Mercurial > repos > matthias > dada2_filterandtrim

annotate dada2_filterAndTrim.xml @ 0:1d6e206b8291 draft

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author matthias
date Fri, 08 Mar 2019 06:36:53 -0500
parents
children ea3c356bff55
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matthias
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1 <tool id="dada2_filterAndTrim" name="dada2: filterAndTrim" version="@DADA2_VERSION@">
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2 <description>Filters and trims an short read data</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 sed -i '1!b;s/^/#dataset/' $outtab
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11 ]]></command>
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12 <configfiles>
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13 <configfile name="dada2_script"><![CDATA[
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14 truncQ <- c($trim.truncQ)
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15 truncLen <- c($trim.truncLen)
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16 trimLeft <- c($trim.trimLeft)
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17 trimRight <- c($trim.trimRight)
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18 #if str($filter.maxLen) == ""
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19 maxLen <- c(Inf)
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20 #else:
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21 maxLen <- c($filter.maxLen)
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22 #end if
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23 minLen <- c($filter.minLen)
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24 maxN <- c($filter.maxN)
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25 minQ <- c($filter.minQ)
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26 #if str($filter.maxEE) == ""
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27 maxEE <- c(Inf)
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28 #else:
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29 maxEE <- c($filter.maxEE)
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30 #end if
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31 #if $paired_cond.paired_select == "TRUE" and $seprev_cond.seprev_select == "yes"
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32 truncQ <- c(truncQ,$seprev_cond.trim.truncQ)
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33 truncLen <- c(truncLen,$seprev_cond.trim.truncLen)
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34 trimLeft <- c(trimLeft,$seprev_cond.trim.trimLeft)
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35 trimRight <- c(trimRight,$seprev_cond.trim.trimRight)
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36 #if str($seprev_cond.filter.maxLen) == ""
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37 maxLen <- c(maxLen,Inf)
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38 #else:
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39 maxLen <- c(maxLen,$seprev_cond.filter.maxLen)
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40 #end if
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41 minLen <- c(minLen,$seprev_cond.filter.minLen)
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42 maxN <- c(maxN,$seprev_cond.filter.maxN)
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43 minQ <- c(minQ,$seprev_cond.filter.minQ)
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44 #if str($seprev_cond.filter.maxEE) == ""
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45 maxEE <- c(maxEE,Inf)
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46 #else:
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47 maxEE <- c(maxEE,$seprev_cond.filter.maxEE)
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48 #end if
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49 #end if
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50
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51 fwd <- NULL
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52 rev <- NULL
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53 filt.fwd <- NULL
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54 filt.rev <- NULL
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55 #if $paired_cond.paired_select == "TRUE"
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56 fwd <- c(fwd, '$paired_cond.reads.forward')
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57 rev <- c(rev, '$paired_cond.reads.reverse')
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58 filt.fwd <- c(filt.fwd, '$paired_output.forward')
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59 filt.rev <- c(filt.rev, '$paired_output.reverse')
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60 #else
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61 fwd <- c(fwd, '$paired_cond.reads')
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62 filt.fwd <- c(filt.fwd, '$output')
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63 #end if
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64
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65 library(dada2, quietly=T)
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66
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67 ftout <- filterAndTrim(fwd, filt.fwd, rev = rev, filt.rev, compress = TRUE,
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68 truncQ = truncQ, truncLen = truncLen, trimLeft = trimLeft, trimRight = trimRight, maxLen = maxLen,
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69 minLen = minLen, maxN = maxN, minQ = minQ, maxEE = maxEE, rm.phix = $rmPhiX, orient.fwd = '$orientFwd')
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70
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71 rownames(ftout) <- c( '$paired_cond.reads.element_identifier' )
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72
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73 write.table(ftout, "$outtab", quote=F, sep="\t", col.names=NA)
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74 ]]></configfile>
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75 </configfiles>
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76 <inputs>
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77 <conditional name="paired_cond">
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78 <param name="paired_select" type="select" label="Paired reads">
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79 <option value="TRUE">yes</option>
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80 <option value="FALSE">no</option>
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81 </param>
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82 <when value="TRUE">
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83 <param name="reads" type="data_collection" collection_type="paired" format="fastqsanger,fastqsanger.gz" label="Paired short read data"/>
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84 </when>
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85 <when value="FALSE">
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86 <param name="reads" type="data" format="fastqsanger,fastqsanger.gz" label="Short read data"/>
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87 </when>
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88 </conditional>
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89 <expand macro="trimmers"/>
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90 <expand macro="filters"/>
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91 <conditional name="seprev_cond">
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92 <param name="seprev_select" type="select" label="Separate filters and trimmers for reverse reads" help="only applies to paired end data">
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93 <option value="no">no</option>
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94 <option value="yes">yes</option>
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95 </param>
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96 <when value="no"/>
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97 <when value="yes">
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98 <expand macro="trimmers"/>
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99 <expand macro="filters"/>
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100 </when>
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101 </conditional>
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102 <param name="rmPhiX" truevalue="TRUE" falsevalue="FALSE" type="boolean" checked="true" label="Discard reads matching PhiX" />
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103 <param name="orientFwd" type="text" value="" optional="true" label="String present at the start of valid reads" />
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104 </inputs>
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105 <outputs>
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106 <collection name="paired_output" type="paired">
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107 <data name="forward" format="fastqsanger.gz" from_work_dir="filt_forward.fastq.gz" />
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108 <data name="reverse" format="fastqsanger.gz" from_work_dir="filt_reverse.fastq.gz" />
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109 <filter>paired_cond['paired_select'] == 'TRUE'</filter>
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110 </collection>
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111 <data name="output" format="fastqsanger.gz" from_work_dir="filt_forward.fastq.gz">
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112 <filter>paired_cond['paired_select'] == 'FALSE'</filter>
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113 </data>
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114 <data name="outtab" format="tabular" label="${tool.name} on ${on_string}: Statistics"/>
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115 </outputs>
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116 <tests>
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117 <!-- paired data -->
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118 <test>
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119 <conditional name="paired_cond">
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120 <param name="paired_select" value="TRUE"/>
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121 <param name="reads">
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122 <collection type="paired">
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123 <element name="forward" value="F3D0_S188_L001_R1_001.fastq" ftype="fastqsanger"/>
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124 <element name="reverse" value="F3D0_S188_L001_R2_001.fastq" ftype="fastqsanger"/>
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125 </collection>
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126 </param>
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127 </conditional>
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128 <output_collection name="paired_output" count="2">
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129 <element name="forward" value="filterAndTrim_paired_F3D0_R1.fq.gz" ftype="fastqsanger.gz" />
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130 <element name="reverse" value="filterAndTrim_paired_F3D0_R2.fq.gz" ftype="fastqsanger.gz" />
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131 </output_collection>
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132 </test>
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133 <!-- paired data -->
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134 <test>
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135 <conditional name="paired_cond">
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136 <param name="paired_select" value="FALSE"/>
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137 <param name="reads" value="F3D0_S188_L001_R1_001.fastq" ftype="fastqsanger"/>
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138 </conditional>
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139 <output name="output" value="filterAndTrim_single_F3D0_R1.fq.gz" ftype="fastqsanger.gz" />
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140 </test>
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141 <!-- TODO parameter tests -->
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142 </tests>
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143
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144 <help><![CDATA[
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145 TODO: Fill in help.
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146 ]]></help>
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147 <expand macro="citations"/>
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148 </tool>