Mercurial > repos > bgruening > deeptools_bam_fingerprint

annotate bamFingerprint.xml @ 8:ab153e5b5428 draft default tip

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4f515024772311c950d277246db548453d24abd7
author bgruening
date Wed, 23 Dec 2015 14:40:57 -0500
parents b97024fb9c9f
children
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1 <tool id="deeptools_bam_fingerprint" 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 <macros>
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4 <token name="@BINARY@">bamFingerprint</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 @multiple_input_bams@
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11 @BINARY@
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12 @THREADS@
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13 --bamfiles #echo " ".join($files)
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14 --labels #echo " ".join($labels)
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15 --plotFile $outFileName
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16
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17 #if $output.showOutputSettings == "yes"
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18 --plotFileFormat $output.outFileFormat
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19 #if $output.saveRawCounts:
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20 --outRawCounts '$outFileRawCounts'
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21 #end if
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22 #else
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23 --plotFileFormat 'png'
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24 #end if
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25
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26 #if str($region).strip() != '':
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27 --region '$region'
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28 #end if
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29
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30 #if $advancedOpt.showAdvancedOpt == "yes":
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31 --binSize '$advancedOpt.binSize'
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32 --numberOfSamples '$advancedOpt.numberOfSamples'
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33
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34 $advancedOpt.ignoreDuplicates
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35 $advancedOpt.skipZeros
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36
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37 #if $advancedOpt.minMappingQuality:
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38 --minMappingQuality '$advancedOpt.minMappingQuality'
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39 #end if
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41 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
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42 --plotTitle '$advancedOpt.plotTitle'
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43 #end if
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44 @ADVANCED_OPTS_READ_PROCESSING@
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45 #end if
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46 ]]>
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47 </command>
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48
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49 <inputs>
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50 <expand macro="multiple_input_bams" />
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51 <expand macro="region_limit_operation" />
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52
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53 <conditional name="advancedOpt">
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54 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
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55 <option value="no" selected="true">no</option>
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56 <option value="yes">yes</option>
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57 </param>
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58 <when value="no" />
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59 <when value="yes">
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60 <param argument="--binSize" type="integer" value="500" min="1"
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61 label="Bin size in bases"
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62 help="Length in bases for a window used to sample the genome."/>
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63 <param argument="--numberOfSamples" type="integer" value="100000" min="1"
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64 label="Number of samples"
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65 help="Number of samples taken from the genome to compute the scaling factors."/>
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66 <expand macro="read_processing_options" />
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67 <expand macro="skipZeros" />
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68 <expand macro="plotTitle" />
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69 </when>
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70 </conditional>
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71
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72 <conditional name="output">
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73 <param name="showOutputSettings" type="select" label="Show advanced output settings">
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74 <option value="no" selected="true">no</option>
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75 <option value="yes">yes</option>
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76 </param>
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77 <when value="no" />
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78 <when value="yes">
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79 <expand macro="input_image_file_format" />
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80 <param name="saveRawCounts" type="boolean" label="Save the bin counts" help="(--outRawCounts)"/>
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81 </when>
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82 </conditional>
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83 </inputs>
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84 <outputs>
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85 <expand macro="output_image_file_format" />
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86 <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
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87 <filter>
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88 ((
2
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89 output['showOutputSettings'] == 'yes' and
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90 output['saveRawCounts'] is True
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91 ))
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92 </filter>
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93 </data>
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94 </outputs>
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95 <tests>
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96 <test>
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97 <param name="bamfiles" value="bowtie2-test1.bam,bowtie2-test1.bam" ftype="bam" />
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98 <param name="showAdvancedOpt" value="no" />
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99 <param name="showOutputSettings" value="no" />
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100 <output name="outFileName" file="bamFingerprint_result1.png" ftype="png" compare="sim_size" />
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101 </test>
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102 <test>
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103 <param name="bamfiles" value="bowtie2-test1.bam,bowtie2-test1.bam" ftype="bam" />
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104 <param name="showAdvancedOpt" value="yes" />
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105 <param name="showOutputSettings" value="yes" />
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106 <param name="saveRawCounts" value="True" />
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107 <param name="plotTitle" value="Test Fingerprint Plot" />
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108 <output name="outFileName" file="bamFingerprint_result2.png" ftype="png" compare="sim_size" />
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109 <output name="outFileRawCounts" file="bamFingerprint_result2.tabular" ftype="tabular" />
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110 </test>
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111 </tests>
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112 <help>
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113 <![CDATA[
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114
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115
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116 **What it does**
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117
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118 This tool is useful for assessing the strength of a ChIP (i.e. how clearly the enrichment signal can be separated from the background)
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119 and is based on a method described in Diaz et al. (2012) Stat Appl Genet Mol Biol 11(3).
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120
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121 The tool first samples indexed BAM files and counts all reads overlapping a window (bin) of the specified length.
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122 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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123 and the cumulative sum of read counts are plotted. An ideal input (control) with a uniform distribution of reads alignments
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124 result in a diagonal line. A very specific and strong ChIP enrichment, on the other hand, would result in a large portion
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125 of reads accumulating in just a few bins and the resulting plot showing a steep rise toward the right-most edge. Such results are
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126 most commonly seen with transcription factors.
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127
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128
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129 .. image:: $PATH_TO_IMAGES/QC_fingerprint.png
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130
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131
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132 You can find more details on the bamFingerprint doc page: https://deeptools.readthedocs.org/en/release-1.6/content/tools/bamFingerprint.html
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133
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134
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135 **Output files**:
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136
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137 - Diagnostic plot
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138 - (optional) Data matrix of raw counts
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139
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140 **Output with test dataset**:
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141
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142 What follows is the output of bamFingerPrint with our test ChIP-Seq datasets, limiting analysis to chromosome X. Single-end reads were extended to
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143 200 bp (advanced options).
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144
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145 .. image:: $PATH_TO_IMAGES/bamFP_galaxy_output.png
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146
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147
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148 -----
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149
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150 @REFERENCES@
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151 ]]>
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152 </help>
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153 <expand macro="citations" />
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154 </tool>