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1 <tool id="signature" name="Small RNA Signatures" version="2.0.0">
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2 <description></description>
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3 <requirements>
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4 <requirement type="package" version="0.12.7">bowtie</requirement>
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5 <requirement type="package" version="0.1.18">samtools</requirement>
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6 <requirement type="package" version="0.7.7">pysam</requirement>
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7 <requirement type="package" version="2.14">biocbasics</requirement>
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8 <requirement type="package" version="3.0.3">R</requirement>
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9 </requirements>
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10 <command interpreter="python">
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11 signature.py
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12 --input $refGenomeSource.input
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13 --inputFormat $refGenomeSource.input.ext
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14 --minquery $minquery
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15 --maxquery $maxquery
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16 --mintarget $mintarget
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17 --maxtarget $maxtarget
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18 --minscope $minscope
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19 --maxscope $maxscope
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20 --outputOverlapDataframe $output
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21 #if $refGenomeSource.genomeSource == "history":
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22 --referenceGenome $refGenomeSource.ownFile
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23 #else:
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24 #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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25 --referenceGenome $reference
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26 --extract_index
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27 #end if
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28 --graph $graph_type
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29 --rcode $sigplotter
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30 </command>
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31
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32 <inputs>
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33 <conditional name="refGenomeSource">
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34 <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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35 <option value="indexed">Use a built-in index</option>
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36 <option value="history">Use one from the history</option>
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37 </param>
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38 <when value="indexed">
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39 <param name="input" type="data" format="tabular,sam,bam" label="Compute signature from this bowtie standard output">
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40 <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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41 </param>
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42 </when>
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43 <when value="history">
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44 <param name="ownFile" type="data" format="fasta" label="Select the fasta reference" />
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45 <param name="input" type="data" format="tabular,sam,bam" label="Compute signature from this bowtie standard output"/>
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46 </when>
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47 </conditional> <!-- refGenomeSource -->
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48 <param name="minquery" type="integer" size="3" value="23" label="Min size of query small RNAs" help="'23' = 23 nucleotides"/>
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49 <param name="maxquery" type="integer" size="3" value="29" label="Max size of query small RNAs" help="'29' = 29 nucleotides"/>
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50 <param name="mintarget" type="integer" size="3" value="23" label="Min size of target small RNAs" help="'23' = 23 nucleotides"/>
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51 <param name="maxtarget" type="integer" size="3" value="29" label="Max size of target small RNAs" help="'29' = 29 nucleotides"/>
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52 <param name="minscope" type="integer" size="3" value="1" label="Minimal relative overlap analyzed" help="'1' = 1 nucleotide overlap"/>
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53 <param name="maxscope" type="integer" size="3" value="26" label="Maximal relative overlap analyzed" help="'1' = 1 nucleotide overlap"/>
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54 <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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55 <option value="global" selected="True">Global</option>
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56 <option value="lattice">Lattice</option>
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57 </param>
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58 </inputs>
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59
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60 <configfiles>
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61 <configfile name="sigplotter">
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62 graph_type = "${graph_type}"
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63
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64 globalgraph = function () {
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65 ## Setup R error handling to go to stderr
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66 options( show.error.messages=F,
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67 error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
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68 signature = read.delim("${output}", header=TRUE)
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69 signaturez=(signature[,2] -mean(signature[,2]))/sd(signature[,2])
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70 YLIM=max(signature[,2])
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71
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72 ## Open output2 PDF file
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73 pdf( "${output2}" )
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74 par(mfrow=c(2,2),oma = c(0, 0, 3, 0))
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75
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76 plot(signature[,1:2], type = "h", main="Numbers of pairs", cex.main=1, xlab="overlap (nt)", ylim=c(0,YLIM), ylab="Numbers of pairs", col="darkslateblue", lwd=4)
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77
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78 plot(signaturez, type = "l", main="Number of pairs Z-scores", cex.main=1, xlab="overlap (nt)", ylab="z-score", pch=19, cex=0.2, col="darkslateblue", lwd=2, cex.lab=1, cex.axis=1, xaxt="n")
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79 axis(1, at=seq(from=1, to=length(signature[,1]), by=3) )
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80
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81 plot(signature[,1], signature[,3]*100, type = "l", main="Overlap probabilities",
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82 cex.main=1, xlab="overlap (nt)", ylab="Probability [%]", ylim=c(0,50),
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83 pch=19, col="darkslateblue", lwd=2, cex.lab=1, cex.axis=1, xaxt="n")
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84 axis(1, at=seq(from=1, to=length(signature[,1]), by=3) )
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85
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86 overlap_prob_z=(signature[,3] -mean(signature[,3]))/sd(signature[,3])
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87 plot(overlap_prob_z, type = "l", main="Overlap Probability Z-scores", cex.main=1, xlab="overlap (nt)", ylab="z-score", pch=19, cex=0.2, col="darkslateblue", lwd=2, cex.lab=1, cex.axis=1, xaxt="n")
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88 axis(1, at=seq(from=1, to=length(signature[,1]), by=3) )
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89
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90 mtext("Overlap Signatures of ${minquery}-${maxquery} against ${mintarget}-${maxtarget}nt small RNAs", outer = TRUE, cex=1)
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91 devname = dev.off()
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92 ## Close the PDF file
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93 }
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94
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95 treillisgraph = function () {
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96 ## Open output2 PDF file
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97 pdf( "${output2}", paper="special", height=11.69, width=8.2677 )
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98 signature = read.delim("${output}", header=TRUE)
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99 options( show.error.messages=F,
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100 error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
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101 library(lattice)
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102 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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103 par.strip.text=list(cex=.5), strip=strip.custom(which.given=1, bg="lightblue"), scales=list(cex=0.5),
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104 cex.main=1, cex=.5, xlab="overlap (nt)", ylab="ping-pong signal [%]",
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105 pch=19, col="darkslateblue", lwd =1.5, cex.lab=1.2, cex.axis=1.2,
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106 layout=c(4,12), as.table=TRUE, newpage = T) )
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107 devnname = dev.off()
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108 }
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109
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110 if (graph_type=="global") {
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111 globalgraph()
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112
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113 }
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114 if(graph_type=="lattice") {
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115 treillisgraph()
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116 }
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117 </configfile>
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118 </configfiles>
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119
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120 <outputs>
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121 <data name="output" format="tabular" label = "signature data frame"/>
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122 <data name="output2" format="pdf" label="Overlap probabilities"/>
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123 </outputs>
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124
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125 <help>
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126
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127 **What it does**
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128
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129 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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130 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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131 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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132
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133 </help>
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134
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135 <test>
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136 <param name="genomeSource" value="history" />
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137 <param name="ownFile" value ="transposons.fasta" ftype="fasta" />
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138 <param name="input" value="sr_bowtie.output" ftype="tabular" />
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139 <param name="minquery" value="23" />
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140 <param name="maxquery" value="29" />
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141 <param name="mintarget" value="23" />
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142 <param name="maxtarget" value="29" />
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143 <param name="minscope" value="1" />
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144 <param name="maxscope" value="26" />
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145 <param name="graph_type" value="global" />
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146 <output name="readmap_dataframe" ftype="tabular" value="signature_data_frame.tab"/>
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147 <output name="readmap_PDF" ftype="pdf" value="Overlap_probabilities.pdf"/>
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148 </test>
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149
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150
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151
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152 </tool>
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153
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