Mercurial > repos > matthias > dada2_seqcounts

annotate dada2_seqCounts.xml @ 4:4e8927c51603 draft

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author matthias
date Mon, 29 Apr 2019 09:51:56 -0400
parents 0c2c91057b4b
children 39e27bd6d230
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1 <tool id="dada2_seqCounts" name="dada2: sequence counts" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@">
0
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2 <description></description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="version_command"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 Rscript '$dada2_script'
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10 ]]></command>
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11 <configfiles>
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12 <configfile name="dada2_script"><![CDATA[
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13 @READ_FOO@
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14 library(dada2, quietly=T)
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15
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16 getN <- function(x){ sum(getUniques(x)) }
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17
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18 df <- NULL
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19 #for $i, $rep in enumerate($inrep)
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20 samples = list()
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21 #for $s in $rep.input:
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22 #if len($rep.input) == 1
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23 samples <- $read_data( $s )
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24 #else
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25 sample_name <- '$s.element_identifier'
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26 samples[[sample_name]] <- $read_data( $s )
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27 #end if
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28 #if $s.ext == "tabular"
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29 tabular <- T
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30 #else
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31 tabular <- F
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32 #end if
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33 #end for
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34
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35 #if str($rep.name) == ""
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36 dname <- '$str(i)'
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37 #else
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38 dname <- '$rep.name'
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39 #end if
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40
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41 if( tabular ){
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42 tdf <- NULL
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43 for( n in names( samples ) ){
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44 if(is.null(tdf)){
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45 tdf <- samples[[n]]
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46 }else{
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47 tdf <- rbind(tdf, samples[[n]])
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48 }
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49 }
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50 names(tdf) <- paste( dname, names(tdf) )
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51 tdf <- cbind( data.frame(samples=names( samples )), tdf)
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52 }else{
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53 if(is.null(names(samples))){
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54 tdf <- data.frame( samples = row.names(samples) )
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55 }else{
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56 tdf <- data.frame( samples = names(samples) )
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57 }
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58 t <- tryCatch({
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59 sapply(samples, getN)
3
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60 },
0
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61 error=function(cond) {
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62 rowSums(samples)
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63 })
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64 tdf[[ dname ]] <- t
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65 }
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66 if(is.null(df)){
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67 df <- tdf
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68 }else{
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69 df <- merge( df, tdf, by="samples", all=T, no.dups=T)
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70 }
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71 #end for
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72 write.table(df, "$counts", quote=F, sep="\t", row.names = F, col.names = T)
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73 ]]></configfile>
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74 </configfiles>
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75 <inputs>
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76 <repeat name="inrep" title="data sets" min="1">
0
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77 <param name="input" type="data" multiple="true" format="tabular,@DADA_UNIQUES@,dada2_sequencetable,dada2_uniques" label="Dataset(s)"/>
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78 <param name="name" type="text" value="" optional="true" label="name"/>
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79 </repeat>
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80 </inputs>
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81 <outputs>
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82 <data name="counts" format="tabular" label="${tool.name} on ${on_string}"/>
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83 </outputs>
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84 <tests>
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85 </tests>
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86 <help><![CDATA[
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87 Description
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88 ...........
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89
0
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90 Get the counts of sequences per sample for the different stages of the dada pipeline.
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91
3
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92 Usage
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93 .....
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94
0
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95 **Inputs:**
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96
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97 Any number of results from derepFastq, dada, mergePairs, makeSequenceTable, and removeBimeraDenovo. Additionally the statistics of filterAndTrim can be used.
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98
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99 **Output:**
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100
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101 A table containing the number of sequences per sample (rows) for each input (columns)
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102
3
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103 Details
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104 .......
0
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105
3
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106 For results from
0
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107
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108 - derepFastq, dada, and mergePairs the sum of the result of dada2's getUniques function is used
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109 - makeSequenceTable, and removeBimeraDenovo R's rowSums function is used
3
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110
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111 @HELP_OVERVIEW@
0
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112 ]]></help>
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113 <expand macro="citations"/>
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114 </tool>