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1 <tool id="deeptools_bamFingerprint" name="bamFingerprint" version="@WRAPPER_VERSION@.0">
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2 <description>plots profiles of BAM files; useful for assesing ChIP signal strength</description>
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3 <expand macro="requirements" />
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4 <expand macro="stdio" />
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5 <macros>
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6 <token name="@BINARY@">bamFingerprint</token>
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7 <import>deepTools_macros.xml</import>
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8 </macros>
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9 <command>
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10 <![CDATA[
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11 @multiple_input_bams@
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12
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13 bamFingerprint
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14
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15 @THREADS@
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16
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17 --bamfiles #echo " ".join($files)
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18 --labels #echo " ".join($labels)
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19
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20 --fragmentLength $fragmentLength
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21
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22 #set newoutFileName=str($outFileName)+".png"
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23 --plotFile $newoutFileName
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24
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25 #if $output.showOutputSettings == "yes"
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26 --plotFileFormat $output.outFileFormat
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27 #if $output.saveRawCounts:
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28 --outRawCounts '$outFileRawCounts'
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29 #end if
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30 #else
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31 --plotFileFormat 'png'
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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 $advancedOpt.showAdvancedOpt == "yes":
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39 --binSize '$advancedOpt.binSize'
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40 --numberOfSamples '$advancedOpt.numberOfSamples'
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41
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42 $advancedOpt.doNotExtendPairedEnds
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43 $advancedOpt.ignoreDuplicates
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44 $advancedOpt.skipZeros
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45
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46 #if $advancedOpt.minMappingQuality:
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47 --minMappingQuality '$advancedOpt.minMappingQuality'
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48 #end if
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49 #end if
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50 ; mv $newoutFileName $outFileName
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51 ; rm $temp_dir -rf
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52 ]]>
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53 </command>
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54
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55 <inputs>
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56 <expand macro="multiple_input_bams" />
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57 <expand macro="fragmentLength" />
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58 <expand macro="region_limit_operation" />
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59
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60 <conditional name="advancedOpt">
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61 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
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62 <option value="no" selected="true">no</option>
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63 <option value="yes">yes</option>
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64 </param>
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65 <when value="no" />
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66 <when value="yes">
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67 <param name="binSize" type="integer" value="500" min="1"
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68 label="Bin size in bp"
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69 help="Length in base pairs for a window used to sample the genome."/>
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70 <param name="numberOfSamples" type="integer" value="100000" min="1"
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71 label="Number of samples"
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72 help="Number of samples taken from the genome to compute the scaling factors. (--numberOfSamples)"/>
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73 <expand macro="doNotExtendPairedEnds" />
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74 <expand macro="ignoreDuplicates" />
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75 <expand macro="minMappingQuality" />
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76 <expand macro="skipZeros" />
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77
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78 </when>
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79 </conditional>
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80 <conditional name="output">
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81 <param name="showOutputSettings" type="select" label="Show advanced output settings">
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82 <option value="no" selected="true">no</option>
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83 <option value="yes">yes</option>
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84 </param>
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85 <when value="no" />
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86 <when value="yes">
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87 <expand macro="input_image_file_format" />
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88 <param name="saveRawCounts" type="boolean" label="Save the bin counts"/>
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89 </when>
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90 </conditional>
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91 </inputs>
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92 <outputs>
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93 <expand macro="output_image_file_format" />
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94 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
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95 <filter>
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96 ((
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97 output['showOutputSettings'] == 'yes' and
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98 output['saveRawCounts'] is True
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99 ))
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100 </filter>
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101 </data>
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102 </outputs>
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103 <tests>
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104 <test>
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105 <repeat name="input_files">
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106 <param name="bamfile" value="bowtie2-test1.bam" ftype="bam" />
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107 </repeat>
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108 <repeat name="input_files">
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109 <param name="bamfile" value="bowtie2-test1.bam" ftype="bam" />
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110 </repeat>
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111 <param name="fragmentLength" value="200" />
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112 <param name="showAdvancedOpt" value="no" />
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113 <param name="showOutputSettings" value="no" />
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114 <output name="outFileName" file="bamFingerprint_result1.png" ftype="png" />
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115 </test>
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116 </tests>
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117 <help>
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118 <![CDATA[
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119 **What it does**
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120
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121 This tool is useful to assess the strength of a ChIP (i.e. how clearly the enrichment signal can be separated from the background signal)
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122 and it is based on a method developed by Diaz et al. (2012) Stat Appl Genet Mol Biol 11(3).
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123
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124 The tool first samples indexed BAM files and counts all reads overlapping a window (bin) of specified length.
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125 These counts are then sorted according to their rank (the bin with the highest number of reads has the highest rank)
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126 and the cumulative sum of read counts are plotted. An ideal input (control sample) with perfect uniform distribution of reads
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127 along the genome (i.e. without enrichments in open chromatin etc.) should
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128 generate a straight diagonal line. A very specific and strong ChIP enrichment will be indicated by a prominent and steep
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129 rise of the cumulative sum towards the highest rank. This means that a big chunk of reads from the ChIP sample is located in
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130 few bins which corresponds to high, narrow enrichments seen for transcription factors.
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131
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132
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133 .. image:: $PATH_TO_IMAGES/QC_fingerprint.png
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134
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135
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136 You can find more details on the bamFingerprint wiki page: https://github.com/fidelram/deepTools/wiki/QC#wiki-bamFingerprint
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137
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138
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139 **Output files**:
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140
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141 - Diagnostic plot
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142 - Data matrix of raw counts
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143
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144 -----
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145
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146 @REFERENCES@
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147 ]]>
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148 </help>
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149 <expand macro="citations" />
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150 </tool>
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