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1 <tool id="piRNAsignature" name="piRNA Signatures" version="1.0.1">
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2 <description></description>
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3 <command interpreter="python">
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4 piRNAsignature.py $refGenomeSource.input $refGenomeSource.input.ext $minquery $maxquery $mintarget $maxtarget $minscope $maxscope $output
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5 #if $refGenomeSource.genomeSource == "history":
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6 $refGenomeSource.ownFile
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7 --do_not_extract_index
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8 #else:
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9 #silent reference= filter( lambda x: str( x[0] ) == str( $input.dbkey ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1]
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10 $reference
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11 --extract_index
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12 #end if
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13 $graph_type
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14 $sigplotter
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15 </command>
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16
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17 <inputs>
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18 <conditional name="refGenomeSource">
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19 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
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20 <option value="indexed">Use a built-in index</option>
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21 <option value="history">Use one from the history</option>
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22 </param>
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23 <when value="indexed">
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24 <param name="input" type="data" format="tabular,sam,bam" label="Compute signature from this bowtie standard output">
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25 <validator type="dataset_metadata_in_data_table" table_name="bowtie_indexes" metadata_name="dbkey" metadata_column="0" message="database not set for this bowtie output. Select the database(=genome used for matching) manually, or select a reference fasta from your history."/>
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26 </param>
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27 </when>
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28 <when value="history">
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29 <param name="ownFile" type="data" format="fasta" label="Select the fasta reference" />
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30 <param name="input" type="data" format="tabular,sam,bam" label="Compute signature from this bowtie standard output"/>
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31 </when>
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32 </conditional> <!-- refGenomeSource -->
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33 <param name="minquery" type="integer" size="3" value="23" label="Min size of query small RNAs" help="'23' = 23 nucleotides"/>
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34 <param name="maxquery" type="integer" size="3" value="29" label="Max size of query small RNAs" help="'29' = 29 nucleotides"/>
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35 <param name="mintarget" type="integer" size="3" value="23" label="Min size of target small RNAs" help="'23' = 23 nucleotides"/>
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36 <param name="maxtarget" type="integer" size="3" value="29" label="Max size of target small RNAs" help="'29' = 29 nucleotides"/>
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37 <param name="minscope" type="integer" size="3" value="1" label="Minimal relative overlap analyzed" help="'1' = 1 nucleotide overlap"/>
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38 <param name="maxscope" type="integer" size="3" value="26" label="Maximal relative overlap analyzed" help="'1' = 1 nucleotide overlap"/>
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39 <param name="graph_type" type="select" label="Graph type" help="Signature can be computed globally or by item present in the alignment file">
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40 <option value="global" selected="True">Global</option>
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41 <option value="lattice">Lattice</option>
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42 </param>
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43 </inputs>
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44
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45 <configfiles>
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46 <configfile name="sigplotter">
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47 graph_type = "${graph_type}"
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48
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49 globalgraph = function () {
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50 ## Setup R error handling to go to stderr
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51 options( show.error.messages=F,
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52 error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
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53 signature = read.delim("${output}", header=TRUE)
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54 ## Open output1 PDF file
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55 pdf( "${output1}" )
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56 signaturez=(signature[,2] -mean(signature[,2]))/sd(signature[,2])
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57 plot(signaturez, type = "b", main="signature", cex.main=2, xlab="overlap (nt)", ylab="z-score", pch=19, cex=0.8, col="darkslateblue", lwd=3, cex.lab=1.5, cex.axis=1.4, xaxt="n")
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58 axis(1, at=seq(from=1, to=length(signature[,1]), by=3) )
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59 devname = dev.off()
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60 ## Close the PDF file
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61 ## Open output2 PDF file
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62 pdf( "${output2}" )
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63 YLIM=max(signature[,2])
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64 plot(signature[,1:2], type = "h", xlab="overlap (nt)", ylim=c(0,YLIM), ylab="number of pairs", col="darkslateblue", lwd=7)
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65 devname = dev.off()
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66 ## Close the PDF file
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67 ## Open output3 PDF file
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68 pdf( "${output3}" )
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69 plot(signature[,1], signature[,3]*100, type = "l", main="ping-pong Signature of ${minquery}-${maxquery} against ${mintarget}-${maxtarget}nt small RNAs",
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70 cex.main=1, xlab="overlap (nt)", ylab="ping-pong signal [%]", ylim=c(0,50),
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71 pch=19, col="darkslateblue", lwd =4, cex.lab=1.2, cex.axis=1, xaxt="n")
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72 axis(1, at=seq(from=1, to=length(signature[,1]), by=3) )
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73 devname = dev.off()
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74 ## Close the PDF file
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75 }
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76
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77 treillisgraph = function () {
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78 ## Open output3 PDF file
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79 pdf( "${output3}", paper="special", height=11.69, width=8.2677 )
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80 signature = read.delim("${output}", header=TRUE)
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81 options( show.error.messages=F,
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82 error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
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83 library(lattice)
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84 print (xyplot(signature[,3]*100~signature[,1]|signature[,4], type = "l", xlim=c(1,26), main="ping-pong Signature of ${minquery}-${maxquery} against ${mintarget}-${maxtarget}nt small RNAs",
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85 par.strip.text=list(cex=.5), strip=strip.custom(which.given=1, bg="lightblue"), scales=list(cex=0.5),
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86 cex.main=1, cex=.5, xlab="overlap (nt)", ylab="ping-pong signal [%]",
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87 pch=19, col="darkslateblue", lwd =1.5, cex.lab=1.2, cex.axis=1.2,
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88 layout=c(4,12), as.table=TRUE, newpage = T) )
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89 devnname = dev.off()
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90 }
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91
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92 if (graph_type=="global") {
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93 globalgraph()
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94
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95 }
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96 if(graph_type=="lattice") {
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97 treillisgraph()
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98 }
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99 </configfile>
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100 </configfiles>
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101
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102 <outputs>
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103 <data name="output" format="tabular" label = "signature data frame"/>
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104 <data name="output2" format="pdf" label="number of pairs signature">
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105 <filter>(graph_type == "global")</filter>
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106 </data>
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107 <data name="output1" format="pdf" label="z-score signature">
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108 <filter>(graph_type == "global")</filter>
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109 </data>
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110 <data name="output3" format="pdf" label="ping-pong signal (hannon algo.)"/>
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111 </outputs>
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112
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113 <help>
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114
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115 **What it does**
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116
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117 This tool computes the number of pairs by overlap classes (in nt) from a bowtie output file, the z-score calculated from these numbers of pairs, and the ping-pong signal as described in Brennecke et al (2009) Science.
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118 The numerical options set the min and max size of both the query small rna class and the target small rna class
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119 Three type of signals are plotted in separate pdf files, the number of pairs founds, the z-score calculated from these numbers of pairs, and the ping-pong signal as described in Brennecke et al (2009) Science.
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120
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121 </help>
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122 </tool>
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