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1 <tool id="je_demultiplex_illu" name="Je-Demultiplex-Illu" version="1.0">
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2 <description>demultiplexes fastq files using Illumina Index file</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 <stdio>
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7 <exit_code range="1:" level="fatal" description="Tool exception" />
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8 </stdio>
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9 <version_command>echo '1.0'</version_command>
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10 <command interpreter="bash">
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11 <![CDATA[
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12 je demultiplex-illu
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13
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14 ## Fastq inputs
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15 @single_or_paired_illu_cmd@
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16
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17 @barcode_option_cmd@
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18
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19 #if str($INTERNAL_BARCODES_CON.INTERNAL_BARCODES) == 'true':
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20 BPOS=${INTERNAL_BARCODES_CON.BPOS}
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21 C=${INTERNAL_BARCODES_CON.CLIP_BARCODE}
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22 #if str( $INTERNAL_BARCODES_CON.LEN ) != "":
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23 BCLEN=$INTERNAL_BARCODES_CON.LEN
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24 #end if
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25 #else:
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26 BPOS=NONE
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27 C=false
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28 #end if
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29
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30 @common_options_cmd@
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31
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32 @demultiplexer_common_output_options_cmd@
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33 @demultiplexer_common_outputs_cmd@
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34 ]]>
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35 </command>
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36 <configfiles>
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37 <expand macro="barcode_config_file"/>
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38 </configfiles>
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39 <inputs>
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40 <!-- single/paired - similar to macro 'single_or_paired_general' -->
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41 <expand macro="single_or_paired_illu">
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42 <expand macro="demultiplex_illu_paired_end_options"/>
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43 </expand>
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44 <expand macro="barcode_option"/>
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45 <conditional name="INTERNAL_BARCODES_CON">
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46 <param name="INTERNAL_BARCODES" type="select"
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47 label="Do your reads contain Unique Molecular Identifiers(UMIs)">
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48 <option value="true">Yes</option>
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49 <option value="false" selected="true">No</option>
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50 </param>
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51 <when value="true">
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52 <param name="BPOS" type="select" label="Barcode read position (BPOS)" help="where are the barcodes.
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53 If not using paired-end it does not matter what you specify here.">
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54 <option value="READ_1" selected="true">READ_1 (beginning of read from the first fastq file)</option>
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55 <option value="READ_2">READ_2 (beginning of read from the second fastq file)</option>
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56 <option value="BOTH">BOTH (beginning of both reads)</option>
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57 </param>
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58 <expand macro="barcode_len_option"/>
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59 <expand macro="clip_barcode"/>
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60 </when>
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61 <when value="false"/>
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62 </conditional>
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63
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64 <expand macro="demultiplexer_common_options"/>
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65
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66 <expand macro="common_options"/>
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67
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68 <expand macro="demultiplexer_common_output_options"/>
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69
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70 </inputs>
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71 <outputs>
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72 <expand macro="demultiplexer_common_outputs"/>
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73 </outputs>
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74
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75 <tests>
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76 <test>
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77 <!-- barcode at both ends, non-redundant -->
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78 <param name="type" value="paired"/>
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79 <param name="input_1" value="illu_file_1_sequence.txt" ftype="fastqsanger"/>
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80 <param name="input_2" value="illu_file_2_sequence.txt" ftype="fastqsanger"/>
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81 <param name="I1" value="illu_file_1_index.txt" ftype="fastqsanger"/>
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82 <param name="I2_AVAILABLE" value="true"/>
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83 <param name="I2" value="illu_file_2_index.txt" ftype="fastqsanger"/>
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84
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85 <param name="INTERNAL_BARCODES" value="true"/>
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86 <param name="barcode_list_type_con" value="file"/>
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87 <param name="BARCODE_FILE" value="illu_dualindexing.txt" ftype="tabular"/>
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88 <param name="LEN" value="8:8"/>
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89 <param name="ZT" value="5:6"/>
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90 <param name="BPOS" value="BOTH"/>
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91 <param name="BM" value="BOTH"/>
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92 <param name="BRED" value="false"/>
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93 <param name="MM" value="3"/>
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94 <param name="MMD" value="2"/>
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95 <param name="Q" value="20"/>
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96 <param name="DIAG" value="false"/>
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97 <output name="METRICS_FILE_NAME" file="illu_summary_PE.txt" ftype="tabular" lines_diff="4">
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98 <discovered_dataset designation="unassigned_1" file="illu_unassigned_1_PE.txt" />
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99 <discovered_dataset designation="unassigned_2" file="illu_unassigned_2_PE.txt" />
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100 <discovered_dataset designation="emb681m5_GGACTCCTCTCTCTAT_2" file="emb681m5_GGACTCCTCTCTCTAT_2.txt"/>
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101 <discovered_dataset designation="emb681m5_GGACTCCTCTCTCTAT_1" file="emb681m5_GGACTCCTCTCTCTAT_1.txt"/>
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102 <discovered_dataset designation="emb681m4_TCCTGAGCCTCTCTAT_2" file="emb681m4_TCCTGAGCCTCTCTAT_2.txt"/>
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103 <discovered_dataset designation="emb681m4_TCCTGAGCCTCTCTAT_1" file="emb681m4_TCCTGAGCCTCTCTAT_1.txt"/>
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104 <discovered_dataset designation="emb681m1_TAAGGCGACTCTCTAT_2" file="emb681m1_TAAGGCGACTCTCTAT_2.txt"/>
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105 <discovered_dataset designation="emb681m1_TAAGGCGACTCTCTAT_1" file="emb681m1_TAAGGCGACTCTCTAT_1.txt"/>
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106 <discovered_dataset designation="emb6801m2_AGGCAGAATAGATCGC_2" file="emb6801m2_AGGCAGAATAGATCGC_2.txt"/>
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107 <discovered_dataset designation="emb6801m2_AGGCAGAATAGATCGC_1" file="emb6801m2_AGGCAGAATAGATCGC_1.txt"/>
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108 <discovered_dataset designation="emb6801m1_CGTACTAGTAGATCGC_2" file="emb6801m1_CGTACTAGTAGATCGC_2.txt"/>
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109 <discovered_dataset designation="emb6801m1_CGTACTAGTAGATCGC_1" file="emb6801m1_CGTACTAGTAGATCGC_1.txt"/>
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110 </output>
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111 </test>
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112 </tests>
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113
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114
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115 <help>
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116 <![CDATA[
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117 **What it does**
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118
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119 Je demultiplex-illu: demultiplex fastq files using Illumina Index files,
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120 with optional handling of Unique Molecular Identifiers for further use in 'markdupes' module
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121 Input files are fastq files, and can be in gzip compressed format.
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122
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123 Author: Charles Girardot (charles.girardot@embl.de).
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124
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125 Wrapper by: Jelle Scholtalbers (jelle.scholtalbers@embl.de).
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126
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127 ------
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128
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129 **Know what you are doing**
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130
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131 .. class:: warningmark
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132
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133 You will want to read the `documentation`__.
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134
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135 .. __: http://gbcs.embl.de/portal/Je
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136
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137 ------
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138
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139 **Parameter list**
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140
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141 This is an exhaustive list of options::
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142
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143 FASTQ_FILE1=File
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144 F1=File
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145
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146 Input fastq file (optionally gzipped) for single end data, or first read in paired end
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147 data.
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148
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149 Required.
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150
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151 FASTQ_FILE2=File
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152 F2=File
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153
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154 Input fastq file (optionally gzipped) for the second read of paired end data.
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155
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156 Default value: null.
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157
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158 INDEX_FILE1=File
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159 I1=File
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160
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161 Fastq file for index 1 (barcode) reads, optionally gzipped
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162
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163 Required.
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164
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165 INDEX_FILE2=File
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166 I2=File
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167
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168 Fastq file for index 2 (barcode) reads, optionally gzipped.
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169 A INDEX_FILE1 MUST be provided when INDEX_FILE2 is given. This situation corresponds to
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170 Illumina dual indexing.
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171
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172 Default value: null.
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173
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174 BARCODE_FILE=File
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175 BF=File
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176
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177 Barcode file describing sequence list and sample names. Tab-delimited file with 2
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178 columns, with the sample in col1 and the corresponding barcode in col2.
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179 Simple barcode file format : 2 tab-delimited colums
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180 If multiple barcode map to the same sample, either line can be duplicated e.g.
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181 sample1 ATAT
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182 sample1 GAGG
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183 sample2 CCAA
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184 sample2 TGTG
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185 Or barcodes can be combined using the OR operator '|' i.e. the file above can be
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186 re-written like
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187 sample1 ATAT|GAGG
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188 sample2 CCAA|TGTG
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189 Finally, for the special situation of paired-end data in which barcodes differ at both
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190 ends (ie BPOS=BOTH BRED=false BM=BOTH , see BRED option description), barcodes for read_1
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191 and read_2 can be distinguished using a ':' separator i.e.
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192 sample1 ATAT:GAGG
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193 sample2 CCAA:TGTG
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194 This above syntax means that sample 1 is encoded with ATAT barcode at read_1 AND GAGG
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195 barcode at read_2. Note that you can still combine barcodes using | e.g.
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196 sample1 ATAT|GAGG:CCAA|TGTG
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197 would mean that sample 1 is mapped by the combination of barcode: ATAT OR GAGG at read_1
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198 AND CCAA OR TGTG at read_2.
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199 Extended barcode file format : 3 (single-end) or 4 (paired-end) tab-delimited colums
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200 same as the simple barcode file format but the extra columns contains the file name(s)
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201 to use to name output files. A unique extra column is expected for single-end while 2
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202 extra columns are expected for paired-end. In case, lines are duplicated (multiple
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203 barcodesmapping the same sample), the same file name should be indicated in the third
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204 (and fourth) column(s).
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205 sample1 ATAT spl1_1.txt.gz spl1_2.txt.gz
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206 sample1 GAGG spl1_1.txt.gz spl1_2.txt.gz
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207 sample2 CCAA spl2_1.txt.gz spl2_2.txt.gz
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208 Or
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209 sample1 ATAT|GAGG:CCAA|TGTG spl1_1.txt.gz spl1_2.txt.gz
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210 Ns in barcode sequence are allowed and are used to flag positions that should be ignored
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211 in sample matching
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212 i.e. they will be clipped off the read sequence (like in iCLIP protocol).
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213
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214 Required.
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215
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216 BARCODE_READ_POS=BarcodePosition
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217 BPOS=BarcodePosition
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218
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219 Indicates the location of additional barcodes present in the read(s). Setting this option
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220 implies setting the LEN option.
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221 Importantly, these additional barcodes must not encode sample identity information but
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222 used for e.g. molecular barcoding (UMIs) or for any purpose other than sample identity encoding.
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223
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224 Default value: BOTH. This option can be set to 'null' to clear the default value.
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225 Possible values: {READ_1, READ_2, BOTH, NONE}
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226
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227 BCLEN=String
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228 LEN=String
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229
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230 Length of the barcode sequences, optional. Taken from barcode file when not given.
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231 In situations where BARCODE_READ_POS == BOTH AND REDUNDANT_BARCODES=false, two distinct
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232 length can be provided using the syntax LEN=X:Z where X and Z are 2 integers representing
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233 the barcode length for read_1 and read_2 respectively.
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234
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235 Default value: null
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236
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237 REDUNDANT_BARCODES=Boolean
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238 BRED=Boolean
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239
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240 This option only applies for paired-end data with *both* INDEX_FILE1 and INDEX_FILE2
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241 provided.
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242 Indicates if both index barcodes encode redundant information i.e. if both barcodes are
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243 supposed to be identical (or resolve to the same sample when a pool of barcodes is used
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244 per sample).
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245 When BRED=true, the STRICT option guides the sample lookup behavior When BRED=false,
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246 barcodes are combined prior to sample lookup.
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247
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248 Default value: true. This option can be set to 'null' to clear the default value.
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249 Possible values: {true, false}
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250
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251 STRICT=Boolean
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252 S=Boolean
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253
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254 For paired-end data and when two distinct barcodes/indices are used to encode samples,
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255 this option tells if both barcodes should resolve to the same sample.
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256 When true and if only one of the two reads has a barcode match, the read pair is
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257 'unassigned'.
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258 When false and if only one of the two reads has a barcode match, the read pair is
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259 assigned to the
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260 corresponding sample
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261 When reads resolve to different samples, the read pair is always 'unassigned'.
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262
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263 Default value: false. This option can be set to 'null' to clear the default value.
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264 Possible values: {true, false}
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265
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266 MAX_MISMATCHES=String
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267 MM=String
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268
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269 Maximum mismatches for a barcode to be considered a match. In situations where both
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270 barcodes are used for sample matching i.e. BPOS=BOTH BM=BOTH (or 2 INDEX_FILE given), two
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271 distinct
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272 values can be given here using the syntax MM=X:Z where X and Z are 2 integers to use for
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273 read_1 and read_2 respectively.
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274 MM=null is like MM=0
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275
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276 Default value: 1. This option can be set to 'null' to clear the default value.
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277
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278 MIN_MISMATCH_DELTA=String
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279 MMD=String
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280
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281 Minimum difference between the number of mismatches against the best and the second best
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282 barcode. When MMD is not respected, the read remains unassigned.
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283 When two distinct barcodes are used for sample matching (dual encoding), two distinct
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284 values can be given using the syntax MMD=X:Z where X and Z are 2 integers to use for
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285 first (e.g. from read_1 or index_1)
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286 MMD=null is like MMD=0
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287
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288 Default value: 1. This option can be set to 'null' to clear the default value.
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289
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290 MIN_BASE_QUALITY=String
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291 Q=String
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292
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293 Minimum base quality during barcode matching: bases which quality is less than this
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294 cutoff are always considered as a mismatch.When two distinct barcodes are used for sample
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295 matching (dual encoding), two distinct values can be given using the syntax Q=X:Z where X
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296 and Z are 2 integers to use for first (e.g. from read_1 or index_1) and second barcode
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297 (e.g. from read_2 or index_2) respectively.
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298 Q=null is like Q=0.
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299
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300 Default value: 10. This option can be set to 'null' to clear the default value.
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301
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302 XTRIMLEN=String
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303 XT=String
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304
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305 Optional extra number of base to be trimmed right after the barcode (only used if
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306 CLIP_BARCODE=true).
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307 When running paired-end, two distinct values can be given using the syntax XT=X:Z where X
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308 and Z are 2 integers to use for read_1 and read_2 respectively. Note that even when
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309 BPOS=READ_1 or BPOS=READ_2, a X:Y synthax can be given to trim the read w/o barcode as to
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310 end up with reads of the same length (note that this can also be operated using ZT). If a
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311 unique value is given, e.g. XT=1, while running paired-end the following rule applies:
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312 (1) BPOS=READ_1 or BPOS=READ_2, no trim is applied at the read w/o barcode
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313 (2) BPOS=BOTH, the value is used for both reads.
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314
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315 Note that XT=null is like XT=0.
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316 Default value: 0. This option can be set to 'null' to clear the default value.
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317
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318 ZTRIMLEN=String
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319 ZT=String
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320
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321 Optional extra number of bases to be trimmed from the read end i.e. 3' end.
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322 When running paired-end, two distinct values can be given here using the syntax ZT=X:Z
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323 where X and Z are 2 integers to use for read_1 and read_2 respectively. Note that even
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324 when BPOS=READ_1 or BPOS=READ_2, a X:Y synthax can be given to trim the read w/o barcode
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325 as to end up with reads of the same length (note that this can also be operated using
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326 XT). Note that if a single value is passed, the value always applies to both reads in
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327 paired-end mode without further consideration.
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328 ZT=null is like ZT=0.
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329
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330 Default value: 0. This option can be set to 'null' to clear the default value.
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331
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332 CLIP_BARCODE=Boolean
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333 C=Boolean
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334
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335 Clip barcode sequence from read sequence, as well as XTRIMLEN (and ZTRIMLEN) bases if
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336 applicable, before writing to output file.
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337 If false, reads are written without modification to output file.
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338 Apply to both barcodes when BPOS=BOTH.
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339
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340 Default value: true. This option can be set to 'null' to clear the default value.
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341 Possible values: {true, false}
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342
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343 ADD_BARCODE_TO_HEADER=Boolean
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344 ADD=Boolean
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345
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346 Add matched barcode at the end of the read header. Applies to both index when INDEX_FILE2
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347 is also provided.
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348 First the sample encoding barcodes from I1 (and I2 when relevant) are added to the read
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349 headers like
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350 @D3FCO8P1:178:C1WLBACXX:7:1101:1836:1965 2:N:0:I1_BARCODE:I2_BARCODE
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351 Then, if BPOS!=NONE, the additional barcodes (UMIs) clipped from the read(s) are added
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352 to their own header, like
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353 @D3FCO8P1:178:C1WLBACXX:7:1101:1836:1965 2:N:0:I1_BARCODE:I2_BARCODE:CLIPPED_SEQ_FROMREAD
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354
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355 Default value: true. This option can be set to 'null' to clear the default value.
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356 Possible values: {true, false}
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357
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358 ENSURE_IDENTICAL_HEADER_NAMES=Boolean
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359 SAME_HEADERS=Boolean
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360
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361 Makes sure that headers of both reads of a pair are identical, using the following read
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362 header pattern (for both reads of a pair):
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363 @D3FCO8P1:178:C1WLBACXX:7:1101:1836:1965 I1_BARCODE:I2_BARCODE(:CLIPPED_SEQ_FROMREAD1:CLIPPED_SEQ_FROMREAD2)
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364 This option only makes sense in paired end mode and ADD=true. Some (if not all) mappers
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365 will indeed complain when the read headers are not identical. When molecular barcodes are
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366 present in reads and the RCHAR is used, you will end with (problematic) read headers like
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367 this:
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368 HISEQ:44:C6KC0ANXX:5:1101:1491:1994:1:N:0:TAGAACAC:TGGAGTAG
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369 HISEQ:44:C6KC0ANXX:5:1101:1491:1994:3:N:0:TAGAACAC:CGTTGTAT
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370 SAME_HEADERS=true will instead genetates the following identical header for both reads:
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371 HISEQ:44:C6KC0ANXX:5:1101:1491:1994:TAGAACAC:TGGAGTAG:CGTTGTAT
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372 Note that we also clipped the useless '1:N:0' and '3:N:0' has they will also result in
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373 generating different headers
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374 Important: this option will force RCHAR=: UNLESS you specify RCHAR=null ; in which
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375 case a space will be preserved ie:
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376 HISEQ:44:C6KC0ANXX:5:1101:1491:1994 TAGAACAC:TGGAGTAG:CGTTGTAT
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377
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378 Default value: true. This option can be set to 'null' to clear the default value.
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379 Possible values: {true, false}
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380
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381 READ_NAME_REPLACE_CHAR=String
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382 RCHAR=String
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383
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384 Replace spaces in read name/header using provided character. This is particularly handy
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385 when you need to retain ADDed barcode in read name/header during mapping (everything
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386 after space in read name is usually clipped in BAM files). For example, with RCHAR=':':
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387 '@D3FCO8P1:178:C1WLBACXX:7:1101:1836:1965 2:N:0:'
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388 becomes
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389 '@D3FCO8P1:178:C1WLBACXX:7:1101:1836:1965:2:N:0:BARCODE'
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390 Default value: null.
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391
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392 QUALITY_FORMAT=FastqQualityFormat
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393 V=FastqQualityFormat
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394
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395 A value describing how the quality values are encoded in the fastq. Either 'Solexa' for
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396 pre-pipeline 1.3 style scores (solexa scaling + 66), 'Illumina' for pipeline 1.3 and
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397 above (phred scaling + 64) or 'Standard' for phred scaled scores with a character shift
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398 of 33. If this value is not specified (or 'null' is given), the quality format will be
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399 detected.
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400
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401 Default value: Standard. This option can be set to 'null' to clear the default value.
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402 Possible values: {Solexa, Illumina, Standard}
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403
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404 KEEP_UNASSIGNED_READ=Boolean
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405 UN=Boolean
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406
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407 Should un-assigned reads be saved in files or simply ignored. File names are
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408 automatically created or can be given using UF1 & UF2 options.
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409
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410 Default value: true. This option can be set to 'null' to clear the default value.
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411 Possible values: {true, false}
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412
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413 BARCODE_DIAG_FILE=String
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414 DIAG=String
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415
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416 Name for a barcode match reporting file (not generated by default).Either a name (in
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417 which case the file will be created in the output dir) or full path. This file will
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418 contain a line per read pair with the barcode best matching the read subsequence or
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419 'null' when no match is found according to matching parameters ; and the final selected
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420 sample. This file is useful for debugging or further processing in case both ends are
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421 barcoded.
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422 N.B: this file will have a size of about one of the fastq input files.
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423
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424 Default value: null.
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425 ]]>
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426 </help>
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427
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428 </tool>
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