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9
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86 <data name="output" format="bed">
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3
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87 <change_format>
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88 <when input="report.report_select" value="hist" format="tabular" />
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89 </change_format>
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90 </data>
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91 </outputs>
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92 <tests>
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93 <test>
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94 <param name="input_type_select" value="bed" />
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95 <param name="input" value="genomeCoverageBed1.bed" ftype="bed" />
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96 <param name="genome_file_opts_selector" value="hist" />
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97 <param name="genome" value="genomeCoverageBed1.len" ftype="tabular" />
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98 <param name="report_select" value="hist" />
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99 <output name="output" file="genomeCoverageBed_result1.bed" ftype="tabular" />
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100 </test>
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101 </tests>
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102 <help><![CDATA[
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103 **What it does**
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104
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105 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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106
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107 .. image:: $PATH_TO_IMAGES/genomecov-glyph.png
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108
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109 .. class:: warningmark
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110
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111 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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112
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113 -----
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114
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115 **Example 1**
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116
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117 Input (BED format)-
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118 Overlapping, un-sorted intervals::
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119
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120 chr1 140 176
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121 chr1 100 130
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122 chr1 120 147
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123
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124
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125 Output (BedGraph format)-
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126 Sorted, non-overlapping intervals, with coverage value on the 4th column::
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127
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128 chr1 100 120 1
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129 chr1 120 130 2
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130 chr1 130 140 1
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131 chr1 140 147 2
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132 chr1 147 176 1
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133
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134 -----
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135
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136 **Example 2 - with ZERO-Regions selected (assuming hg19)**
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137
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138 Input (BED format)-
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139 Overlapping, un-sorted intervals::
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140
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141 chr1 140 176
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142 chr1 100 130
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143 chr1 120 147
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144
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145
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146 BedGraph output will contain five columns:
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147
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148 * 1. Chromosome name (or 'genome' for whole-genome coverage)
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149 * 2. Coverage depth
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150 * 3. The number of bases on chromosome (or genome) with depth equal to column 2.
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151 * 4. The size of chromosome (or entire genome) in base pairs
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152 * 5. The fraction of bases on chromosome (or entire genome) with depth equal to column 2.
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153
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154 **Example Output**:
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155
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156 chr2L 0 1379895 23011544 0.0599653
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157 chr2L 1 837250 23011544 0.0363839
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158 chr2L 2 904442 23011544 0.0393038
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159 chr2L 3 913723 23011544 0.0397072
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160 chr2L 4 952166 23011544 0.0413778
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161 chr2L 5 967763 23011544 0.0420555
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162 chr2L 6 986331 23011544 0.0428624
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163 chr2L 7 998244 23011544 0.0433801
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164 chr2L 8 995791 23011544 0.0432735
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165 chr2L 9 996398 23011544 0.0432999
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166
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167
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168 @REFERENCES@
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169 ]]></help>
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170 <expand macro="citations" />
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171 </tool>
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