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annotate readmap.xml @ 4:4efe210c91f3 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 9237338d798251fb2667280d597746e852f3ffcc-dirty
author mvdbeek
date Wed, 03 Feb 2016 11:35:00 -0500
parents ebfc73c72652
children 68f58363f1c6
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4efe210c91f3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit 9237338d798251fb2667280d597746e852f3ffcc-dirty
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1 <tool id="Readmap" name="Generate readmap and histograms from alignment files" version="1.1.3">
0
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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="0.7.7">pysam</requirement>
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6 <requirement type="package" version="3.1.2">R</requirement>
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7 <requirement type="package" version="2.14">biocbasics</requirement>
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8 <requirement type="package" version="1.9">numpy</requirement>
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9 </requirements>
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10 <command interpreter="python">
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11 readmap.py
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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12 #if $refGenomeSource.genomeSource == "history":
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13 --reference_fasta ## sys.argv[2]
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14 $refGenomeSource.ownFile ## index source
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15 #else:
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16 #silent reference= filter( lambda x: str( x[0] ) == str( $refGenomeSource.series[0].input.dbkey ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1]
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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17 --reference_bowtie_index
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18 $reference
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19 #end if
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20 --rcode
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21 $plotCode
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22 --output_readmap
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23 $readmap_dataframe
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24 --output_size_distribution
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25 $size_distribution_dataframe
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26 --minquery
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27 $minquery
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28 --maxquery
ac7d8e55bb67 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_readmap_and_size_histograms commit fe40dec87779c1fcfbd03330e653aa886f4a2cda
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29 $maxquery
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30 --input
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31 #for $i in $refGenomeSource.series
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32 $i.input
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33 #end for
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34 --ext
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35 #for $i in $refGenomeSource.series
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36 $i.input.ext
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37 #end for
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38 --label
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39 #for $i in $refGenomeSource.series
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40 "$i.input.name"
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41 #end for
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42 --normalization_factor
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43 #for $i in $refGenomeSource.series
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44 $i.norm
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45 #end for
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46 #if $gff:
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47 --gff
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48 $gff
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49 #end if
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50
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51 </command>
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52 <inputs>
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53 <conditional name="refGenomeSource">
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54 <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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55 <option value="indexed">Use a built-in index</option>
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56 <option value="history">Use one from the history</option>
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57 </param>
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58 <when value="indexed">
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59 <repeat name="series" title="Add alignment files">
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60 <param name="input" type="data" label="Select multiple alignments to parse" format="tabular,sam,bam">
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61 <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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62 </param>
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63 <param name="norm" type="float" value="1" label="Indicate a normalization factor to compare multiple aligments"/>
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64 </repeat>
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65 </when>
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66 <when value="history">
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67 <param name="ownFile" type="data" format="fasta" label="Select a fasta file, that served as the reference index for the alignments" />
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68 <repeat name="series" title="Add alignment files">
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69 <param name="input" type="data" label="Select multiple alignments to parse" format="tabular,sam,bam"/>
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70 <param name="norm" type="float" value="1" label="Indicate a normalization factor to compare multiple aligments"/>
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71 </repeat>
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72 </when>
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73 </conditional>
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74 <param name="gff" type="data" format="gff3" optional="true" label="Optional: select a GFF to investigate regions of interest" help="GFF must match genome build"/>
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75 <!-- <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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76 <param name="minquery" type="integer" size="3" value="18" label="Min size of query small RNAs" help="'18' = 18 nucleotides"/>
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77 <param name="maxquery" type="integer" size="3" value="28" label="Max size of query small RNAs" help="'28' = 28 nucleotides"/>
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78 <param name="title" type="text" size="15" value= "Readmaps and size distributions" label="Main Titles"/>
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79 <param name="xlabel" type="text" size="15" value="Coordinates/read size" label="x axis label"/>
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80 <param name="ylabel" type="text" size="15" value="Number of reads" label="y axis label"/>
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81 <param name="yrange" type="integer" size="3" value="0" label="y axis range for readmaps. 0 means auto-scaling."/>
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82 <param name="rows_per_page" type="text" size="9" value="8" label="How many items to display per page?">
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83 <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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84 </param>
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85 </inputs>
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86 <configfiles>
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87 <configfile name="plotCode">
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88 ## Setup R error handling to go to stderr
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89 options( show.error.messages=F,
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90 error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
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91 library(RColorBrewer)
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92 library(lattice)
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93 library(latticeExtra)
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94 library(grid)
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95 library(gridExtra)
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96
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97 ## data frames implementation
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98
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99 rm=read.delim("${readmap_dataframe}", header=T, row.names=NULL)
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100 n_samples=length(unique(rm\$sample))
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101 genes=unique(levels(rm\$gene))
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102 per_gene_readmap=lapply(genes, function(x) subset(rm, gene==x)) ####### ?
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103 n_genes=length(per_gene_readmap)
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104
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105 size=read.delim("${size_distribution_dataframe}", header=T, row.names=NULL)
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106 per_gene_size=lapply(genes, function(x) subset(size, gene==x)) ###### ?
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107
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108 ## end of data frames implementation
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109
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110 ## functions
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111
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112 plot_readmap=function(df, ...) {
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113 combineLimits(xyplot(count~coord|factor(sample, levels=unique(sample))+reorder(gene, count, function(x) -sum(abs(x))),
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114 data=df,
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115 type='h',
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116 scales= list(relation="free", x=list(rot=0, cex=0.7, axs="i", tck=0.5), y=list(tick.number=4, rot=90, cex=0.7)),
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117 xlab=NULL, main=NULL, ylab=NULL,
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118 as.table=T,
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119 origin = 0,
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120 horizontal=FALSE,
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121 group=polarity,
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122 col=c("red","blue"),
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123 par.strip.text = list(cex=0.7),
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124 ...))
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125 }
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126
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127 plot_size_distribution= function(df, ...) {
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128 smR.prepanel=function(x,y,...){; yscale=c(-max(abs(y)), max(abs(y)));list(ylim=yscale);}
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129 bc= barchart(count~as.factor(size)|factor(sample, levels=unique(sample))+gene, data = df, origin = 0,
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130 horizontal=FALSE,
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131 group=polarity,
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132 stack=TRUE,
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133 col=c('red', 'blue'),
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134 cex=0.75,
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135 scales=list(y=list(tick.number=4, rot=90, relation="free", cex=0.7), x=list(cex=0.7) ),
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136 prepanel=smR.prepanel,
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137 xlab = NULL,
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138 ylab = NULL,
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139 main = NULL,
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140 as.table=TRUE,
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141 newpage = T,
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142 par.strip.text = list(cex=0.7),
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143 ...)
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144 combineLimits(bc)
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145 }
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146
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147 ## end of functions
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148
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149 ## function parameters'
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150
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151 par.settings.readmap=list(layout.heights=list(top.padding=0, bottom.padding=-2.5), strip.background = list(col=c("lightblue","lightgreen")) )
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152 par.settings.size=list(layout.heights=list(top.padding=-1, bottom.padding=-2.5), strip.background = list(col=c("lightblue","lightgreen")) )
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153 par.settings.combination.readmap=list(layout.heights=list(top.padding=0, bottom.padding=-3), strip.background=list(col=c("lightblue","lightgreen")) )
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154 par.settings.combination.size=list(layout.heights=list(top.padding=-2, bottom.padding=-0.5), strip.background=list(col=c("lightblue", "lightgreen")) )
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155
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156 ## end of function parameters'
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157
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158 ## GRAPHS
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159
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160 if (n_genes > 7) {page_height_simple = 11.69; page_height_combi=11.69; rows_per_page=${rows_per_page}; extrarow=0 } else {
1
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161 rows_per_page= 8; page_height_simple = 11.69; page_height_combi=11.69; extrarow=0 }
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162 ## rows_per_page= 8; page_height_simple = 11.69/7*n_genes; page_height_combi=11.69/9*(n_genes*2); extrarow=0 }
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163 ## rows_per_page= n_genes; page_height_simple = 11.69/n_genes/4; page_height_combi=11.69/(n_genes*2); extrarow=1 }
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164 if (n_samples > 4) {page_width = 8.2677*n_samples/4} else {page_width = 8.2677*n_samples/3} # to test
0
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165
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166 pdf(file="${readmap_PDF}", paper="special", height=page_height_simple, width=page_width)
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167 for (i in seq(1,n_genes,rows_per_page)) {
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168 start=i
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169 end=i+rows_per_page-1
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170 if (end>n_genes) {end=n_genes}
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171 if (${yrange} == 0) { readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, par.settings=par.settings.readmap)) } else {
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172 readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, ylim=c(-${yrange}, ${yrange}) , par.settings=par.settings.readmap)) }
0
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173 args.list=c(readmap_plot.list, list(nrow=rows_per_page, ncol=1,
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174 main=textGrob("Read Maps (nucleotide coordinates)", gp=gpar(cex=1), just="top"),
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175 left=textGrob("${ylabel}", gp=gpar(cex=1), vjust=1, rot=90)
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176 #sub=textGrob("readmap coordinates", gp=gpar(cex=.75), just="bottom")
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177 )
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178 )
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179 do.call(grid.arrange, args.list)
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180 }
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181 devname=dev.off()
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182
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183
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184 pdf(file="${size_PDF}", paper="special", height=page_height_simple, width=page_width)
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185 for (i in seq(1,n_genes,rows_per_page)) {
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186 start=i
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187 end=i+rows_per_page-1
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188 if (end>n_genes) {end=n_genes}
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189 plot.list=lapply(per_gene_size[start:end], function(x) plot_size_distribution(x, par.settings=par.settings.size) )
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190 args.list=c(plot.list, list(nrow=rows_per_page, ncol=1,
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191 main=textGrob("Size distributions (in nucleotides)", gp=gpar(cex=1), just="top"),
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192 left=textGrob("${ylabel}", gp=gpar(cex=1), vjust=1, rot=90)
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193 #sub="readsize in nucleotides"
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194 )
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195 )
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196 do.call(grid.arrange, args.list)
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197 }
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198 devname=dev.off()
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199
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200 pdf(file="${combi_PDF}", paper="special", height=page_height_combi, width=page_width)
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201 for (i in seq(1,n_genes,rows_per_page/2)) {
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202 start=i
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203 end=i+rows_per_page/2-1
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204 if (end>n_genes) {end=n_genes}
2
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205 if (${yrange} == 0) {readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, par.settings=par.settings.readmap)) } else {
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206 readmap_plot.list=lapply(per_gene_readmap[start:end], function(x) plot_readmap(x, ylim=c(-${yrange}, ${yrange}), par.settings=par.settings.readmap)) }
0
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207 size_plot.list=lapply(per_gene_size[start:end], function(x) plot_size_distribution(x, strip=FALSE, par.settings=par.settings.combination.size))
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208 plot.list=rbind(readmap_plot.list, size_plot.list )
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209 args.list=c(plot.list, list(nrow=rows_per_page + extrarow, ncol=1,
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210 main=textGrob("${title}", gp=gpar(cex=1), just="top"),
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211 left=textGrob("${ylabel}", gp=gpar(cex=1), vjust=1, rot=90),
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212 sub=textGrob("${xlabel}", gp=gpar(cex=1), just="bottom")
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213 )
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214 )
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215 do.call(grid.arrange, args.list)
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216 }
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217 devname=dev.off()
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218
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219
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220 </configfile>
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221 </configfiles>
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222
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223 <outputs>
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224 <data format="tabular" name="readmap_dataframe" label="Readmap dataframe"/>
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225 <data format="tabular" name="size_distribution_dataframe" label="Size distribution dataframe"/>
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226 <data format="pdf" name="readmap_PDF" label="Readmaps"/>
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227 <data format="pdf" name="size_PDF" label="Size distribution"/>
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228 <data format="pdf" name="combi_PDF" label="Size distribution and Readmaps"/>
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229 </outputs>
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230 <help>
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231
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232 **What it does**
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233
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234 Takes one or more alignment files (BAM, SAM or tabular bowtie output) as input and produces a "Readmap",
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235 where by default for each "chromosome" the position of the read is recorded on the x-axis, and the y-axis indicates
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236 the number of reads per position. Reads that map in sense are on the top, reads that map antisense are on the bottom.
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237
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238
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239 .. class:: warningmark
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240
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241 '''TIP''' The input data can be produced using the sRbowtie tool.
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242
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243 ----
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244
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245 '''Example'''
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246
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247 Query sequence::
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248 For a SAM file as the following:
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249
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250 5 16 2L_79 24393 255 17M * 0 0 CCTTCATCTTTTTTTTT IIIIIIIIIIIIIIIII XA:i:0 MD:Z:17 NM:i:0
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251
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252 11 0 2R_1 12675 255 21M * 0 0 AAAAAAAACGCGTCCTTGTGC IIIIIIIIIIIIIIIIIIIII XA:i:0 MD:Z:21 NM:i:0
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253
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254 2 16 2L_5 669 255 23M * 0 0 TGTTGCTGCATTTCTTTTTTTTT IIIIIIIIIIIIIIIIIIIIIII XA:i:0 MD:Z:23 NM:i:0
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255
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256 produce a plot like this:
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257
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258 ----
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259
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260 .. image:: static/images/readmap.png
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261 :height: 800
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262 :width: 500
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263
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264 </help>
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265 <tests>
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266 <test>
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267 <param name="genomeSource" value="history" />
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268 <param name="ownFile" value ="transposons.fasta" ftype="fasta" />
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269 <param name="series_0|input" value="sample1.srbowtie_out" ftype="tabular"/>
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270 <param name="series_0|norm" value="1" />
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271 <param name="series_1|input" value="sample2.srbowtie_out" ftype="tabular"/>
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272 <param name="series_1|norm" value="1" />
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273 <param name="series_2|input" value="sample3.srbowtie_out" ftype="tabular"/>
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274 <param name="series_2|norm" value="1" />
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275 <param name="minquery" value="20" />
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276 <param name="maxquery" value="30" />
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277 <param name="title" value="Readmaps and size distributions" />
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278 <param name="xlabel" value="Coordinates/read size" />
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279 <param name="ylabel" value="Number of reads" />
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280 <param name="rows_per_page" value="8" />
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281 <output name="readmap_dataframe" ftype="tabular" file="Readmap_dataframe.tab" />
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282 <output name="size_distribution_dataframe" ftype="tabular" file="Size_distribution_dataframe.tab" />
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283 <output name="readmap_PDF" ftype="pdf" file="Readmaps.pdf" />
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284 <output name="size_PDF" ftype="pdf" file="Size_distribution.pdf" />
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285 <output name="combi_PDF" ftype="pdf" file="Size_distribution_and_Readmaps.pdf" />
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286 </test>
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287 </tests>
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288 </tool>