Mercurial > repos > bgruening > deeptools_bam_coverage

annotate bamCoverage.xml @ 5:5c5c6aff3732 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4b6c1004addf9496c85fb8566173e4f9f9e9d356
author bgruening
date Fri, 18 Mar 2016 08:47:18 -0400
parents 10e697ec9bfb
children 115aa2cbf152
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1 <tool id="deeptools_bam_coverage" name="bamCoverage" version="@WRAPPER_VERSION@.0">
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2 <description>generates a coverage bigWig file from a given BAM file</description>
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3 <macros>
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4 <token name="@BINARY@">bamCoverage</token>
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5 <import>deepTools_macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command>
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9 <![CDATA[
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10 ln -s '$bamInput' one.bam &&
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11 ln -s '${bamInput.metadata.bam_index}' one.bam.bai &&
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13 @BINARY@
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14 @THREADS@
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16 --bam one.bam
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17 --outFileName '$outFileName'
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18 --outFileFormat '$outFileFormat'
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20 --binSize $binSize
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22 #if $scaling.type=='rpkm':
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23 --normalizeUsingRPKM
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24 --scaleFactor $scaling.scaleFactor
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25 #elif $scaling.type=='1x':
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26 #if $scaling.effectiveGenomeSize.effectiveGenomeSize_opt == "specific":
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27 --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize
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28 #else:
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29 --normalizeTo1x $scaling.effectiveGenomeSize.effectiveGenomeSize_opt
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30 #end if
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31 --scaleFactor $scaling.scaleFactor
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32 #end if
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33
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34 #if str($region).strip() != '':
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35 --region '$region'
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36 #end if
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38 #if $advancedOpt.showAdvancedOpt == "yes":
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39 #if $advancedOpt.smoothLength:
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40 --smoothLength '$advancedOpt.smoothLength'
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41 #end if
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43 @ADVANCED_OPTS_READ_PROCESSING@
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44 $advancedOpt.skipNAs
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46 #if str($advancedOpt.ignoreForNormalization).strip() != '':
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47 --ignoreForNormalization $advancedOpt.ignoreForNormalization
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48 #end if
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50 #if str($advancedOpt.filterRNAstrand) != 'no':
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51 --filterRNAstrand '$advancedOpt.filterRNAstrand'
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52 #end if
0
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53 #end if
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54 ]]>
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55 </command>
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56
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57 <inputs>
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58 <param name="bamInput" format="bam" type="data" label="BAM file"
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59 help=""/>
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61 <param name="binSize" type="integer" value="50" min="1"
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62 label="Bin size in bases"
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63 help="The genome will be divided into bins of the specified size. For each bin, the overlaping number of fragments (or reads) will be reported. If only half a fragment overlaps, this fraction will be reported. "/>
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64
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65 <conditional name="scaling">
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66 <param name="type" type="select" label="Scaling/Normalization method" >
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67 <option value="1x">Normalize coverage to 1x</option>
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68 <option value="rpkm">Normalize to fragments (reads) per kilobase per million (RPKM)</option>
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69 <option value="no">Do not normalize or scale</option>
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70 </param>
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71 <when value="rpkm">
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72 <expand macro="scaleFactor" />
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73 </when>
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74 <when value="no"/>
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75 <when value="1x">
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76 <expand macro="effectiveGenomeSize" />
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77 <expand macro="scaleFactor" />
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78 </when>
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79 </conditional>
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80
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81 <param name="outFileFormat" type="select" label="Coverage file format">
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82 <option value="bigwig" selected="true">bigwig</option>
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83 <option value="bedgraph">bedgraph</option>
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84 </param>
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85
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86 <expand macro="region_limit_operation" />
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87
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88 <conditional name="advancedOpt">
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89 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
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90 <option value="no" selected="true">no</option>
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91 <option value="yes">yes</option>
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92 </param>
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93 <when value="no" />
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94 <when value="yes">
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95 <expand macro="smoothLength" />
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96
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97 <param argument="ignoreForNormalization" type="text" value=""
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98 label="Regions that should be excluded for normalization"
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99 help="A list of chromosome names separated by spaces
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100 containing those chromosomes that should be excluded
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101 during normalization. This is useful when
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102 considering samples with unequal coverage across
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103 chromosomes, like male and female samples. Example: chrX chrM" />
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104
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105 <expand macro="skipNAs" />
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106 <expand macro="read_processing_options" />
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107
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108 <param argument="--MNase" type="boolean" truevalue="--MNase" falsevalue=""
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109 label="Determine nucleosome positions from MNase-seq data"
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110 help="Only the 3 nucleotides at the center of each fragment are counted. The fragment ends are defined by the two mate reads. *NOTE*: Requires paired-end data." />
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111
3
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112 <param argument="filterRNAstrand" type="select" label="Only include reads originating from fragments from the forward or reverse strand."
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113 help="By default (the no option), all reads are processed, regardless of the strand they originated from. For RNAseq, it can be useful to separately create bigWig files for the forward or reverse strands.
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114 Note that this tools assumes that a dUTP-based method was used, so fragments will be assigned to the reverse strand if the second read in a pair is reverse complemented.">
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115 <option value="no" selected="true">no</option>
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116 <option value="forward">forward</option>
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117 <option value="reverse">reverse</option>
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118 </param>
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119
0
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120 </when>
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121 </conditional>
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122 </inputs>
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123 <outputs>
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124 <data format="bigwig" name="outFileName">
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125 <change_format>
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126 <when input="outFileFormat" value="bigwig" format="bigwig" />
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127 <when input="outFileFormat" value="bedgraph" format="bedgraph" />
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128 </change_format>
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129 </data>
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130 </outputs>
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131 <tests>
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132 <test>
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133 <param name="bamInput" value="bowtie2-test1.bam" ftype="bam" />
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134 <param name="outFileFormat" value="bigwig" />
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135 <param name="showAdvancedOpt" value="no" />
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136 <param name="binSize" value="10" />
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137 <param name="type" value="no" />
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138 <output name="outFileName" file="bamCoverage_result1.bw" ftype="bigwig" />
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139 </test>
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140 <test>
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141 <param name="bamInput" value="bowtie2-test1.bam" ftype="bam" />
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142 <param name="outFileFormat" value="bigwig" />
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143 <param name="showAdvancedOpt" value="no" />
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144 <param name="binSize" value="10" />
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145 <output name="outFileName" file="bamCoverage_result2.bw" ftype="bigwig" />
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146 </test>
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147 <test>
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148 <param name="bamInput" value="bowtie2-test1.bam" ftype="bam" />
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149 <param name="outFileFormat" value="bedgraph" />
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150 <param name="showAdvancedOpt" value="no" />
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151 <param name="binSize" value="10" />
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152 <output name="outFileName" file="bamCoverage_result3.bg" ftype="bedgraph" />
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153 </test>
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154 <test>
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155 <param name="bamInput" value="phiX.bam" ftype="bam" />
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156 <param name="outFileFormat" value="bigwig" />
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157 <param name="showAdvancedOpt" value="no" />
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158 <param name="binSize" value="10" />
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159 <output name="outFileName" file="bamCoverage_result4.bw" ftype="bigwig" />
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160 </test>
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161 <test>
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162 <param name="bamInput" value="phiX.bam" ftype="bam" />
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163 <param name="outFileFormat" value="bedgraph" />
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164 <param name="showAdvancedOpt" value="yes" />
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165 <param name="binSize" value="10" />
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166 <output name="outFileName" file="bamCoverage_result4.bg" ftype="bedgraph" />
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167 </test>
3
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168 <test>
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169 <param name="bamInput" value="phiX.bam" ftype="bam" />
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170 <param name="outFileFormat" value="bigwig" />
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171 <param name="showAdvancedOpt" value="yes" />
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172 <param name="filterRNAstrand" value="reverse" />
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173 <param name="binSize" value="10" />
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174 <output name="outFileName" file="bamCoverage_result5.bw" ftype="bigwig" />
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175 </test>
0
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176 </tests>
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177 <help>
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178 <![CDATA[
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180 What it does
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181 --------------
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183 Given a BAM file, this tool generates a bigWig or bedGraph file of fragment or
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184 read coverages. The way the method works is by first calculating all the
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185 number of reads (either extended to match the fragment length or not) that
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186 overlap each bin in the genome. The resulting read counts can be normalized
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187 using either a given scaling factor, the RPKM formula or to get a 1x depth of
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188 coverage (RPGC). In the case of paired-end mapping, each read mate is treated
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189 independently to avoid a bias when a mixture of concordant and discordant
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190 pairs is present. This means that *each end* will be extended to match the
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191 fragment length.
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192
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193 See the usage hints below.
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195 .. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png
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196 :width: 600
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197 :height: 336
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199 Output
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200 -------------
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201
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202 ``bamCoverage`` produces a coverage file, either in bigWig or bedGraph format, where for each bin the number of overlapping reads (possibly normalized) is noted.
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204 Like BAM files, bigWig files are compressed, binary files. If you would like to see the coverage values, choose the bedGraph output. For more information on typical NGS file formats, see our `Glossary <http://deeptools.readthedocs.org/en/latest/content/help_glossary.html#file-formats>`_
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206 .. image:: $PATH_TO_IMAGES/bamCoverage_output.png
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207 :width: 600
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208 :height: 450
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210 Usage hints
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211 ------------
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213 * A smaller ``bin size`` value will result in a higher resolution of the coverage track but also in a larger file size.
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214 * The ``1x normalization`` (RPGC) requires the input of a value for the **effective genome size**, which is the mappable part of the reference genome. Of course, this value is species-specific.
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215 * It might be useful for some studies to exclude certain chromosomes in order to avoid biases, e.g. chromosome X for many mammals where the males contain a pair of each autosome, but often only a single X chromosome.
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216 * By default, the read length is **NOT** extended! This is the preferred setting for **spliced-read** data like RNA-seq, where one usually wants to rely on the detected read locations only. A read extension would neglect potential splice sites in the unmapped part of the fragment.
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217 Other data, e.g. ChIP-seq, where fragments are known to map contiuously, should be processed with read extension (``--extendReads [INT]``).
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218 * For paired-end data, the fragment length is generally defined by the two read mates. The user-provided fragment length is only used as a fallback for singletons or mate reads that map too far apart (with a distance greater than four times the fragment length or if the mates are located on different chromosomes).
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220 WARNING: If you already normalized for GC bias using ``correctGCbias``, you should absolutely **NOT** set the parameter ``--ignoreDuplicates``!
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221
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223 -----
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225 @REFERENCES@
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226 ]]>
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227 </help>
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228 <expand macro="citations" />
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229 </tool>