Mercurial > repos > bgruening > deeptools_bam_compare

annotate bamCompare.xml @ 0:105b9da2445c draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 0a9265a12a303b54cdaa974e82e87c2ac60962ee-dirty
author bgruening
date Mon, 25 Jan 2016 20:25:37 -0500
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children e237a134059a
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1 <tool id="deeptools_bam_compare" name="bamCompare" version="@WRAPPER_VERSION@.0">
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2 <description>normalizes and compares two BAM files to obtain the ratio, log2ratio or difference between them</description>
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3 <macros>
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4 <token name="@BINARY@">bamCompare</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 '$bamFile1' one.bam &&
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11 ln -s '${bamFile1.metadata.bam_index}' one.bam.bai &&
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12 ln -s '$bamFile2' two.bam &&
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13 ln -s '${bamFile2.metadata.bam_index}' two.bam.bai &&
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15 @BINARY@
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16 @THREADS@
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17 --bamfile1 one.bam
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18 --bamfile2 two.bam
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19
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20 --outFileName '$outFileName'
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21 --outFileFormat '$outFileFormat'
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22
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23 --binSize $binSize
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24
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25 #if $scaling.method == 'SES':
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26 --scaleFactorsMethod SES
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27 --sampleLength $scaling.sampleLength
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28 --numberOfSamples $scaling.numberOfSamples
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29 #elif $scaling.method == 'readCount':
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30 --scaleFactorsMethod readCount
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31 #elif $scaling.method == 'own':
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32 --scaleFactors '$scaling.scaleFactor1:$scaling.scaleFactor2'
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33 #end if
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34
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35 --ratio $comparison.type
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36
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37 #if $comparison.type == 'subtract':
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38 #if $comparison.normalization.type == 'rpkm':
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39 --normalizeUsingRPKM
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40 #elif $comparison.normalization.type == '1x':
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41
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42 #if $comparison.normalization.effectiveGenomeSize.effectiveGenomeSize_opt == "specific":
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43 --normalizeTo1x $comparison.normalization.effectiveGenomeSize.effectiveGenomeSize
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44 #else:
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45 --normalizeTo1x $comparison.normalization.effectiveGenomeSize.effectiveGenomeSize_opt
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46 #end if
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47
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48 #end if
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49 #elif $comparison.type in ['ratio','log2']:
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50 --pseudocount $comparison.pseudocount
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51 #end if
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52
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53 #if str($region).strip() != '':
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54 --region '$region'
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55 #end if
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56
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57 #if $advancedOpt.showAdvancedOpt == "yes":
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58 #if $advancedOpt.smoothLength:
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59 --smoothLength '$advancedOpt.smoothLength'
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60 #end if
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61
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62 @ADVANCED_OPTS_READ_PROCESSING@
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63 $advancedOpt.skipNAs
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64
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65 #if str($advancedOpt.ignoreForNormalization).strip() != '':
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66 --ignoreForNormalization '$advancedOpt.ignoreForNormalization'
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67 #end if
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68 #end if
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69 ]]>
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70 </command>
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71 <inputs>
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72 <param argument="--bamFile1" format="bam" type="data" label="First BAM file (e.g. treated sample)"
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73 help="The BAM file must be sorted."/>
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74 <param argument="--bamFile2" format="bam" type="data" label="Second BAM file (e.g. control sample)"
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75 help="The BAM file must be sorted."/>
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76
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77 <param argument="--binSize" type="integer" value="50" min="1"
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78 label="Bin size in bases"
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79 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.
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80 If only half a fragment overlaps then this fraction will be reported."/>
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81
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82 <conditional name="scaling">
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83 <param name="method" type="select"
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84 label="Method to use for scaling the largest sample to the smallest">
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85 <option value="readCount" selected="true">read count</option>
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86 <option value="SES">signal extraction scaling (SES), check with plotFingerprint before using it!</option>
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87 <option value="own">enter own scaling factors</option>
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88 </param>
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89 <when value="SES">
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90 <param argument="--sampleLength" type="integer" value="1000" min="10"
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91 label="Length in bases used to sample the genome and compute the size or scaling factors."
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92 help="The default is fine. Only change it if you know what you are doing." />
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93 <param argument="--numberOfSamples" type="integer" value="100000" min="0"
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94 label="Number of samplings taken from the genome to compute the scaling factors"
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95 help="" />
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96 </when>
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97 <when value="readCount" />
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98 <when value="own">
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99 <expand macro="scaleFactors" />
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100 </when>
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101 </conditional>
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102
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103 <conditional name="comparison">
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104 <param name="type" type="select"
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105 label="How to compare the two files"
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106 help="The default is to output the log2ratio between the two samples.
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107 The reciprocal ratio returns the negative of the inverse of the ratio if
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108 the ratio is less than 0. The resulting values are interpreted as negative fold changes.">
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109 <option value="log2" selected="true">Compute log2 of the number of reads ratio</option>
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110 <option value="ratio">Compute the ratio of the number of reads</option>
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111 <option value="subtract">Compute difference (subtract input from treatment) of the number of reads</option>
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112 <option value="add">Compute the sum of number of reads</option>
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113 <option value="reciprocal_ratio">Computes the fold change. If the fold change is less than 1, the negative of the inverse is reported. E.g. A fold change of 10 to 5 would be reported not as 0.5 but as -2</option>
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114 </param>
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115 <when value="log2">
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116 <expand macro="pseudocount" />
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117 </when>
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118 <when value="ratio">
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119 <expand macro="pseudocount" />
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120 </when>
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121 <when value="add" />
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122 <when value="reciprocal_ratio">
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123 <expand macro="pseudocount" />
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124 </when>
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125 <when value="subtract">
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126 <conditional name="normalization">
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127 <param name="type" type="select" label="Normalization method" >
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128 <option value="1x">Normalize coverage to 1x</option>
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129 <option value="rpkm">Normalize to fragments (reads) per kilobase per million (RPKM)</option>
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130 <option value="no">Do not normalize or scale</option>
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131 </param>
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132 <when value="rpkm" />
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133 <when value="no" />
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134 <when value="1x">
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135 <expand macro="effectiveGenomeSize" />
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136 </when>
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137 </conditional>
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138 </when>
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139 </conditional>
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140
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141 <param name="outFileFormat" type="select" label="Coverage file format">
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142 <option value="bigwig" selected="true">bigwig</option>
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143 <option value="bedgraph">bedgraph</option>
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144 </param>
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145 <expand macro="region_limit_operation" />
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146 <conditional name="advancedOpt">
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147 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
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148 <option value="no" selected="true">no</option>
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149 <option value="yes">yes</option>
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150 </param>
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151 <when value="no" />
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152 <when value="yes">
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153 <expand macro="smoothLength" />
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154 <expand macro="read_processing_options" />
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155
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156 <expand macro="skipNAs" />
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157 <param argument="--ignoreForNormalization" type="text" value="" size="50"
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158 label="regions that should be excluded for calculating the scaling factor"
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159 help="Sometimes it makes sense to exclude certain regions when calculating the scaling factor.
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160 For example, if you know of copy number variations between samples then you may want to exclude these.
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161 Another typical example is the difference in chromosome X copies between males and females in many species.
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162 Example inputs are chrX,chrY,chr3 or chr10:12220-128932" />
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163 </when>
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164 </conditional>
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165 </inputs>
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166 <outputs>
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167 <data format="bigwig" name="outFileName">
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168 <change_format>
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169 <when input="outFileFormat" value="bigwig" format="bigwig" />
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170 <when input="outFileFormat" value="bedgraph" format="bedgraph" />
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171 </change_format>
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172 </data>
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173 </outputs>
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174 <tests>
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175 <test>
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176 <param name="bamFile1" value="bowtie2-test1.bam" ftype="bam" />
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177 <param name="bamFile2" value="bowtie2-test1.bam" ftype="bam" />
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178 <param name="showAdvancedOpt" value="no" />
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179 <param name="outFileFormat" value="bigwig" />
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180 <param name="outFileFormat" value="bedgraph" />
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181 <param name="binSize" value="5" />
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182 <param name="type" value="ratio" />
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183 <output name="outFileName" file="bamCompare_result1.bg" ftype="bedgraph" />
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184 </test>
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185 <test>
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186 <param name="bamFile1" value="bowtie2-test1.bam" ftype="bam" />
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187 <param name="bamFile2" value="bowtie2-test1.bam" ftype="bam" />
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188 <param name="showAdvancedOpt" value="yes" />
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189 <param name="outFileFormat" value="bigwig" />
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190 <param name="outFileFormat" value="bigwig" />
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191 <param name="binSize" value="10" />
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192 <param name="type" value="ratio" />
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193 <output name="outFileName" file="bamCompare_result2.bw" ftype="bigwig" />
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194 </test>
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195 </tests>
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196 <help>
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197 <![CDATA[
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198
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199 **What it does**
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200
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201 This tool compares two BAM files based on the number of mapped reads. To
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202 compare the BAM files, the genome is partitioned into bins of equal size, then
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203 the number of reads found in each BAM file is counted per bin and
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204 finally a summary value reported. This value can be the ratio of the
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205 number of reads per bin, the log2 of the ratio or the difference. This tool
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206 can normalize the number of reads in each BAM file using the SES method
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207 proposed in Diaz et al. (2012). "Normalization, bias correction, and peak
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208 calling for ChIP-seq". Statistical applications in genetics and molecular
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209 biology, 11(3). Normalization based on read counts is also available. The
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210 output is either a bedgraph or a bigwig file containing the bin location and
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211 the resulting comparison values. By default, if reads are mated, the fragment
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212 length reported in the BAM file is used. In the case of paired-end mapping,
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213 each read mate is treated independently to avoid a bias when a mixture of
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214 concordant and discordant pairs are present. This means that *each end* will be
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215 extended to match the fragment length.
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216
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217
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218 .. image:: $PATH_TO_IMAGES/norm_IGVsnapshot_indFiles.png
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219
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220
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221 You can find more details on the bamCompare doc page: https://deeptools.readthedocs.org/en/master/content/tools/bamCompare.html
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222
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223
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224 **Output files**:
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225
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226 - same as for bamCoverage, except that you now obtain 1 coverage file that is based on 2 BAM files.
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227
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228 -----
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229
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230 @REFERENCES@
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231 ]]>
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232 </help>
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233 <expand macro="citations" />
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234 </tool>