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1 <tool id="signature" name="Small RNA Signatures" version="2.0.1">
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2 <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 <requirement type="package" version="1.9">numpy</requirement>
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10 <requirement type="package" version="0.14">scipy</requirement>
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11 </requirements>
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12 <command interpreter="python">
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13 signature.py
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14 --input $refGenomeSource.input
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15 --inputFormat $refGenomeSource.input.ext
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16 --minquery $minquery
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17 --maxquery $maxquery
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18 --mintarget $mintarget
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19 --maxtarget $maxtarget
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20 --minscope $minscope
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21 --maxscope $maxscope
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22 --outputOverlapDataframe $output
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23 #if $refGenomeSource.genomeSource == "history":
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24 --referenceGenome $refGenomeSource.ownFile
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25 #else:
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26 #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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27 --referenceGenome $reference
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28 --extract_index
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29 #end if
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30 --graph $graph_type
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31 --rcode $sigplotter
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32 </command>
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33 <inputs>
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34 <conditional name="refGenomeSource">
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35 <param help="Built-ins were indexed using default options" label="Will you select a reference genome from your history or use a built-in index?" name="genomeSource" type="select">
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36 <option value="indexed">Use a built-in index</option>
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37 <option value="history">Use one from the history</option>
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38 </param>
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39 <when value="indexed">
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40 <param format="tabular,sam,bam" label="Compute signature from this bowtie standard output" name="input" type="data">
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41 <validator message="database not set for this bowtie output. Select the database(=genome used for matching) manually, or select a reference fasta from your history." metadata_column="0" metadata_name="dbkey" table_name="bowtie_indexes" type="dataset_metadata_in_data_table" />
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42 </param>
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43 </when>
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44 <when value="history">
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45 <param format="fasta" label="Select the fasta reference" name="ownFile" type="data" />
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46 <param format="tabular,sam,bam" label="Compute signature from this bowtie standard output" name="input" type="data" />
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47 </when>
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48 </conditional>
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49 <param help="'23' = 23 nucleotides" label="Min size of query small RNAs" name="minquery" size="3" type="integer" value="23" />
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50 <param help="'29' = 29 nucleotides" label="Max size of query small RNAs" name="maxquery" size="3" type="integer" value="29" />
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51 <param help="'23' = 23 nucleotides" label="Min size of target small RNAs" name="mintarget" size="3" type="integer" value="23" />
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52 <param help="'29' = 29 nucleotides" label="Max size of target small RNAs" name="maxtarget" size="3" type="integer" value="29" />
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53 <param help="'1' = 1 nucleotide overlap" label="Minimal relative overlap analyzed" name="minscope" size="3" type="integer" value="1" />
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54 <param help="'1' = 1 nucleotide overlap" label="Maximal relative overlap analyzed" name="maxscope" size="3" type="integer" value="26" />
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55 <param help="Signature can be computed globally or by item present in the alignment file" label="Graph type" name="graph_type" type="select">
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56 <option selected="True" value="global">Global</option>
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57 <option value="lattice">Lattice</option>
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58 </param>
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59 </inputs>
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60 <outputs>
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61 <data format="tabular" label="signature data frame" name="output" />
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62 <data format="pdf" label="Overlap probabilities" name="output2" />
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63 </outputs>
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64 <tests>
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65 <test>
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66 <param name="genomeSource" value="history" />
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67 <param ftype="fasta" name="ownFile" value="ensembl.fa" />
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68 <param ftype="bam" name="input" value="sr_bowtie.bam" />
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69 <param name="minquery" value="23" />
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70 <param name="maxquery" value="29" />
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71 <param name="mintarget" value="23" />
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72 <param name="maxtarget" value="29" />
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73 <param name="minscope" value="5" />
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74 <param name="maxscope" value="15" />
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75 <param name="graph_type" value="global" />
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76 <output file="signature.tab" ftype="tabular" name="output" />
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77 <output file="signature.pdf" ftype="pdf" name="output2" />
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78 </test>
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79 </tests>
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80 <help>
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81
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82 **What it does**
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83
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84 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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85 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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86 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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87
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88 </help>
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89 <citations>
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90 <citation type="doi">10.1007/978-1-4939-0931-5_12</citation>
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91 </citations>
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92 <configfiles>
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93 <configfile name="sigplotter">
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94 graph_type = "${graph_type}"
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95
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96 globalgraph = function () {
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97 ## Setup R error handling to go to stderr
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98 options( show.error.messages=F,
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99 error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
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100 signature = read.delim("${output}", header=TRUE)
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101 signaturez=data.frame(signature[,1], (signature[,2] -mean(signature[,2]))/sd(signature[,2]))
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102 overlap_prob_z=data.frame(signature[,1], (signature[,3] -mean(signature[,3]))/sd(signature[,3]))
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103 YLIM=max(signature[,2])
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104
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105 ## Open output2 PDF file
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106 pdf( "${output2}" )
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107 par(mfrow=c(2,2),oma = c(0, 0, 3, 0))
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108
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109 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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110
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111 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)
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112
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113 plot(signature[,1], signature[,3]*100, type = "l", main="Overlap probabilities",
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114 cex.main=1, xlab="overlap (nt)", ylab="Probability [%]", ylim=c(0,50),
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115 pch=19, col="darkslateblue", lwd=2)
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116
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117 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)
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118
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119 mtext("Overlap Signatures of ${minquery}-${maxquery} against ${mintarget}-${maxtarget}nt small RNAs", outer = TRUE, cex=1)
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120 devname = dev.off()
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121 ## Close the PDF file
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122 }
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123
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124 treillisgraph = function () {
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125 ## Open output2 PDF file
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126 pdf( "${output2}", paper="special", height=11.69, width=8.2677 )
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127 signature = read.delim("${output}", header=TRUE)
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128 options( show.error.messages=F,
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129 error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
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130 library(lattice)
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131 print (xyplot(signature[,3]*100~signature[,1]|signature[,4], type = "l", xlim=c(${minscope},${maxscope}), main="ping-pong Signature of ${minquery}-${maxquery} against ${mintarget}-${maxtarget}nt small RNAs",
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132 par.strip.text=list(cex=.5), strip=strip.custom(which.given=1, bg="lightblue"), scales=list(cex=0.5),
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133 cex.main=1, cex=.5, xlab="overlap (nt)", ylab="ping-pong signal [%]",
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134 pch=19, col="darkslateblue", lwd =1.5, cex.lab=1.2, cex.axis=1.2,
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135 layout=c(4,12), as.table=TRUE, newpage = T) )
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136 devnname = dev.off()
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137 }
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138
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139 if (graph_type=="global") {
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140 globalgraph()
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141
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142 }
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143 if(graph_type=="lattice") {
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144 treillisgraph()
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145 }
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146 </configfile>
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147 </configfiles>
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148 </tool>
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