Mercurial > repos > iuc > bedtools

annotate coverageBed.xml @ 48:2f457890d8c8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
author iuc
date Tue, 11 Dec 2018 13:59:34 -0500
parents b176b1c7949e
children df28283b3778
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48
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1 <tool id="bedtools_coveragebed" name="bedtools Compute both the depth and breadth of coverage" version="@WRAPPER_VERSION@">
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2 <description>of features in file B on the features in file A (bedtools coverage)</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 <requirement type="package" version="@SAMTOOLS_VERSION@">samtools</requirement>
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8 </expand>
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9 <expand macro="stdio" />
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10 <command>
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11 <![CDATA[
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12 bedtools coverage
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13 $d
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14 $hist
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15 $split
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16 $strandedness
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17 #if str($overlap_a) != "None" and str($overlap_a):
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18 -f '$overlap_a'
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19 #end if
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20 #if str($overlap_b) != "None" and str($overlap_b):
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21 -F '$overlap_b'
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22 #end if
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23 $reciprocal_overlap
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24 $a_or_b
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25 -a '$inputA'
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26 #if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate':
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27 -b '$reduce_or_iterate.inputB'
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28 #if $reduce_or_iterate.inputB.is_of_type('bam'):
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29 -sorted -g <(samtools view -H $reduce_or_iterate.inputB | grep '^@SQ' | sed $'s/\tSN:/\tSN\t/' | sed $'s/\tLN:/\tLN\t/' | cut -f 3,5)
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30 #end if
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31 #else:
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32 #set inputBs = "' '".join([str($file) for $file in $reduce_or_iterate.inputB])
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33 -b '$inputBs'
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34 #end if
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35 #if $inputA.is_of_type('gff') or $inputA.is_of_type('gff3'):
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36 | sort -k1,1 -k4,2n
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37 #else:
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38 | sort -k1,1 -k2,2n
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39 #end if
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40 > '$output'
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41 ]]>
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42 </command>
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43 <inputs>
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44 <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="File A (on which coverage is calculated)" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format" />
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45 <conditional name="reduce_or_iterate">
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46 <param name='reduce_or_iterate_selector' type='select' label='Combined or separate output files'>
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47 <option value='iterate' selected='true'>One output file per 'input B' file</option>
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48 <option value='reduce'>Single output containing results for all 'input B' files</option>
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49 </param>
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50 <when value='iterate'>
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51 <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputB" type="data"
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52 label="File(s) B (for which coverage is calculated)" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format"/>
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53 </when>
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54 <when value='reduce'>
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55 <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputB" type="data" multiple="true"
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56 label="File(s) B (for which coverage is calculated)" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format"/>
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57 </when>
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58 </conditional>
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59 <expand macro="split" />
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60 <param name="strandedness" type="boolean" label="Force strandedness" truevalue="-s" falsevalue="" checked="false"
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61 help="Only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand (-s)"/>
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62 <param name="d" type="boolean" checked="false" truevalue="-d" falsevalue=""
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63 label="Report the depth at each position in each A feature"
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64 help="Positions reported are one based. Each position and depth follow the complete B feature (-d)" />
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65 <param name="hist" type="boolean" checked="false" truevalue="-hist" falsevalue=""
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66 label="Report a histogram of coverage for each feature in A as well as a summary histogram for all features in A"
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67 help="Additional columns after each feature in A: 1) depth 2) # bases at depth 3) size of A 4) % of A at depth (-hist)" />
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68 <param name="overlap_a" type="text"
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69 label="Minimum overlap required as a fraction of A."
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70 help="Default is 1E-9 (i.e., 1bp). (-f)">
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71 <sanitizer invalid_char="">
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72 <valid initial="string.digits"><add value=",."/></valid>
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73 </sanitizer>
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74 </param>
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75 <param name="overlap_b" type="text"
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76 label="Minimum overlap required as a fraction of B."
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77 help="Default is 1E-9 (i.e., 1bp). (-F)">
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78 <sanitizer invalid_char="">
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79 <valid initial="string.digits"><add value=",."/></valid>
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80 </sanitizer>
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81 </param>
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82 <param name="reciprocal_overlap" type="boolean" checked="false" truevalue="-r" falsevalue=""
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83 label="Require that the fraction overlap be reciprocal for A AND B."
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84 help="if -f is 0.90 and -r is used, this requires that B overlap 90% of A and A _also_ overlaps 90% of B (-r)" />
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85 <param name="a_or_b" type="boolean" checked="false" truevalue="-e" falsevalue=""
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86 label="Require that the minimum fraction be satisfied for A OR B."
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87 help="if -e is used with -f 0.90 and -F 0.10 this requires that either 90% of A is covered OR 10% of B is covered. Without -e, both fractions would have to be satisfied. (-e)" />
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88 </inputs>
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89 <outputs>
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90 <data format="bed" name="output" metadata_source="inputA" label="Count of overlaps on ${inputA.name}"/>
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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="inputA" value="coverageBedA.bed" ftype="bed" />
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95 <param name="inputB" value="coverageBedB.bed" ftype="bed" />
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96 <output name="output" file="coverageBed_result1.bed" ftype="bed" />
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97 </test>
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98 <test>
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99 <param name="inputA" value="multiCov1.bed" ftype="bed" />
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100 <param name="inputB" value="srma_in3.bam" ftype="bam" />
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101 <output name="output" file="multicov1_by_srma_in3.cov.bed" ftype="bed" />
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102 </test>
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103 <test>
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104 <param name="inputA" value="multiCov1.bed" ftype="bed" />
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105 <param name="reduce_or_iterate_selector" value="reduce" />
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106 <param name="inputB" value="srma_in3.bam" ftype="bam" />
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107 <output name="output" file="multicov1_by_srma_in3.cov.bed" ftype="bed" />
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108 </test>
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109 <test>
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110 <param name="inputA" value="coverageBedA.bed" ftype="bed" />
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111 <param name="inputB" value="coverageBedB.bed" ftype="bed" />
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112 <param name="overlap_b" value="1" />
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113 <output name="output" file="coverageBed_result2_F1.bed" ftype="bed" />
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114 </test>
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115 <test>
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116 <param name="inputA" value="coverageBedA.bed" ftype="bed" />
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117 <param name="inputB" value="coverageBedB.bed" ftype="bed" />
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118 <param name="overlap_a" value="1" />
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119 <param name="reciprocal_overlap" value="true" />
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120 <output name="output" file="coverageBed_result3_f1r.bed" ftype="bed" />
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121 </test>
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122 </tests>
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123 <help>
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124 <![CDATA[
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125 **What it does**
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126
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127 `bedtools coverage`_ computes both the *depth* and *breadth* of coverage of features in
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128 file B on the features in file A. For example, ``bedtools coverage`` can compute the coverage of sequence alignments
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129 (file B) across 1 kilobase (arbitrary) windows (file A) tiling a genome of interest.
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130 One advantage that ``bedtools coverage`` offers is that it not only *counts* the number of features that
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131 overlap an interval in file A, it also computes the fraction of bases in the interval in A that were overlapped by one or more features.
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132 Thus, ``bedtools coverage`` also computes the *breadth* of coverage for each interval in A.
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133
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134 .. _bedtools coverage: http://bedtools.readthedocs.org/en/latest/content/tools/coverage.html
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135
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136 .. class:: infomark
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137
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138 The lines in the output will be comprised of each interval in A, followed by:
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139
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140 1. The number of features in B that overlapped (by at least one base pair) the A interval.
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141 2. The number of bases in A that had non-zero coverage from features in B.
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142 3. The length of the entry in A.
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143 4. The fraction of bases in A that had non-zero coverage from features in B.
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144
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145 @REFERENCES@
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146 ]]>
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147 </help>
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148 <expand macro="citations" />
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149 </tool>