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1 <tool id="diffbind" name="DiffBind" version="2.0.2">
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2 <description> differential binding analysis of ChIP-Seq peak data</description>
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3 <requirements>
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4 <requirement type="package" version="3.0.3">R</requirement>
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5 <requirement type="package" version="1.2.10">deseq2</requirement>
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6 <requirement type="package" version="1.8.3">diffbind</requirement>
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7 </requirements>
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8 <command>
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9 <![CDATA[
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10 ## seems that diffbind also needs file extensions to work properly
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11 #set $counter = 1
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12 #for $sample in $samples:
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13 ln -s $sample.bamreads #echo str($counter) + "_bamreads.bam"# &&
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14 ln -s ${sample.bamreads.metadata.bam_index} #echo str($counter) + "_bamreads.bai"# &&
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15 ln -s $sample.bamcontrol #echo str($counter) + "_bamcontrol.bam"# &&
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16 ln -s ${sample.bamcontrol.metadata.bam_index} #echo str($counter) + "_bamcontrol.bai"# &&
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17 #set $counter = $counter + 1
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18 #end for
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19
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20 Rscript $__tool_directory__/diffbind.R
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21 -i $infile
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22 -o $outfile
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23 -p $plots
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24 -f $format
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25 ]]>
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26 </command>
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27 <stdio>
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28 <regex match="Execution halted"
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29 source="both"
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30 level="fatal"
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31 description="Execution halted." />
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32 <regex match="Input-Error 01"
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33 source="both"
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34 level="fatal"
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35 description="Error in your input parameters: Make sure you only apply factors to selected samples." />
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36 <regex match="Error in"
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37 source="both"
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38 level="fatal"
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39 description="An undefined error occured, please check your intput carefully and contact your administrator." />
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40 </stdio>
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41 <inputs>
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42 <repeat name="samples" title="Samples" min="2">
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43 <param name="sample_id" type="text" value="Sample ID" label="Specify a sample id" help="e.g. BT474.1-" />
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44 <param name="tissue" type="text" value="Tissue" label="Specify the tissue" help="e.g. BT474" />
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45 <param name="factor" type="text" value="Factor Name" label="Specify a factor name" help="e.g. ER" />
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46 <param name="condition" type="text" value="Condition" label="Specify the condition" help="e.g. Resistent" />
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47 <param name="replicate" type="integer" value="1" label="Specify the replicate number" help="e.g. 1" />
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48 <param format="bam" name="bamreads" type="data" label="Read BAM file" help="Specify the Read BAM file, used for Peak calling."/>
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49 <param format="bam" name="bamcontrol" type="data" label="Control BAM file" help="Specify the Control BAM file, used for Peak calling."/>
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50 <param format="bed" name="peaks" type="data" label="Peak file" help="Result of your Peak calling experiment."/>
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51 </repeat>
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52 <param name="pdf" type="boolean" truevalue="" falsevalue="" checked="true"
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53 label="Visualising the analysis results"
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54 help="output an additional PDF files" />
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55 <param name="format" type="select" label="Output Format">
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56 <option value="bed">BED</option>
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57 <option value="gff">GFF</option>
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58 <option value="wig">WIG</option>
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59 </param>
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60 </inputs>
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61 <configfiles>
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62 <configfile name="infile">
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63 SampleID,Tissue,Factor,Condition,Replicate,bamReads,bamControl,Peaks
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64 #set $counter = 1
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65 #for $sample in $samples:
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66 $sample.sample_id,$sample.tissue,$sample.factor,$sample.condition,$sample.replicate,#echo str($counter) + '_bamreads.bam'#,#echo str($counter) + '_bamcontrol.bam'#,$sample.peaks
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67 #set $counter = $counter + 1
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68 #end for
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69 </configfile>
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70 </configfiles>
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71 <outputs>
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72 <data format="bed" name="outfile" label="Differential binding sites on ${on_string}">
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73 <change_format>
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74 <when input="format" value="wig" format="wig" />
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75 <when input="format" value="gff" format="gff" />
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76 </change_format>
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77 </data>
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78 <data format="pdf" name="plots" label="Differential binding sites on ${on_string}">
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79 <filter>pdf == True</filter>
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80 </data>
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81 </outputs>
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82
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83 <help>
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84 <![CDATA[
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85
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86
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87 **What it does**
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88
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89 Diffbind provides functions for processing ChIP-Seq data enriched for genomic loci where specific protein/DNA binding occurs, including peak sets identified by ChIP-Seq peak callers and aligned sequence read datasets.
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90
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91 **Input**
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92
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93 - You have to specify your samples. Here is one example:
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94
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95 ID Tissue Factor Condition Treatment Replicate Caller Intervals
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96 BT4741 BT474 ER Resistant Full-Media 1 raw 1084
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97
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98 - BAM file which contains the mapped sequencing reads can be associated with each
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99 peakset
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100
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101 - Control BAM file represents a control dataset
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102
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103 - Peak file: Result of your Peak calling experiment
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104
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105
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106 **Output**
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107
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108 As output format you can choose BED, GFF, WIG.
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109
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110
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111 **References**
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112
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113 DiffBind_ Authors: Rory Stark, Gordon Brown (2011)
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114
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115 .. _DiffBind: http://www.bioconductor.org/packages/release/bioc/html/DiffBind.html
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116
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117 Wrapper authors: Bjoern Gruening, Pavankumar Videm
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118
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119 ]]>
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120 </help>
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121 </tool>
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