annotate je-clip.xml @ 8:b2977ee0d42d draft

planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit bc2365188e0dd0f20925884276a27914bb714280
author gbcs-embl-heidelberg
date Mon, 23 Apr 2018 05:46:19 -0400
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1 <tool id="je_clip" name="Je-Clip" version="@VERSION_STRING@">
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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 <expand macro="requirements" />
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7 <stdio>
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8 <exit_code range="1:" level="fatal" description="Tool exception" />
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9 </stdio>
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10 <expand macro="version_command" />
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11 <command>
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12 <![CDATA[
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13 je clip
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14
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15 ## Fastq inputs
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16 @single_or_paired_cmd@
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17 #if str( $library.type ) != "single":
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18 BPOS=${library.BPOS}
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19 #end if
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20
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21 @common_options_cmd@
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22 @barcode_len_cmd@
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23 ADD=${ADD}
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24 #if str($ADD) == "false":
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25 BARCODE_RESULT_FILENAME=${BARCODE_RESULT_FILENAME}
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26 #end if
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27
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28 OF1=${OF1}
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29 #if str( $library.type ) != "single":
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30 OF2=${OF2}
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31 #end if
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32
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33 FORCE=true
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34 ]]>
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35 </command>
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36 <inputs>
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37 <!-- single/paired -->
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38 <expand macro="single_or_paired_general">
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39 <param name="BPOS" type="select" label="Barcode read position (BPOS)" help="where are the barcodes.">
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40 <option value="READ_1" selected="true">READ_1 (beginning of read from the first fastq file)</option>
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41 <option value="READ_2">READ_2 (beginning of read from the second fastq file)</option>
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42 <option value="BOTH">BOTH (beginning of both reads)</option>
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43 </param>
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44 </expand>
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45 <expand macro="barcode_len_option"/>
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46 <param name="ADD" type="boolean"
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47 label="Add matched barcode at the end of the read header (ADD)"
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48 truevalue="true"
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49 falsevalue="false"
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50 checked="true"
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51 />
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52
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53 <expand macro="common_options"/>
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54
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55
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56 </inputs>
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57 <outputs>
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58 <data name="BARCODE_RESULT_FILENAME" format="tabular" label="Je-Clipped Barcodes">
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59 <filter>!ADD</filter>
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60 </data>
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61 <data name="OF1" format_source="input_1" label="Je-Clip OF1: ${on_string}"/>
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62 <data name="OF2" format_source="input_2" label="Je-Clip OF2: ${on_string}">
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63 <filter>library["type"] != "single"</filter>
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64 </data>
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65 </outputs>
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66
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67 <tests>
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68 <test>
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69 <!-- simple test on single end data -->
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70 <param name="type" value="single"/>
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71 <param name="input_1" value="file_1_sequence.txt" ftype="fastqsanger"/>
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72 <param name="LEN" value="6"/>
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73 <param name="ADD" value="false"/>
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74 <output name="BARCODE_RESULT_FILENAME" file="clip_barcode_result_file.txt"/>
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75 <output name="OF1" file="clip_dataset1_SE.fastq"/>
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76 </test>
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77 <test>
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78 <!-- more complex test on paired end data with different barcode for fwd/rev -->
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79 <param name="type" value="paired"/>
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80 <param name="input_1" value="file_1_sequence.txt" ftype="fastqsanger"/>
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81 <param name="input_2" value="file_2_sequence.txt" ftype="fastqsanger"/>
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82 <param name="LEN" value="6"/>
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83 <param name="BPOS" value="BOTH"/>
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84 <output name="OF1" file="clip_dataset1_PE.fastq"/>
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85 <output name="OF2" file="clip_dataset2_PE.fastq"/>
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86 </test>
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87 </tests>
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88
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89 <help>
0
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90 <![CDATA[
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91 **What it does**
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92
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93 Je clip: Clips barcodes or Unique Molecular Identifiers (UMIs) from the input fastq files
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94 Input files are fastq files, and can be in gzip compressed format.
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95
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96 Author: Charles Girardot (charles.girardot@embl.de).
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97
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98 Wrapper by: Jelle Scholtalbers (jelle.scholtalbers@embl.de).
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99
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100 ------
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101
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102 **Know what you are doing**
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103
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104 .. class:: warningmark
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105
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106 You will want to read the `documentation`__.
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107
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108 .. __: http://gbcs.embl.de/portal/Je
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109
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110 ------
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111
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112 **Parameter list**
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113
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114 This is an exhaustive list of options::
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115
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116 FASTQ_FILE1=File
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117 F1=File
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118
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119 Input fastq file (optionally gzipped) for single end data, or first read in paired end data.
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120 Required.
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121
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122 FASTQ_FILE2=File
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123 F2=File
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124
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125 Input fastq file (optionally gzipped) for the second read of paired end data.
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126 Default value: null.
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127
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128 BCLEN=String
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129 LEN=String
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130
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131 Length of the barcode sequences. When BARCODE_READ_POS == BOTH, two distinct lengths can
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132 be provided using the syntax LEN=X:Z where X and Z are 2 integers representing the
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133 barcode length for read_1 and read_2 respectively.
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134 Required.
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135
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136 BARCODE_READ_POS=BarcodePosition
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137 BPOS=BarcodePosition
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138
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139 Reads containing the sequence (i.e. UMIs) to clip:
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140 READ_1 (beginning of read from FASTQ_FILE_1),
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141 READ_2 (beginning of read from FASTQ_FILE_2),
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142 BOTH (beginning of both reads).
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143
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144 Automatically set to READ_1 in single end mode and BOTH in paired end mode. Actually not
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145 relevant for single end data
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146 Default value: BOTH. This option can be set to 'null' to clear the default value.
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147 Possible values: {READ_1, READ_2, BOTH, NONE}
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148
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149 ADD_BARCODE_TO_HEADER=Boolean
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150 ADD=Boolean
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151
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152 Should clipped UMIs be added to the read header (at the end); apply to both barcodes when
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153 BPOS=BOTH.
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154 If ADD=true, the string ':barcode' is added at the end of the read header with a ':'
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155 added only if current read header does not end with ':'.
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156 If both reads of the pair contains a UMI (i.e. BARCODE_READ_POS == BOTH), the UMI from
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157 the second read is also added to the read header.
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158 Else, the header of the read without UMI receives the UMI from the other read.
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159 For example:
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160 @D3FCO8P1:178:C1WLBACXX:7:1101:1836:1965 2:N:0:
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161 becomes
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162 @D3FCO8P1:178:C1WLBACXX:7:1101:1836:1965 2:N:0:BARCODE
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163 Default value: true. This option can be set to 'null' to clear the default value.
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164 Possible values: {true, false}
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165
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166 ENSURE_IDENTICAL_HEADER_NAMES=Boolean
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167 SAME_HEADERS=Boolean
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168
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169 Makes sure headers of both reads of a pair are identical.
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170 Read name (or headers) will follow the pattern (for both reads of a pair):
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171 @D3FCO8P1:178:C1WLBACXX:7:1101:1836:1965 CLIPPED_SEQ_FROMREAD1:CLIPPED_SEQ_FROMREAD2
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172 This option only makes sense in paired end mode and ADD=true.Some (if not all) mappers
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173 will indeed complain when read headers of a read pair are not identical.
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174 When SAME_HEADERS=FALSE and the RCHAR is used, read headers look like this:
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175 HISEQ:44:C6KC0ANXX:5:1101:1491:1994:1:N:0:TGGAGTAG
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176 HISEQ:44:C6KC0ANXX:5:1101:1491:1994:3:N:0:CGTTGTAT
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177
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178 SAME_HEADERS=true will instead generates the following identical header for both reads :
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179 HISEQ:44:C6KC0ANXX:5:1101:1491:1994:TGGAGTAG:CGTTGTAT
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180 Note that we also clipped the useless '1:N:0' amd '3:N:0' as they also result in
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181 different headers
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182 Important : this option will force RCHAR=: UNLESS you specify RCHAR=null ; in which case
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183 a space will be preserved i.e.:
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184 HISEQ:44:C6KC0ANXX:5:1101:1491:1994 TAGAACAC:TGGAGTAG:CGTTGTAT
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185
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186 Default value: true.
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187 This option can be set to 'null' to clear the default value. Possible values: {true,
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188 false}
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189
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190 READ_NAME_REPLACE_CHAR=String
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191 RCHAR=String
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192
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193 Replace spaces in read name/header using provided character.
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194 This is needed when you need to retain ADDed barcode in read name/header during mapping
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195 as everything after space in read name is usually clipped in BAM files.
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196 For example, with RCHAR=':':
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197 @D3FCO8P1:178:C1WLBACXX:7:1101:1836:1965 1:N:0:
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198 becomes
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199 @D3FCO8P1:178:C1WLBACXX:7:1101:1836:1965:1:N:0:BARCODE
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200
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201 Default value: ':'. This option can be set to 'null' to clear the default value.
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202
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203 XTRIMLEN=String
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204 XT=String
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205
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206 Optional extra number of base(s) to be trimmed right after the barcode. These extra bases
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207 are not added to read headers.
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208 When running paired-end, two distinct values can be given using the syntax XT=X:Z where X
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209 and Z are 2 integers to use for read_1 and read_2 respectively. Note that even when
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210 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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211 end up with reads of identical length (note that this can also be operated using ZT). If
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212 a unique value is given, e.g. XT=1, while running paired-end the following rule applies :
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213 (1) BPOS=READ_1 or BPOS=READ_2, no trim is applied at the read w/o barcode
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214 (2) BPOS=BOTH, the value is used for both reads.
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215 Note that XT=null is like XT=0.
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216 Default value: 0. This option can be set to 'null' to clear the default value.
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217
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218 ZTRIMLEN=String
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219 ZT=String
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220
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221 Optional extra number of bases to be trimmed from the read end i.e. 3' end. These extra
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222 bases are not added to read headers.
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223 When running paired-end, two distinct values can be given here using the syntax ZT=X:Z
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224 where X and Z are 2 integers to use for read_1 and read_2 respectively. Note that even
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225 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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226 as to end up with reads of the same length (note that this can also be operated using
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227 XT). Note that if a single value is passed, the value always applies to both reads in
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228 paired-end mode without further consideration.
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229
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230 Default value: 0. This option can be set to 'null' to clear the default value.
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231
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232 BARCODE_RESULT_FILENAME=String
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233 BF=String
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234
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235 Optional file name where to write clipped barcodes, default name is clipped_barcodes.txt.
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236 This file is automatically created if ADD=FALSE i.e. even if this option is not provided
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237 by user (and always created if this option is given).
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238 File format is tab delimited with:
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239 ``read header (col 1) barcode from read_1 (col 2) barcode quality from read_1 (col 2)``
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240 + barcode + quality from read_2 (col 4 and 5 respectively) when relevant.
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241 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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242 Default value: null.
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243
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244 ]]>
5
8b4ccdf5f7dd planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 0eefd837333dae6fbecaf4f55b053268d844eff6
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245 </help>
8b4ccdf5f7dd planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit 0eefd837333dae6fbecaf4f55b053268d844eff6
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246 <expand macro="citations"/>
0
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247 </tool>