Mercurial > repos > pimarin > bedtools

annotate coverageBed.xml @ 0:4cacc5b8001b draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
author pimarin
date Thu, 23 Feb 2023 09:50:24 +0000
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0
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1 <tool id="bedtools_coveragebed" name="bedtools Compute both the depth and breadth of coverage" version="@TOOL_VERSION@" profile="@PROFILE@">
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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="bio_tools" />
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7 <expand macro="requirements">
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8 <requirement type="package" version="@SAMTOOLS_VERSION@">samtools</requirement>
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9 </expand>
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10 <expand macro="stdio" />
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11 <command><![CDATA[
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12 bedtools coverage
4cacc5b8001b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools
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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 $mean
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18 #if str($overlap_a):
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19 -f $overlap_a
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20 #end if
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21 #if str($overlap_b):
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22 -F $overlap_b
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23 #end if
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24 $reciprocal_overlap
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25 $a_or_b
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26 -a '$inputA'
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27 #if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate':
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28 -b '$reduce_or_iterate.inputB'
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29 #else:
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30 -b
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31 #for $file in $reduce_or_iterate.inputB
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32 '$file'
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33 #end for
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34 #end if
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35 @SORTED@
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36 #if $inputA.is_of_type('gff'):
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37 | sort -k1,1 -k4,2n
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38 #else:
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39 | sort -k1,1 -k2,2n
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40 #end if
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41 > '$output'
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42 ]]></command>
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43 <inputs>
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44 <param name="inputA" argument="-a" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" 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 name="inputB" argument="-b" type="data" format="bam,@STD_BEDTOOLS_INPUTS@"
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52 label="File 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 name="inputB" argument="-b" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" 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" argument="-s" 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"/>
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62 <param argument="-d" type="boolean" truevalue="-d" falsevalue="" checked="false"
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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" />
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65 <param argument="-hist" type="boolean" truevalue="-hist" falsevalue="" checked="false"
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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" />
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68 <param name="mean" argument="-mean" type="boolean" label="Mean depth" truevalue="-mean" falsevalue="" checked="false"
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69 help="Report the mean depth of all positions in each A feature."/>
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70 <expand macro="overlap" name="overlap_a" />
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71 <expand macro="overlap" name="overlap_b" argument="-F" fracof="B" />
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72 <param name="reciprocal_overlap" argument="-r" type="boolean" truevalue="-r" falsevalue="" checked="false"
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73 label="Require that the fraction overlap be reciprocal for A AND B."
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74 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" />
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75 <param name="a_or_b" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="false"
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76 label="Require that the minimum fraction be satisfied for A OR B."
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77 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" />
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78 <!-- -sorted -g -->
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79 <expand macro="sorted" />
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80 </inputs>
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81 <outputs>
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82 <data name="output" format="bed" metadata_source="inputA" label="Count of overlaps on ${inputA.name}"/>
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83 </outputs>
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84 <tests>
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85 <test>
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86 <param name="inputA" value="coverageBedA.bed" ftype="bed" />
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87 <param name="inputB" value="coverageBedB.bed" ftype="bed" />
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88 <output name="output" file="coverageBed_result1.bed" ftype="bed" />
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89 </test>
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90 <test>
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91 <param name="inputA" value="multiCov1.bed" ftype="bed" />
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92 <param name="inputB" value="srma_in3.bam" ftype="bam" />
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93 <param name="sorted" value="true"/>
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94 <output name="output" file="multicov1_by_srma_in3.cov.bed" ftype="bed" />
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95 </test>
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96 <test>
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97 <param name="inputA" value="multiCov1.bed" ftype="bed" />
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98 <param name="reduce_or_iterate_selector" value="reduce" />
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99 <param name="inputB" value="srma_in3.bam" ftype="bam" />
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100 <param name="sorted" value="true"/>
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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="coverageBedA.bed" ftype="bed" />
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105 <param name="inputB" value="coverageBedB.bed" ftype="bed" />
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106 <param name="overlap_b" value="1" />
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107 <output name="output" file="coverageBed_result2_F1.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_a" value="1E-5" />
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113 <param name="reciprocal_overlap" value="true" />
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114 <output name="output" file="coverageBed_result3_f1r.bed" ftype="bed" />
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115 </test>
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116 <test>
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117 <param name="inputA" value="multiCov1.bed" ftype="bed" />
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118 <param name="reduce_or_iterate_selector" value="reduce" />
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119 <param name="inputB" value="srma_in3.bam,coverageBed.bam" ftype="bam" />
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120 <param name="sorted" value="true"/>
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121 <output name="output" file="coverageBed_result4_2bam.bed" ftype="bed" />
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122 </test>
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123 <test>
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124 <param name="inputA" value="coverageBedA2.bed" ftype="bed" />
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125 <param name="inputB" value="coverageBed.bam" ftype="bam" />
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126 <output name="output" file="coverageBed_result5_unsorted.bed" ftype="bed" />
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127 </test>
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128 <test>
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129 <param name="inputA" value="coverageBedA2.bed" ftype="bed" />
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130 <param name="inputB" value="coverageBed.bam" ftype="bam" />
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131 <param name="mean" value="true"/>
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132 <output name="output" file="mean_coverage.bed" ftype="bed" />
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133 </test>
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134 </tests>
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135 <help><![CDATA[
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136 **What it does**
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137
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138 `bedtools coverage`_ computes both the *depth* and *breadth* of coverage of features in
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139 file B on the features in file A. For example, ``bedtools coverage`` can compute the coverage of sequence alignments
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140 (file B) across 1 kilobase (arbitrary) windows (file A) tiling a genome of interest.
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141 One advantage that ``bedtools coverage`` offers is that it not only *counts* the number of features that
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142 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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143 Thus, ``bedtools coverage`` also computes the *breadth* of coverage for each interval in A.
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144
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145 .. _bedtools coverage: http://bedtools.readthedocs.org/en/latest/content/tools/coverage.html
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146
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147 .. class:: infomark
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148
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149 The lines in the output will be comprised of each interval in A, followed by:
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150
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151 1. The number of features in B that overlapped (by at least one base pair) the A interval.
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152 2. The number of bases in A that had non-zero coverage from features in B.
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153 3. The length of the entry in A.
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154 4. The fraction of bases in A that had non-zero coverage from features in B.
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155
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156 @REFERENCES@
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157 ]]></help>
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158 <expand macro="citations" />
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159 </tool>