Mercurial > repos > bgruening > deeptools_bam_coverage

annotate bamCoverage.xml @ 13:892146aaf356 draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 13910e1a5ebcfc740c1bc5e38fc676592ef44f11
author bgruening
date Mon, 15 Feb 2016 10:04:26 -0500
parents 300e98d37770
children b7e2129ad348
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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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12
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13 @BINARY@
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14 @THREADS@
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15
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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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19
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20 --binSize $binSize
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21
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22 #if $scaling.type=='rpkm':
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23 --normalizeUsingRPKM
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24 --scaleFactor $scaling.scaleFactor
0
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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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37
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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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42
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43 @ADVANCED_OPTS_READ_PROCESSING@
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44 $advancedOpt.skipNAs
0
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45
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46 #if str($advancedOpt.ignoreForNormalization).strip() != '':
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47 --ignoreForNormalization $advancedOpt.ignoreForNormalization
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48 #end if
0
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49 #end if
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50 ]]>
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51 </command>
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52
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53 <inputs>
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54 <param name="bamInput" format="bam" type="data" label="BAM file"
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55 help="The BAM file must be sorted."/>
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56
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57 <param name="binSize" type="integer" value="50" min="1"
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58 label="Bin size in bases"
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59 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. "/>
0
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60
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61 <conditional name="scaling">
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62 <param name="type" type="select" label="Scaling/Normalization method" >
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63 <option value="1x">Normalize coverage to 1x</option>
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64 <option value="rpkm">Normalize to fragments (reads) per kilobase per million (RPKM)</option>
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65 <option value="no">Do not normalize or scale</option>
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66 </param>
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67 <when value="rpkm">
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68 <expand macro="scaleFactor" />
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69 </when>
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70 <when value="no"/>
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71 <when value="1x">
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72 <expand macro="effectiveGenomeSize" />
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73 <expand macro="scaleFactor" />
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74 </when>
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75 </conditional>
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76
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77 <param name="outFileFormat" type="select" label="Coverage file format">
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78 <option value="bigwig" selected="true">bigwig</option>
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79 <option value="bedgraph">bedgraph</option>
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80 </param>
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81
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82 <expand macro="region_limit_operation" />
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83
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84 <conditional name="advancedOpt">
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85 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
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86 <option value="no" selected="true">no</option>
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87 <option value="yes">yes</option>
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88 </param>
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89 <when value="no" />
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90 <when value="yes">
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91 <expand macro="smoothLength" />
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92
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93 <param argument="ignoreForNormalization" type="text" value=""
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94 label="Regions that should be excluded for normalization"
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95 help="A list of chromosome names separated by spaces
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96 containing those chromosomes that should be excluded
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97 during normalization. This is useful when
0
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98 considering samples with unequal coverage across
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99 chromosomes, like male and female samples. Example: chrX chrM" />
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100
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101 <expand macro="skipNAs" />
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102 <expand macro="read_processing_options" />
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103
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104 <param argument="--MNase" type="boolean" truevalue="--MNase" falsevalue=""
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105 label="Determine nucleosome positions from MNase-seq data"
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106 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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107
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108 </when>
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109 </conditional>
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110 </inputs>
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111 <outputs>
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112 <data format="bigwig" name="outFileName">
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113 <change_format>
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114 <when input="outFileFormat" value="bigwig" format="bigwig" />
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115 <when input="outFileFormat" value="bedgraph" format="bedgraph" />
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116 </change_format>
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117 </data>
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118 </outputs>
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119 <tests>
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120 <test>
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121 <param name="bamInput" value="bowtie2-test1.bam" ftype="bam" />
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122 <param name="outFileFormat" value="bigwig" />
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123 <param name="showAdvancedOpt" value="no" />
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124 <param name="binSize" value="10" />
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125 <param name="type" value="no" />
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126 <output name="outFileName" file="bamCoverage_result1.bw" ftype="bigwig" />
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127 </test>
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128 <test>
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129 <param name="bamInput" value="bowtie2-test1.bam" ftype="bam" />
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130 <param name="outFileFormat" value="bigwig" />
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131 <param name="showAdvancedOpt" value="no" />
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132 <param name="binSize" value="10" />
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133 <output name="outFileName" file="bamCoverage_result2.bw" ftype="bigwig" />
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134 </test>
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135 <test>
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136 <param name="bamInput" value="bowtie2-test1.bam" ftype="bam" />
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137 <param name="outFileFormat" value="bedgraph" />
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138 <param name="showAdvancedOpt" value="no" />
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139 <param name="binSize" value="10" />
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140 <output name="outFileName" file="bamCoverage_result3.bg" ftype="bedgraph" />
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141 </test>
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142 <test>
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143 <param name="bamInput" value="phiX.bam" ftype="bam" />
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144 <param name="outFileFormat" value="bigwig" />
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145 <param name="showAdvancedOpt" value="no" />
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146 <param name="binSize" value="10" />
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147 <output name="outFileName" file="bamCoverage_result4.bw" ftype="bigwig" />
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148 </test>
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149 <test>
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150 <param name="bamInput" value="phiX.bam" ftype="bam" />
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151 <param name="outFileFormat" value="bedgraph" />
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152 <param name="showAdvancedOpt" value="yes" />
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153 <param name="binSize" value="10" />
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154 <output name="outFileName" file="bamCoverage_result4.bg" ftype="bedgraph" />
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155 </test>
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156 </tests>
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157 <help>
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158 <![CDATA[
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159
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160 What it does
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161 --------------
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162
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163 Given a BAM file, this tool generates a bigWig or bedGraph file of fragment or
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164 read coverages. The way the method works is by first calculating all the
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165 number of reads (either extended to match the fragment length or not) that
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166 overlap each bin in the genome. The resulting read counts can be normalized
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167 using either a given scaling factor, the RPKM formula or to get a 1x depth of
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168 coverage (RPGC). In the case of paired-end mapping, each read mate is treated
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169 independently to avoid a bias when a mixture of concordant and discordant
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170 pairs is present. This means that *each end* will be extended to match the
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171 fragment length.
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172
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173 See the usage hints below.
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174
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175 .. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png
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176 :width: 600
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177 :height: 336
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178
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179 Output
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180 -------------
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181
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182 ``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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183
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184 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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185
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186 .. image:: $PATH_TO_IMAGES/bamCoverage_output.png
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187 :width: 600
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188 :height: 450
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189
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190 Usage hints
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191 ------------
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192
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193 * 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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194 * 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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195 * 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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196 * 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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197 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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198 * 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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199
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200 WARNING: If you already normalized for GC bias using ``correctGCbias``, you should absolutely **NOT** set the parameter ``--ignoreDuplicates``!
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201
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203 -----
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204
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205 @REFERENCES@
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206 ]]>
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207 </help>
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208 <expand macro="citations" />
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209 </tool>