Mercurial > repos > iuc > dada2_seqcounts

annotate dada2_seqCounts.xml @ 0:448c54392221 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
author iuc
date Fri, 08 Nov 2019 18:45:01 -0500
parents
children d006780246bf
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448c54392221 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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1 <tool id="dada2_seqCounts" name="dada2: sequence counts" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@" profile="19.09">
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2 <description></description>
448c54392221 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
448c54392221 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
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9 <command detect_errors="exit_code"><![CDATA[
448c54392221 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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10 Rscript '$dada2_script'
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11 ]]></command>
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12 <configfiles>
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13 <configfile name="dada2_script"><![CDATA[
448c54392221 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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14 @READ_FOO@
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15 library(dada2, quietly=T)
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16
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17 getN <- function(x){ sum(getUniques(x)) }
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18
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19 df <- NULL
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20 #for $i, $rep in enumerate($inrep)
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21 samples = list()
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22 #for $s in $rep.input:
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23 ## for collection input assume identifiers are sample names
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24 #if $s.ext in ["tabular", "dada2_dada", "dada2_mergepairs"]
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25 sample_name <- '$s.element_identifier'
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26 samples[[sample_name]] <- $read_data( $s )
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27 #else
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28 samples <- $read_data( $s )
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29 #end if
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30 #if $s.ext == "tabular"
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31 tabular <- T
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32 #else
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33 tabular <- F
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34 #end if
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35 #end for
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36
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37 #if str($rep.name) == ""
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38 dname <- '$str(i)'
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39 #else
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40 dname <- '$rep.name'
448c54392221 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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41 #end if
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42
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43 if( tabular ){
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44 tdf <- NULL
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45 for( n in names( samples ) ){
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46 if(is.null(tdf)){
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47 tdf <- samples[[n]]
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48 }else{
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49 tdf <- rbind(tdf, samples[[n]])
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50 }
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51 }
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52 names(tdf) <- paste( dname, names(tdf) )
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53 tdf <- cbind( data.frame(samples=names( samples )), tdf)
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54 }else{
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55 if(is.null(names(samples))){
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56 tdf <- data.frame( samples = row.names(samples) )
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57 }else{
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58 tdf <- data.frame( samples = names(samples) )
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59 }
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60 t <- tryCatch({
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61 sapply(samples, getN)
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62 },
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63 error=function(cond) {
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64 rowSums(samples)
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65 })
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66 tdf[[ dname ]] <- t
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67 }
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68 if(is.null(df)){
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69 df <- tdf
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70 }else{
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71 df <- merge( df, tdf, by="samples", all=T, no.dups=T)
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72 }
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73 #end for
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74 write.table(df, "$counts", quote=F, sep="\t", row.names = F, col.names = T)
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75 ]]></configfile>
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76 </configfiles>
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77 <inputs>
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78 <repeat name="inrep" title="data sets" min="1">
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79 <param name="input" type="data" multiple="true" format="tabular,@DADA_UNIQUES@,dada2_sequencetable,dada2_uniques" label="Dataset(s)"/>
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80 <param name="name" type="text" value="" optional="true" label="name"/>
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81 </repeat>
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82 </inputs>
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83 <outputs>
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84 <data name="counts" format="tabular" label="${tool.name} on ${on_string}"/>
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85 </outputs>
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86 <tests>
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87 <!-- test for the separate inputs (didn't implement as single test using the repeat
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88 since the sample name won't match anyway [galaxy does not allow to specify the
448c54392221 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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89 names of the elements of the input collection for <param ... multiple="true">]) -->
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90 <test>
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91 <repeat name="inrep">
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92 <param name="input" value="filterAndTrim_F3D0.tab" ftype="tabular"/>
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93 <param name="name" value="filter"/>
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94 </repeat>
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95 <output name="counts" value="seqCounts_F3D0_filter.tab" ftype="tabular" />
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96 </test>
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97 <test>
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98 <repeat name="inrep">
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99 <param name="input" value="dada_F3D0_R1.Rdata" ftype="dada2_dada"/>
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100 <param name="name" value="dadaF"/>
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101 </repeat>
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102 <output name="counts" value="seqCounts_F3D0_dadaF.tab" ftype="tabular" />
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103 </test>
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104 <test>
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105 <repeat name="inrep">
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106 <param name="input" value="mergePairs_F3D0.Rdata" ftype="dada2_mergepairs"/>
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107 <param name="name" value="merge"/>
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108 </repeat>
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109 <output name="counts" value="seqCounts_F3D0_merge.tab" ftype="tabular" />
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110 </test>
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111 <test>
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112 <repeat name="inrep">
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113 <param name="input" value="makeSequenceTable_F3D0.tab" ftype="dada2_sequencetable"/>
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114 <param name="name" value="seqtab"/>
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115 </repeat>
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116 <output name="counts" value="seqCounts_F3D0_seqtab.tab" ftype="tabular" />
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117 </test>
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118 <test>
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119 <repeat name="inrep">
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120 <param name="input" value="removeBimeraDenovo_F3D0.tab" ftype="dada2_sequencetable"/>
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121 <param name="name" value="nochim"/>
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122 </repeat>
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123 <output name="counts" value="seqCounts_F3D0_nochim.tab" ftype="tabular" />
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124 </test>
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125 </tests>
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126 <help><![CDATA[
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127 Description
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128 ...........
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129
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130 Get the counts of sequences per sample for the different stages of the dada pipeline.
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131
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132 Usage
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133 .....
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134
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135 **Inputs:**
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136
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137 Any number of results of dada2 steps in the following form:
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138 - a collection of results from dada, or mergePairs; or the collection of statistics from filterAndTrim (the identifiers of the collection elements are used as sample names)
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139 - the result of makeSequenceTable or removeBimeraDenovo
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140
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141 **Output:**
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142
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143 A table containing the number of sequences per sample (rows) for each input (columns)
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144
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145 Details
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146 .......
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147
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148 For results from
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149
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150 - dada, and mergePairs the sum of the result of dada2's getUniques function is used
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151 - makeSequenceTable, and removeBimeraDenovo R's rowSums function is used
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152
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153 @HELP_OVERVIEW@
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154 ]]></help>
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155 <expand macro="citations"/>
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156 </tool>