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1 <tool id="Size_histogram" name="Generate size histograms from alignment files" version="0.9.5">
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2 <description>from sRbowtie aligment</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 <parallelism method="basic"></parallelism>
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11 <command interpreter="python">
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12 size_histogram.py
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13 #if $refGenomeSource.genomeSource == "history":
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14 --reference_fasta ## sys.argv[2]
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15 $refGenomeSource.ownFile ## index source
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16 #else:
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17 #silent reference= filter( lambda x: str( x[0] ) == str( $refGenomeSource.series[0].input.dbkey ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1]
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18 --reference_bowtie_index
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19 $reference
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20 #end if
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21 --rcode
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22 $plotCode
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23 --output_size_distribution
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24 $size_distribution_dataframe
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25 --minquery
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26 $minquery
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27 --maxquery
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28 $maxquery
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29 --input
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30 #for $i in $refGenomeSource.series
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31 $i.input
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32 #end for
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33 --ext
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34 #for $i in $refGenomeSource.series
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35 $i.input.ext
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36 #end for
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37 --label
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38 #for $i in $refGenomeSource.series
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39 "$i.input.name"
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40 #end for
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41 --normalization_factor
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42 #for $i in $refGenomeSource.series
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43 $i.norm
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44 #end for
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45 #if $gff:
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46 --gff
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47 $gff
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48 #end if
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49 #if $global.value == 'yes':
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50 --global_size
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51 #end if
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52 #if $collapsestrands.value == 'yes':
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53 --collapse
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54 #end if
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55
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56 </command>
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57 <inputs>
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58 <conditional name="refGenomeSource">
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59 <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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60 <option value="indexed">Use a built-in index</option>
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61 <option value="history">Use one from the history</option>
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62 </param>
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63 <when value="indexed">
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64 <repeat name="series" title="Add alignment files">
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65 <param name="input" type="data" label="Select multiple alignments to parse">
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66 <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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67 </param>
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68 <param name="norm" type="float" value="1" label="Indicate a normalization factor to compare multiple aligments"/>
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69 </repeat>
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70 </when>
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71 <when value="history">
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72 <param name="ownFile" type="data" format="fasta" label="Select a fasta file, to serve as index reference" />
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73 <repeat name="series" title="Add alignment files">
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74 <param name="input" type="data" label="Select multiple alignments to parse"/>
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75 <param name="norm" type="float" value="1" label="Indicate a normalization factor to compare multiple aligments"/>
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76 </repeat>
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77 </when>
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78 </conditional>
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79 <param name="gff" type="data" optional="true" label="Optional: select a GFF to investigate regions of interest" help="GFF must match genome build"/>
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80 <!-- <validator type="dataset_metadata_in_data_table" table_name="bowtie_indexes" metadata_name="dbkey" metadata_column="0" message="GFF database and alignment file databse do not match!"/> -->
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81 <param name="global" type="select" label="Generate size distribution for each item, or generate a global alignment">
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82 <option value="no">for each item</option>
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83 <option value="yes">global</option>
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84 </param>
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85 <param name="collapsestrands" type="select" label="Whether + and - reads should be collapsed or not">
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86 <option value="no">Do not collapse</option>
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87 <option value="yes">Collapse + and - reads</option>
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88 </param>
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89 <param name="minquery" type="integer" size="3" value="18" label="Min size of reads to plot" help="'15' = 15 nucleotides"/>
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90 <param name="maxquery" type="integer" size="3" value="28" label="Max size of reads to plot" help="'30' = 30 nucleotides"/>
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91 <param name="title" type="text" size="15" value="Size distribution" label="Main Titles"/>
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92 <param name="xlabel" type="text" size="15" value="Size in nucleotides" label="x axis label"/>
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93 <param name="ylabel" type="text" size="15" value="Number of reads" label="y axis label"/>
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94 <param name="rows_per_page" type="text" size="9" value="8" label="How many items to display per page?">
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95 <validator type="in_range" min="6" max="20" message="Select between 6 and 20 rows, as the readability will suffer otherwise."/>
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96 </param>
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97 </inputs>
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98 <configfiles>
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99 <configfile name="plotCode">
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100 ## Setup R error handling to go to stderr
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101 options( show.error.messages=F,
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102 error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
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103 library(RColorBrewer)
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104 library(lattice)
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105 library(latticeExtra)
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106 library(grid)
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107 library(gridExtra)
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108
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109 ##cheetahtemplate data frame implementation
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110 size=read.delim("${size_distribution_dataframe}", header=T, row.names=NULL)
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111 n_samples = length(unique (size\$sample))
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112 n_genes = length (unique (levels(size\$gene)))
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113
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114 par.settings.size=list(layout.heights=list(top.padding=1, bottom.padding=1),
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115 strip.background = list(col = c("lightblue", "lightgreen"))
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116 )
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117
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118 smR.prepanel=function(x,y,...){; yscale=c(-max(abs(y)), max(abs(y)));list(ylim=yscale);} # use if one want y axis in the middle of the plot
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119
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120 plot_size_distribution= function(df, ...) {
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121 bc= barchart(count~as.factor(size)|factor(sample, levels=unique(sample))+gene, data = df, origin = 0,
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122 horizontal=FALSE,
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123 group=polarity,
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124 stack=TRUE,
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125 col=c('red', 'blue'),
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126 cex=0.75,
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127 scales=list(y=list(tick.number=4, rot=90, relation="free", cex=0.5, alternating=T), x=list(cex=.6 ) ),
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128 xlab = "readsize in nucleotides",
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129 ylab = "${ylabel}",
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130 main="${title}" ,
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131 par.strip.text = list(cex=0.75),
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132 as.table=TRUE,
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133 newpage = T,
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134 ...)
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135
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136 combineLimits(update(useOuterStrips(bc,
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137 strip.left = strip.custom(par.strip.text = list(cex=0.5))
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138 ),
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139 layout=c(n_samples,${rows_per_page})),
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140 margin.x=F, margin.y=1)
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141 }
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142
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143 # per_gene_size=lapply(genes, function(x) subset(size, gene==x)) # no object in this script
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144
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145 global = "no"
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146 #if $global.value == 'yes':
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147 global = "yes"
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148 #end if
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149
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150 if (global=="no") {
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151
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152 options(warn=-1)
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153 pdf(file="${size_PDF}", paper="special", height=11.69, width=8.2677*n_samples/4)
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154 plot_size_distribution(size, par.settings=par.settings.size) # removed , prepanel=smR.prepanel
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155
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156 } else {
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157
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158 pdf(file="${size_PDF}", paper="special", height=11.69, width=8.2677)
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159 bc= barchart(count~as.factor(size)|factor(sample, levels=unique(sample)), data = size, origin = 0,
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160 horizontal=FALSE,
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161 group=polarity,
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162 stack=TRUE,
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163 col=c('red', 'blue'),
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164 # par.settings=list(fontsize = list(text=8, points=8)),
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165 scales=list(y=list(tick.number=4, rot=90, relation="same"), cex=1),
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166 xlab = "readsize in nucleotides",
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167 ylab = "${ylabel}",
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168 main="${title}" , as.table=TRUE, newpage = T,
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169 aspect=0.5,
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170 strip = strip.custom(par.strip.text = list(cex = 1), which.given=1, bg="lightblue")
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171 )
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172 bc
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173 }
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174 devname=dev.off()
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175
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176 </configfile>
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177 </configfiles>
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178
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179 <outputs>
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180 <data format="tabular" name="size_distribution_dataframe" label="Size_distribution_dataframe.tab"/>
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181 <data format="pdf" name="size_PDF" label="Size_distribution.pdf"/>
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182 </outputs>
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183 <help>
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184
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185 **What it does**
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186
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187 Takes one or more alignment files (BAM, SAM or tabular bowtie output) as input and produces a histogram of read sizes,
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188 where by default for each "chromosome" a histogram of read sizes is drawn.
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189 Reads that map in sense are on the top (red), reads that map antisense are on the bottom (blue).
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190
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191
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192 .. class:: warningmark
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193
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194 '''TIP''' The input data can be produced using the sRbowtie tool.
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195
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196 ----
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197
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198 '''Example'''
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199
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200 Query sequence::
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201 For a SAM file as the following:
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202
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203 5 16 2L_79 24393 255 17M * 0 0 CCTTCATCTTTTTTTTT IIIIIIIIIIIIIIIII XA:i:0 MD:Z:17 NM:i:0
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204
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205 11 0 2R_1 12675 255 21M * 0 0 AAAAAAAACGCGTCCTTGTGC IIIIIIIIIIIIIIIIIIIII XA:i:0 MD:Z:21 NM:i:0
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206
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207 2 16 2L_5 669 255 23M * 0 0 TGTTGCTGCATTTCTTTTTTTTT IIIIIIIIIIIIIIIIIIIIIII XA:i:0 MD:Z:23 NM:i:0
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208
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209 produce a plot like this:
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210
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211 ----
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212
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213 .. image:: static/images/size_histogram.png
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214 :height: 800
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215 :width: 500
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216
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217 </help>
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218 <test>
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219 <param name="genomeSource" value="history" />
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220 <param name="ownFile" value ="transposons.fasta" ftype="fasta" />
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221 <param name="input" value="sample1.srbowtie_out, sample2.srbowtie_out, sample3.srbowtie_out" ftype="tabular" />
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222 <param name="norm" value="1,1,1" />
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223 <param name="global" value="no" />
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224 <param name="collapsestrands" value="no" />
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225 <param name="minquery" value="18"/>
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226 <param name="maxquery" value="30"/>
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227 <param name="title" value="Size distribution"/>
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228 <param name="xlabel" value="Size in nucleotides"/>
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229 <param name="ylabel" value="Number of reads"/>
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230 <param name="rows_per_page" value="10"/>
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231 <output name="size_distribution_dataframe" ftype="tabular" value="Size_distribution_dataframe.tab" />
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232 <output name="size_PDF" ftype="pdf" value="Size_distribution.pdf" />
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233 </test>
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234 </tool>
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235
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