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1 <tool id="MirParser" name="Parse miRNAs" version="0.9.1">
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2 <description>from sRbowtie aligment</description>
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3 <requirements><requirement type='package'>bowtie-inspect</requirement></requirements>
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4 <parallelism method="basic"></parallelism>
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5 <command interpreter="python">
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6 MirParser.py
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7 #if $refGenomeSource.genomeSource == "history":
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8 $refGenomeSource.ownFile ## index source sys.arg[1]
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9 --do_not_extract_index ## sys.argv[2]
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10 #else:
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11 #silent reference= filter( lambda x: str( x[0] ) == str( $input_list.dbkey ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1]
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12 $reference ## sys.argv[1]
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13 --extract_index ## sys.argv[2]
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14 #end if
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15 $output1 ## for pre-mirs ## sys.argv[3]
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16 $output2 ## for mature mirs ## sys.argv[4]
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17 $GFF3 ## sys.argv[5]
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18 #if $plotting.plottingOption == "yes":
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19 $lattice_dataframe ## sys.argv[6]
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20 $plotCode ## sys.argv[7]
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21 $latticePDF ## sys.argv[8]
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22 #else:
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23 "dummy_dataframe_path" ## sys.argv[6]
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24 "dummy_plotCode" ## sys.argv[7]
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25 "dummy_latticePDF" ## sys.argv[8]
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26 #end if
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27 #for $i in $refGenomeSource.input_list
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28 $i $i.ext "$i.name" ## sys.argv[9,10,11] modulo 3
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29 #end for
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30 #silent plottingoption = $plotting.plottingOption
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31 </command>
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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_list" type="data" label="Select multiple alignments to parse" multiple="true">
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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="input_list" type="data" label="Select multiple alignments to parse" multiple="true"/>
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45 <param name="ownFile" type="data" format="fasta" label="Select the fasta reference" />
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46 </when>
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47 </conditional> <!-- refGenomeSource -->
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48 <param name="GFF3" type="data" label="miRbase GFF3 guide" />
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49 <conditional name="plotting">
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50 <param name="plottingOption" type="select" label="Additional mir coverage graphs">
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51 <option value="no" selected="True">No</option>
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52 <option value="yes">YES</option>
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53 </param>
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54 <when value="yes">
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55 <param name="display" type="select" label="Display Coverage with absolute number of reads or relatively to the total number of read matching the gene or mir">
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56 <option value="relative" selected="True">Relative Coverage</option>
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57 <option value="absolute">Absolute Coverage</option>
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58 </param>
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59 </when>
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60 </conditional>
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61 </inputs>
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62 <configfiles>
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63 <configfile name="plotCode">
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64 #if $plotting.plottingOption == "yes":
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65 graph_type = "${plotting.display}" ## "relative" or "absolute"
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66 ## Setup R error handling to go to stderr
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67 options( show.error.messages=F,
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68 error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
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69 library(lattice)
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70 coverage = read.delim("${lattice_dataframe}", header=T)
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71 Numb_of_biosamples = length(levels(coverage\$sample))
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72 if (graph_type=="relative") {
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73 graph = xyplot(countsNorm~offsetNorm | mir, data=coverage, groups=polarity, col=c("red", "blue"), type="l", lwd=1,
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74 scales=list(x=list(cex=.5), y=list(cex=.5)), par.strip.text=list(cex=.5), strip=strip.custom(which.given=1, bg="lightblue"), layout=c(Numb_of_biosamples,15), as.table=TRUE, main="miRNA coverage maps")
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75 } else {
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76 graph = xyplot(counts~offset | mir, data=coverage, groups=polarity, col=c("red", "blue"), type="l", lwd=1,
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77 scales=list(x=list(cex=.5), y=list(cex=.5)), par.strip.text=list(cex=.5), strip=strip.custom(which.given=1, bg="lightblue"), layout=c(Numb_of_biosamples,15), as.table=TRUE, main="miRNA coverage maps")
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78 }
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79 ## pdf output
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80 pdf(file="${latticePDF}", paper="special", height=11.69, width=8.2677)
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81 plot(graph, newpage = T)
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82 dev.off()
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83 #end if
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84 </configfile>
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85 </configfiles>
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86
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87 <outputs>
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88 <data format="tabular" name="output1" label="Premirs Count Lists"/>
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89 <data format="tabular" name="output2" label="Mature Mirs Count Lists"/>
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90 <data format="tabular" name="lattice_dataframe" label="Lattice Dataframe">
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91 <filter>plotting['plottingOption'] == "yes"</filter>
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92 </data>
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93 <data format="pdf" name="latticePDF" label="Mir coverage">
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94 <filter>plotting['plottingOption'] == "yes"</filter>
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95 </data>
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96 </outputs>
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97 <help>
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98
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99 **What it does**
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100
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101 This tool uses a specie-specific GFF3 file from mirBase_ to guide the parsing of an alignment file produced with the sRbowtie tool.
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102
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103 .. _mirBase: ftp://mirbase.org/pub/mirbase/CURRENT/genomes/
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104
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105 ------
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106
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107 .. class:: warningmark
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108
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109 the Guide GFF3 file must be in the following format:
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110
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111 2L . miRNA_primary_transcript 243035 243141 . - . ID=MI0005821;Alias=MI0005821;Name=dme-mir-965
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112
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113 2L . miRNA 243055 243076 . - . ID=MIMAT0005480;Alias=MIMAT0005480;Name=dme-miR-965-3p;Derives_from=MI0005821
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114
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115 2L . miRNA 243096 243118 . - . ID=MIMAT0020861;Alias=MIMAT0020861;Name=dme-miR-965-5p;Derives_from=MI0005821
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116
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117 2L . miRNA_primary_transcript 857542 857632 . + . ID=MI0005813;Alias=MI0005813;Name=dme-mir-375
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118
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119 2L . miRNA 857596 857617 . + . ID=MIMAT0005472;Alias=MIMAT0005472;Name=dme-miR-375-3p;Derives_from=MI0005813
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120
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121 2L . miRNA 857556 857579 . + . ID=MIMAT0020853;Alias=MIMAT0020853;Name=dme-miR-375-5p;Derives_from=MI0005813
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122
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123 2L . miRNA_primary_transcript 1831685 1831799 . - . ID=MI0011290;Alias=MI0011290;Name=dme-mir-2280
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124
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125 With name for mature miRNA (3rd column = miRNA) containing either the -3p or -5p string in the attribute Name (Name=dme-miR-965-3p, for instance)
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126
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127 ------
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128
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129 **Input formats**
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130
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131 1. One or sereral alignment files generated with sRbowtie tool and **renamed** according to the name of the biosample (avoid spaces in biosample labels)
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132
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133 .. class:: warningmark
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134
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135 Alignment datasets generated with sRbowtie must be renamed according to a biosample name
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136
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137 2. A GFF3 file retrieved from mirBase_
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138
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139 ------
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140
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141 **Outputs**
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142
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143 Two count list files for counts of reads aligned to pre-mir or mature miRNA
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144
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145 A pdf of pre-mir coverages. Red coverages indicate that the mir gene is in the genomic up strand, blue coverages indicate that the mir gene is in the genomic down strand.
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146
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147 </help>
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148 </tool>
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