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1 <tool id="je_clip" name="Je-Clip" version="1.0">
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2 <description>clips Unique Molecular Identifiers (UMIs) from fastq files</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 clip
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13
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14 ## Fastq inputs
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15 @single_or_paired_cmd@
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16 #if str( $library.type ) != "single":
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17 BPOS=${library.BPOS}
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18 #end if
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19
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20 @common_options_cmd@
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21 @barcode_len_cmd@
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22 ADD=${ADD}
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23 #if str($ADD) == "false":
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24 BARCODE_RESULT_FILENAME=$BARCODE_RESULT_FILENAME
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25 #end if
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26
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27 OF1=${OF1}
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28 #if str( $library.type ) != "single":
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29 OF2=${OF2}
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30 #end if
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31
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32 FORCE=true
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33 ]]>
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34 </command>
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35 <inputs>
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36 <!-- single/paired -->
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37 <expand macro="single_or_paired_general">
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38 <param name="BPOS" type="select" label="Barcode read position (BPOS)" help="where are the barcodes.">
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39 <option value="READ_1" selected="true">READ_1 (beginning of read from the first fastq file)</option>
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40 <option value="READ_2">READ_2 (beginning of read from the second fastq file)</option>
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41 <option value="BOTH">BOTH (beginning of both reads)</option>
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42 </param>
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43 </expand>
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44 <expand macro="barcode_len_option"/>
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45 <param name="ADD" type="boolean"
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46 label="Add matched barcode at the end of the read header (ADD)"
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47 truevalue="true"
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48 falsevalue="false"
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49 checked="true"
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50 />
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51
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52 <expand macro="common_options"/>
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53
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54
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55 </inputs>
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56 <outputs>
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57 <data name="BARCODE_RESULT_FILENAME" format="tabular" label="Je-Clipped Barcodes"/>
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58 <data name="OF1" format_source="input_1" label="Je-Clipped {on_string}"/>
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59 <data name="OF2" format_source="input_1" label="Je-Clipped {on_string}">
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60 <filter>(type != "single")</filter>
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61 </data>
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62 </outputs>
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63
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64 <tests>
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65 <test>
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66 <!-- simple test on single end data -->
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67 <param name="type" value="single"/>
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68 <param name="input_1" value="file_1_sequence.txt" ftype="fastqsanger"/>
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69 <param name="LEN" value="6"/>
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70 <param name="ADD" value="false"/>
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71 <output name="BARCODE_RESULT_FILENAME" file="clip_barcode_result_file.txt"/>
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72 <output name="OF1" file="clip_dataset1_SE.fastq"/>
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73 </test>
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74 <test>
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75 <!-- more complex test on paired end data with different barcode for fwd/rev -->
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76 <param name="type" value="paired"/>
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77 <param name="input_1" value="file_1_sequence.txt" ftype="fastqsanger"/>
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78 <param name="input_2" value="file_2_sequence.txt" ftype="fastqsanger"/>
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79 <param name="LEN" value="6"/>
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80 <param name="BPOS" value="BOTH"/>
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81 <output name="OF1" file="clip_dataset1_PE.fastq"/>
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82 <output name="OF2" file="clip_dataset2_PE.fastq"/>
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83 </test>
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84 </tests>
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85
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86
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87 <help>
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88 <![CDATA[
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89 **What it does**
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90
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91 Je clip: Clips barcodes or Unique Molecular Identifiers (UMIs) from the input fastq files
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92 Input files are fastq files, and can be in gzip compressed format.
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93
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94 Author: Charles Girardot (charles.girardot@embl.de).
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95
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96 Wrapper by: Jelle Scholtalbers (jelle.scholtalbers@embl.de).
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97
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98 ------
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99
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100 **Know what you are doing**
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101
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102 .. class:: warningmark
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103
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104 You will want to read the `documentation`__.
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105
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106 .. __: http://gbcs.embl.de/portal/Je
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107
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108 ------
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109
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110 **Parameter list**
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111
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112 This is an exhaustive list of options::
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113
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114 FASTQ_FILE1=File
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115 F1=File
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116
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117 Input fastq file (optionally gzipped) for single end data, or first read in paired end data.
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118 Required.
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119
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120 FASTQ_FILE2=File
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121 F2=File
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122
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123 Input fastq file (optionally gzipped) for the second read of paired end data.
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124 Default value: null.
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125
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126 BCLEN=String
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127 LEN=String
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128
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129 Length of the barcode sequences. When BARCODE_READ_POS == BOTH, two distinct lengths can
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130 be provided using the syntax LEN=X:Z where X and Z are 2 integers representing the
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131 barcode length for read_1 and read_2 respectively.
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132 Required.
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133
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134 BARCODE_READ_POS=BarcodePosition
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135 BPOS=BarcodePosition
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136
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137 Reads containing the sequence (i.e. UMIs) to clip:
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138 READ_1 (beginning of read from FASTQ_FILE_1),
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139 READ_2 (beginning of read from FASTQ_FILE_2),
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140 BOTH (beginning of both reads).
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141
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142 Automatically set to READ_1 in single end mode and BOTH in paired end mode. Actually not
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143 relevant for single end data
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144 Default value: BOTH. This option can be set to 'null' to clear the default value.
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145 Possible values: {READ_1, READ_2, BOTH, NONE}
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146
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147 ADD_BARCODE_TO_HEADER=Boolean
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148 ADD=Boolean
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149
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150 Should clipped UMIs be added to the read header (at the end); apply to both barcodes when
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151 BPOS=BOTH.
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152 If ADD=true, the string ':barcode' is added at the end of the read header with a ':'
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153 added only if current read header does not end with ':'.
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154 If both reads of the pair contains a UMI (i.e. BARCODE_READ_POS == BOTH), the UMI from
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155 the second read is also added to the read header.
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156 Else, the header of the read without UMI receives the UMI from the other read.
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157 For example:
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158 @D3FCO8P1:178:C1WLBACXX:7:1101:1836:1965 2:N:0:
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159 becomes
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160 @D3FCO8P1:178:C1WLBACXX:7:1101:1836:1965 2:N:0:BARCODE
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161 Default value: true. This option can be set to 'null' to clear the default value.
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162 Possible values: {true, false}
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163
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164 ENSURE_IDENTICAL_HEADER_NAMES=Boolean
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165 SAME_HEADERS=Boolean
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166
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167 Makes sure headers of both reads of a pair are identical.
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168 Read name (or headers) will follow the pattern (for both reads of a pair):
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169 @D3FCO8P1:178:C1WLBACXX:7:1101:1836:1965 CLIPPED_SEQ_FROMREAD1:CLIPPED_SEQ_FROMREAD2
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170 This option only makes sense in paired end mode and ADD=true.Some (if not all) mappers
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171 will indeed complain when read headers of a read pair are not identical.
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172 When SAME_HEADERS=FALSE and the RCHAR is used, read headers look like this:
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173 HISEQ:44:C6KC0ANXX:5:1101:1491:1994:1:N:0:TGGAGTAG
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174 HISEQ:44:C6KC0ANXX:5:1101:1491:1994:3:N:0:CGTTGTAT
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175
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176 SAME_HEADERS=true will instead generates the following identical header for both reads :
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177 HISEQ:44:C6KC0ANXX:5:1101:1491:1994:TGGAGTAG:CGTTGTAT
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178 Note that we also clipped the useless '1:N:0' amd '3:N:0' as they also result in
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179 different headers
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180 Important : this option will force RCHAR=: UNLESS you specify RCHAR=null ; in which case
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181 a space will be preserved i.e.:
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182 HISEQ:44:C6KC0ANXX:5:1101:1491:1994 TAGAACAC:TGGAGTAG:CGTTGTAT
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183
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184 Default value: true.
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185 This option can be set to 'null' to clear the default value. Possible values: {true,
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186 false}
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187
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188 READ_NAME_REPLACE_CHAR=String
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189 RCHAR=String
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190
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191 Replace spaces in read name/header using provided character.
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192 This is needed when you need to retain ADDed barcode in read name/header during mapping
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193 as everything after space in read name is usually clipped in BAM files.
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194 For example, with RCHAR=':':
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195 @D3FCO8P1:178:C1WLBACXX:7:1101:1836:1965 1:N:0:
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196 becomes
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197 @D3FCO8P1:178:C1WLBACXX:7:1101:1836:1965:1:N:0:BARCODE
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198
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199 Default value: ':'. This option can be set to 'null' to clear the default value.
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200
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201 XTRIMLEN=String
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202 XT=String
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203
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204 Optional extra number of base(s) to be trimmed right after the barcode. These extra bases
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205 are not added to read headers.
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206 When running paired-end, two distinct values can be given using the syntax XT=X:Z where X
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207 and Z are 2 integers to use for read_1 and read_2 respectively. Note that even when
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208 BPOS=READ_1 or BPOS=READ_2, a X:Y synthax can be given to trim the read w/o barcode to
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209 end up with reads of identical length (note that this can also be operated using ZT). If
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210 a unique value is given, e.g. XT=1, while running paired-end the following rule applies :
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211 (1) BPOS=READ_1 or BPOS=READ_2, no trim is applied at the read w/o barcode
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212 (2) BPOS=BOTH, the value is used for both reads.
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213 Note that XT=null is like XT=0.
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214 Default value: 0. This option can be set to 'null' to clear the default value.
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215
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216 ZTRIMLEN=String
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217 ZT=String
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218
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219 Optional extra number of bases to be trimmed from the read end i.e. 3' end. These extra
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220 bases are not added to read headers.
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221 When running paired-end, two distinct values can be given here using the syntax ZT=X:Z
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222 where X and Z are 2 integers to use for read_1 and read_2 respectively. Note that even
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223 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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224 as to end up with reads of the same length (note that this can also be operated using
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225 XT). Note that if a single value is passed, the value always applies to both reads in
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226 paired-end mode without further consideration.
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227
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228 Default value: 0. This option can be set to 'null' to clear the default value.
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229
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230 BARCODE_RESULT_FILENAME=String
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231 BF=String
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232
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233 Optional file name where to write clipped barcodes, default name is clipped_barcodes.txt.
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234 This file is automatically created if ADD=FALSE i.e. even if this option is not provided
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235 by user (and always created if this option is given).
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236 File format is tab delimited with:
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237 ``read header (col 1) barcode from read_1 (col 2) barcode quality from read_1 (col 2)``
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238 + barcode + quality from read_2 (col 4 and 5 respectively) when relevant.
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239 Can either be a name (in which case the file will be created in the output dir) or a full path.
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240 Default value: null.
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241
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242 ]]>
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243 </help>
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244
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245 </tool>
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