annotate macros.xml @ 14:f1d33e4c7bd8 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit 31bad8c5bf75981eafcd19ec6b00593f184fdeb8"
author iuc
date Thu, 18 Nov 2021 08:25:56 +0000
parents aa9a4233c641
children 04e09969d376
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1 <?xml version="1.0"?>
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2 <macros>
12
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3
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4 <!-- macros applying to all umi_tools -->
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5
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6 <token name="@TOOL_VERSION@">1.1.2</token>
14
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7 <token name="@VERSION_SUFFIX@">2</token>
12
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8 <token name="@PROFILE@">21.01</token>
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9 <xml name="requirements">
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10 <requirements>
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11 <requirement type="package" version="@TOOL_VERSION@">umi_tools</requirement>
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12 <yield />
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13 </requirements>
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14 </xml>
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15 <xml name="citations">
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16 <citations>
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17 <citation type="doi">10.1101/gr.209601.116</citation>
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18 <citation type="bibtex">
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19 @misc{githubUMI-tools,
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20 title = {UMI-tools},
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21 publisher = {GitHub},
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22 journal = {GitHub repository},
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23 url = {https://github.com/CGATOxford/UMI-tools},
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24 }
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25 </citation>
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26 </citations>
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27 </xml>
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28 <xml name="advanced_options_macro">
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29 <section name="advanced" title="Extra parameters" expanded="false">
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30 <param argument="--random-seed" type="integer" min="0" optional="true" label="Random Seed" />
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31 </section>
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32 </xml>
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33 <token name="@ADVANCED_OPTIONS@"><![CDATA[
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34 #if str($advanced.random_seed) != ''
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35 --random-seed='$advanced.random_seed'
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36 #end if
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37 ]]></token>
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38
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39 <!-- macros for extract and whitelist-->
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40
8
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41 <macro name="barcode_sanitizer" >
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42 <sanitizer invalid_char="">
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43 <valid initial="string.letters,string.digits">
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44 <add value="&#42;" /><!-- asterisk -->
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45 <add value="&#44;" /><!-- comma -->
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46 <add value="&#46;" /><!-- period -->
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47 <add value="&#60;" /><!-- less than -->
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48 <add value="&#61;" /><!-- equals sign -->
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49 <add value="&#62;" /><!-- greater than -->
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50 <add value="&#63;" /><!-- question mark -->
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51 <add value="&#95;" /><!-- underscore -->
9
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52 <add value="&#40;" /><!-- left bracket -->
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53 <add value="&#41;" /><!-- right bracket -->
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54 <add value="&#91;"/> <!-- left square bracket -->
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55 <add value="&#93;"/> <!-- right square bracket -->
8
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56 <add value="&#123;"/><!-- left brace -->
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57 <add value="&#125;"/><!-- right brace -->
9
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58 <add value="&#94;"/> <!-- caret -->
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59 <add value="&#36;"/> <!-- dollar sign-->
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60 <add value="&#43;" /><!-- plus sign -->
9
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61 <add value="-"/>
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62 <add value="!"/>
8
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63 </valid>
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64 </sanitizer>
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65 </macro>
12
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66 <xml name="sanitize_tag" >
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67 <sanitizer invalid_char="">
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68 <valid initial="string.letters,string.digits" />
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69 </sanitizer>
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70 </xml>
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71 <macro name="barcode1_macro" >
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72 <param argument="--bc-pattern" type="text" label="Barcode pattern for first read"
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73 help="Use this option to specify the format of the UMI/barcode. Use Ns to
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74 represent the random positions and Xs to indicate the bc positions.
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75 Bases with Ns will be extracted and added to the read name. Remaining
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76 bases, marked with an X will be reattached to the read">
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77 <validator type="empty_field" />
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78 <expand macro="barcode_sanitizer" />
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79 </param>
2
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80 </macro>
12
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81 <macro name="barcode2_macro" >
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82 <param argument="--bc-pattern2" type="text" value="" label="Barcode pattern for second read"
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83 help="Use this option to specify the format of the UMI/barcode for
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84 the second read pair if required" >
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85 <expand macro="barcode_sanitizer" />
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86 </param>
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87 </macro>
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88 <!-- not just fastq because this would allow also fastqcsanger -->
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89 <token name="@FASTQ_FORMATS@">fastqsanger,fastqsanger.gz,fastqillumina,fastqillumina.gz,fastqsolexa,fastqsolexa.gz</token>
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90 <xml name="bio_tools">
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91 <xrefs>
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92 <xref type="bio.tools">umi-tools</xref>
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93 </xrefs>
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94 </xml>
2
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95 <xml name="input_types">
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96 <conditional name="input_type_cond">
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97 <param name="input_type" type="select" label="Library type">
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98 <option value="single">Single-end</option>
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99 <option value="paired">Paired-end</option>
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100 <option value="paired_collection">Paired-end Dataset Collection</option>
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101 </param>
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102 <when value="single">
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103 <param name="input_read1" type="data" format="@FASTQ_FORMATS@" label="Reads in FASTQ format" />
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104 <expand macro="barcode1_macro"/>
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105 </when>
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106 <when value="paired">
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107 <param name="input_read1" type="data" format="@FASTQ_FORMATS@" label="Reads in FASTQ format" />
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108 <param name="input_read2" type="data" format="@FASTQ_FORMATS@" label="Reads in FASTQ format" />
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109 <expand macro="barcode1_macro"/>
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110 <expand macro="barcode2_macro"/>
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111 <yield/>
2
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112 </when>
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113 <when value="paired_collection">
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114 <param name="input_readpair" type="data_collection" collection_type="paired" format="@FASTQ_FORMATS@" label="Reads in FASTQ format" />
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115 <expand macro="barcode1_macro"/>
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116 <expand macro="barcode2_macro"/>
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117 <yield/>
2
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118 </when>
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119 </conditional>
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120 </xml>
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121 <token name="@COMMAND_LINK@"><![CDATA[
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122 #set $gz = False
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123 #if $input_type_cond.input_type == 'single':
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124 #if $input_type_cond.input_read1.is_of_type("fastq.gz", "fastqsanger.gz"):
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125 ln -s '$input_type_cond.input_read1' input_single.gz &&
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126 #set $gz = True
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127 #else
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128 ln -s '$input_type_cond.input_read1' input_single.txt &&
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129 #end if
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130 #elif $input_type_cond.input_type == 'paired':
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131 #if $input_type_cond.input_read1.is_of_type("fastq.gz", "fastqsanger.gz"):
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132 ln -s '$input_type_cond.input_read1' input_read1.gz &&
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133 ln -s '$input_type_cond.input_read2' input_read2.gz &&
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134 #set $gz = True
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135 #else
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136 ln -s '$input_type_cond.input_read1' input_read1.txt &&
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137 ln -s '$input_type_cond.input_read2' input_read2.txt &&
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138 #end if
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139 #else ## paired_collection
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140 #if $input_type_cond.input_readpair.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
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141 ln -s '$input_type_cond.input_readpair.forward' input_read1.gz &&
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142 ln -s '$input_type_cond.input_readpair.reverse' input_read2.gz &&
2
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143 #set $gz = True
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144 #else
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145 ln -s '$input_type_cond.input_readpair.forward' input_read1.txt &&
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146 ln -s '$input_type_cond.input_readpair.reverse' input_read2.txt &&
2
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147 #end if
12
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148 #end if
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149 ]]></token>
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150
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151 <!-- macros for count, dedup, and group -->
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152
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153 <token name="@LINK_SAM_BAM_INPUT@"><![CDATA[
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154 #if $input.is_of_type("sam"):
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155 ## TODO dedup has problems with SAM input in some cases
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156 ## https://github.com/CGATOxford/UMI-tools/issues/483
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157 ## so convert it to sorted BAM for now
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158 ## #set $input_file = $input
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159 samtools sort --no-PG '$input' > 'input.bam' &&
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160 samtools index -b 'input.bam' &&
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161 #set $input_file = 'input.bam'
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162 #else:
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163 ln -sf '${input}' 'input.bam' &&
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164 ln -sf '$input.metadata.bam_index' 'input.bam.bai' &&
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165 #set $input_file = 'input.bam'
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166 #end if
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167 ]]></token>
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168 <token name="@SET_INPUT_TYPE@"><![CDATA[
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169 ## TODO see comment in LINK_SAM_BAM_INPUT
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170 ## #if $input.is_of_type("sam"):
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171 ## --in-sam
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172 ## #end if
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173 ]]></token>
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174
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175 <xml name="fastq_barcode_extraction_options_macro">
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176 <conditional name="extract_method_cond">
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177 <param argument="--extract-method" type="select" label="Barcode Extraction Method"
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178 help="If bracketed expressions are used in the above barcode pattern, then set this to 'regex'. Otherwise leave as 'string'" >
14
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179 <option value="string" selected="true">String</option>
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180 <option value="regex">Regex</option>
12
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181 </param>
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182 <when value="string">
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183 <param argument="--3prime" name="prime3" type="boolean" label="Is barcode on 3' end of the read?"
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184 truevalue="--3prime" falsevalue=""
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185 help="By default the barcode is assumed to be on the 5' end of the read, but
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186 use this option to specify that it is on the 3' end instead.
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187 This option only works with ``--extract-method=string``
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188 since 3' encoding can be specified explicitly with a regex, e.g
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189 ``.*(?P&lt;umi_1&gt;.{5})$``" />
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190 </when>
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191 <when value="regex">
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192 <param name="filtered_out_bool" type="boolean" label="Write out reads not matching regex pattern"/>
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193 </when>
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194 </conditional>
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195 <param argument="--ignore-read-pair-suffixes" type="boolean" truevalue="--ignore-read-pair-suffixes" falsevalue="" label="Ignore '\1' and '\2' read name suffixes"/>
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196 </xml>
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197 <token name="@FASTQ_BARCODE_EXTRACTION_OPTIONS@"><![CDATA[
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198 ## fastq barcode extraction options:
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199 --extract-method='$extract_method_cond.extract_method'
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200 --bc-pattern='$input_type_cond.bc_pattern'
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201 #if $input_type_cond.input_type != 'single' and $input_type_cond.bc_pattern2 != ''
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202 --bc-pattern2='$input_type_cond.bc_pattern2'
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203 #end if
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204 #if $extract_method_cond.extract_method == 'string'
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205 $extract_method_cond.prime3
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206 #else if $extract_method_cond.filtered_out_bool
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207 #if $input_type_cond.input_type == 'single':
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208 --filtered-out='$filtered_out'
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209 #else if $input_type_cond.input_type == 'paired':
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210 --filtered-out='$filtered_out'
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211 --filtered-out2='$filtered_out_paired'
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212 #else
12
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213 --filtered-out='$filtered_out_paired_collection.forward'
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214 --filtered-out2='$filtered_out_paired_collection.reverse'
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215 #end if
12
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216 #end if
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217 $ignore_read_pair_suffixes
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218 ]]></token>
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219 <token name="@FASTQ_BARCODE_EXTRACTION_HELP@"><![CDATA[
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220 There are two methods enabled to extract the umi barcode (+/-
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221 cell barcode). For both methods, the patterns should be provided
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222 using the ``--bc-pattern`` and ``--bc-pattern2`` options.x
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223
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224 - ``string``
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225 This should be used where the barcodes are always in the same
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226 place in the read.
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227
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228 - N = UMI position (required)
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229 - C = cell barcode position (optional)
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230 - X = sample position (optional)
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231
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232 Bases with Ns and Cs will be extracted and added to the read
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233 name. The corresponding sequence qualities will be removed from
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234 the read. Bases with an X will be reattached to the read.
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235
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236 E.g. If the pattern is `NNNNCC`,
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237 Then the read::
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238
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239 @HISEQ:87:00000000 read1
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240 AAGGTTGCTGATTGGATGGGCTAG
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241 +
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242 DA1AEBFGGCG01DFH00B1FF0B
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243
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244 will become::
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245
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246 @HISEQ:87:00000000_TT_AAGG read1
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247 GCTGATTGGATGGGCTAG
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248 +
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249 1AFGGCG01DFH00B1FF0B
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250
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251 where 'TT' is the cell barcode and 'AAGG' is the UMI.
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252
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253 - ``regex``
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254 This method allows for more flexible barcode extraction and
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255 should be used where the cell barcodes are variable in
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256 length. Alternatively, the regex option can also be used to
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257 filter out reads which do not contain an expected adapter
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258 sequence. UMI-tools uses the regex module rather than the more
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259 standard re module since the former also enables fuzzy matching
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260
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261 The regex must contain groups to define how the barcodes are
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262 encoded in the read. The expected groups in the regex are:
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263
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264 umi_n = UMI positions, where n can be any value (required)
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265 cell_n = cell barcode positions, where n can be any value (optional)
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266 discard_n = positions to discard, where n can be any value (optional)
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267
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268 UMI positions and cell barcode positions will be extracted and
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269 added to the read name. The corresponding sequence qualities
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270 will be removed from the read.
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271
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272 Discard bases and the corresponding quality scores will be
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273 removed from the read. All bases matched by other groups or
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274 components of the regex will be reattached to the read sequence
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275
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276 For example, the following regex can be used to extract reads
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277 from the Klein et al inDrop data::
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278
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279 (?P<cell_1>.{8,12})(?P<discard_1>GAGTGATTGCTTGTGACGCCTT)(?P<cell_2>.{8})(?P<umi_1>.{6})T{3}.*
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280
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281 Where only reads with a 3' T-tail and `GAGTGATTGCTTGTGACGCCTT` in
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282 the correct position to yield two cell barcodes of 8-12 and 8bp
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283 respectively, and a 6bp UMI will be retained.
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284
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285 You can also specify fuzzy matching to allow errors. For example if
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286 the discard group above was specified as below this would enable
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287 matches with up to 2 errors in the discard_1 group.
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288
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289 ::
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290
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291 (?P<discard_1>GAGTGATTGCTTGTGACGCCTT){s<=2}
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292
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293 Note that all UMIs must be the same length for downstream
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294 processing with dedup, group or count commands]]></token>
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295
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296 <xml name="barcode_options_macro">
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297 <conditional name="bc" >
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298 <param argument="--extract-umi-method" type="select" label="Umi Extract Method" help="How are the barcodes encoded in the read?" >
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299 <option value="read_id" selected="true">Barcodes are contained at the end of the read seperated by a delimiter</option>
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300 <option value="tag" >Barcodes are contained in tags</option>
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301 <option value="umis" >Barcodes were extracted using umis</option>
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302 </param>
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303 <when value="read_id" >
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304 <param argument="--umi-separator" type="text" label="Delimiter between read id and the UMI" value="_" >
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305 <sanitizer invalid_char="" >
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306 <valid initial="string.punctuation" />
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307 </sanitizer>
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308 </param>
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309 </when>
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310 <when value="tag" >
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311 <param argument="--umi-tag" type="text" label="Tag which contains the UMI" value="RX" >
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312 <expand macro="sanitize_tag" />
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313 </param>
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314 <param argument="--umi-tag-split" type="text" label="Separate the UMI in tag by SPLIT" help="and take the first element"/>
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315 <param argument="--umi-tag-delimiter" type="text" label="Separate the UMI in tag by DELIMITER" help="and concatenate the elements"/>
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316 <param argument="--cell-tag" type="text" label="Tag which contains the cell barcode" >
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317 <expand macro="sanitize_tag" />
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318 </param>
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319 <param argument="--cell-tag-split" type="text" label="Separate the cell barcode in tag by SPLIT" help="and take the first element"/>
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320 <param argument="--cell-tag-delimiter" type="text" label="Separate the cell barcode in tag by DELIMITER" help="and concatenate the elements"/>
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321 </when>
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322 <when value="umis"/>
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323 </conditional>
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324 </xml>
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325 <token name="@BARCODE_OPTIONS@"><![CDATA[
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326 --extract-umi-method $bc.extract_umi_method
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327 #if str($bc.extract_umi_method) == 'read_id':
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328 --umi-separator '$bc.umi_separator'
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329 #else if str($bc.extract_umi_method) == 'tag':
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330 --umi-tag '$bc.umi_tag'
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331 #if $bc.umi_tag_split != ''
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332 --umi-tag-split '$bc.umi_tag_split'
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333 #end if
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334 #if $bc.umi_tag_delimiter != ''
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335 --umi-tag-delimiter '$bc.umi_tag_delimiter'
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336 #end if
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337 --cell-tag '$bc.cell_tag'
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338 #if $bc.cell_tag_split != ''
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339 --cell-tag-split '$bc.cell_tag_split'
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340 #end if
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341 #if $bc.cell_tag_delimiter != ''
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342 --cell-tag-delimiter '$bc.cell_tag_delimiter'
2
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343 #end if
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344 #end if
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345 ]]></token>
12
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346 <token name="@BARCODE_HELP@"><![CDATA[
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347 Extracting barcodes
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348 -------------------
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349
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350 It is assumed that the FASTQ files were processed with ``umi_tools
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351 extract`` before mapping and thus the UMI is the last word of the read
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352 name. e.g:
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353
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354 @HISEQ:87:00000000_AATT
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355
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356 where ``AATT`` is the UMI sequeuence.
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357
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358 If you have used an alternative method which does not separate the
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359 read id and UMI with a "_", such as bcl2fastq which uses ":", you can
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360 specify the separator with the option ``--umi-separator=<sep>``,
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361 replacing <sep> with e.g ":".
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362
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363 Alternatively, if your UMIs are encoded in a tag, you can specify this
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364 by setting the option --extract-umi-method=tag and set the tag name
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365 with the --umi-tag option. For example, if your UMIs are encoded in
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366 the 'UM' tag, provide the following options:
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367 ``--extract-umi-method=tag`` ``--umi-tag=UM``
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368
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369 Finally, if you have used umis to extract the UMI +/- cell barcode,
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370 you can specify ``--extract-umi-method=umis``
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371
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372 The start position of a read is considered to be the start of its alignment
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373 minus any soft clipped bases. A read aligned at position 500 with
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374 cigar 2S98M will be assumed to start at position 498.]]></token>
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375
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376
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377 <xml name="umi_grouping_options_macro">
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378 <section name="umi" title="UMI grouping options">
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379 <param argument="--method" type="select" label="Method used to identify PCR duplicates within reads" help="All methods start by identifying the reads with the same mapping position">
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380 <option value="unique">Reads group share the exact same UMI</option>
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381 <option value="percentile">Reads group share the exact same UMI. UMIs with counts less than 1% of the median counts for UMIs at the same position are ignored</option>
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382 <option value="cluster">Identify clusters based on hamming distance</option>
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383 <option value="adjacency">Identify clusters based on hamming distance and resolve networks by using the node counts</option>
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384 <option value="directional">Identify clusters based on distance and counts, restrict network expansion by threshold</option>
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385 </param>
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386 <param argument="--edit-distance-threshold" type="integer" value="1" label="Edit distance threshold" help="For the adjacency and cluster methods the threshold for the edit distance to connect two UMIs in the network can be increased. The default value of 1 works best unless the UMI is very long (&gt;14bp)" />
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387 <param argument="--spliced-is-unique" type="boolean" truevalue="--spliced-is-unique" falsevalue="" label="Spliced reads are unique" help="Causes two reads that start in the same position on the same strand and having the same UMI to be considered unique if one is spliced and the other is not. (Uses the 'N' cigar operation to test for splicing)" />
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388 <param argument="--soft-clip-threshold" type="integer" value="4" label="Soft clip threshold" help="Mappers that soft clip, will sometimes do so rather than mapping a spliced read if there is only a small overhang over the exon junction. By setting this option, you can treat reads with at least this many bases soft-clipped at the 3' end as spliced" />
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389 <param argument="--read-length" type="boolean" truevalue="--read-length" falsevalue="" label="Use the read length as as a criterion when deduping" />
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390 </section>
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391 </xml>
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392 <token name="@UMI_GROUPING_OPTIONS@"><![CDATA[
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393 --method $umi.method
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394 --edit-distance-threshold $umi.edit_distance_threshold
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395 $umi.spliced_is_unique
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396 --soft-clip-threshold $umi.soft_clip_threshold
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397 $umi.read_length
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398 ]]></token>
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399 <token name="@UMI_GROUPING_HELP@"><![CDATA[
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400 UMI grouping options
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401 --------------------
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402
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403 Grouping Method
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404 ...............
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405
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406 What method to use to identify group of reads with the same (or
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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407 similar) UMI(s)?
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408
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409 All methods start by identifying the reads with the same mapping position.
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410
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411 The simplest methods, unique and percentile, group reads with
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412 the exact same UMI. The network-based methods, cluster, adjacency and
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413 directional, build networks where nodes are UMIs and edges connect UMIs
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414 with an edit distance <= threshold (usually 1). The groups of reads
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415 are then defined from the network in a method-specific manner. For all
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416 the network-based methods, each read group is equivalent to one read
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417 count for the gene.
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418
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419 - unique
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420 Reads group share the exact same UMI
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421
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422 - percentile
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423 Reads group share the exact same UMI. UMIs with counts < 1% of the
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424 median counts for UMIs at the same position are ignored.
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425
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426 - cluster
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427 Identify clusters of connected UMIs (based on hamming distance
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428 threshold). Each network is a read group
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429
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430 - adjacency
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431 Cluster UMIs as above. For each cluster, select the node (UMI)
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432 with the highest counts. Visit all nodes one edge away. If all
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433 nodes have been visited, stop. Otherwise, repeat with remaining
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434 nodes until all nodes have been visted. Each step
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435 defines a read group.
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436
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437 - directional (default)
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438 Identify clusters of connected UMIs (based on hamming distance
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439 threshold) and umi A counts >= (2* umi B counts) - 1. Each
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440 network is a read group.
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441
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442 ]]></token>
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443
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444 <xml name="sambam_options_macro">
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445 <section name="sambam" title="SAM/BAM options">
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446 <param argument="--mapping-quality" type="integer" value="0" label="Minimum mapping quality for a read to be retained"/>
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447 <param argument="--unmapped-reads" type="select" label="How to handle unmapped reads">
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448 <option value="discard">discard</option>
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449 <option value="use">use</option>
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450 <option value="correct">correct</option>
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451 </param>
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452 <param argument="--chimeric-pairs" type="select" optional="true" label="How to handle chimeric read pairs (default: use)">
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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453 <option value="discard">discard</option>
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454 <option value="use">use</option>
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455 <option value="correct">correct</option>
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456 </param>
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457 <param argument="--unpaired-reads" type="select" optional="true" label="How to handle unpaired reads (default: use)">
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458 <option value="discard">discard</option>
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459 <option value="use">use</option>
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460 <option value="correct">correct</option>
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461 </param>
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462 <param argument="--ignore-umi" type="boolean" truevalue="--ignore-umi" falsevalue="" label="Ignore UMI and dedup only on position"/>
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463 <param argument="--ignore-tlen" type="boolean" truevalue="--ignore-tlen" falsevalue="" label="Dedup paired end reads based solely on read1" help="whether or not the template length is the same"/>
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464 <param argument="--chrom" type="text" value="" label="Consider only chromosome" help="If a value is given only a single chromosome with the given name is considered"/>
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465 <param argument="--subset" type="float" min="0.0" max="1.0" value="1.0" label="Only consider a random selection of the reads" />
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466 <!--in-sam is set automatically-->
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467 <param argument="--paired" type="boolean" truevalue="--paired" falsevalue="" label="BAM is paired end" help="This will also force the use of the template length to determine reads with the same mapping coordinates" />
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468 </section>
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469 </xml>
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470 <token name="@SAMBAM_OPTIONS@"><![CDATA[
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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471 --mapping-quality $sambam.mapping_quality
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472 --unmapped-reads $sambam.unmapped_reads
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473 #if $sambam.chimeric_pairs
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474 --chimeric-pairs $sambam.chimeric_pairs
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475 #end if
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diff changeset
476 #if $sambam.unpaired_reads
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477 --unpaired-reads $sambam.unpaired_reads
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478 #end if
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479 $sambam.ignore_umi
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480 $sambam.ignore_tlen
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481 #if str($sambam.chrom) != ''
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482 --chrom '$sambam.chrom'
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483 #end if
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484 --subset $sambam.subset
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485 $sambam.paired
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486 @SET_INPUT_TYPE@
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487 ]]></token>
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diff changeset
488
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489 <!-- per-gene is hard coded in count https://github.com/CGATOxford/UMI-tools/blob/c3ead0792ad590822ca72239ef01b8e559802da9/umi_tools/count.py#L92
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490 hence we need a specialized macro here
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491 TODO count used XF as default for gene-tag now I set it explicitly for the tests but we could as well parametrize the macro and set tool specific defaults
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492 -->
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diff changeset
493
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diff changeset
494 <xml name="fullsc_options_macro">
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diff changeset
495 <expand macro="sc_options_macro">
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496 <param argument="--per-gene" type="boolean" truevalue="--per-gene" falsevalue="" label="Deduplicate per gene"
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497 help="Must combine with either --gene-tag or --per-contig. As for --per-contig except with this option you can align to a reference transcriptome with more than one transcript per gene. You need to also provide a map of genes to transcripts. This will also add a metacontig ('MC') tag to the output BAM file" />
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498 </expand>
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499 </xml>
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500 <token name="@FULLSC_OPTIONS@"><![CDATA[
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501 $sc.per_gene
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502 @SC_OPTIONS@
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503 ]]></token>
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504
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505 <xml name="sc_options_macro">
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506 <section name="sc" title="Single-cell RNA-Seq options">
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diff changeset
507 <yield/>
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508 <param argument="--gene-tag" type="text" optional="true" label="Deduplicate by this gene tag" help="As --per-gene except here the gene information is encoded in the bam read tag specified so you do not need to supply the mapping file">
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509 <expand macro="sanitize_tag" />
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510 </param>
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511 <param argument="--assigned-status-tag" type="text" optional="true" label="Bam tag describing whether read is assigned to a gene" help="By default, this is set as the same tag as --gene-tag">
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512 <expand macro="sanitize_tag" />
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513 </param>
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514 <param argument="--skip-tags-regex" name="skip_tags_regex" type="text" label="Skip any reads where the gene matches this tag" value="" >
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515 <expand macro="barcode_sanitizer" />
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516 </param>
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517 <param argument="--per-contig" type="boolean" truevalue="--per-contig" falsevalue="" label="Deduplicate per contig" help="Field 3 in BAM; RNAME. All reads with the same contig will be considered to have the same alignment position. This is useful if your library prep generates PCR duplicates with non identical alignment positions such as CEL-Seq. In this case, you would align to a reference transcriptome with one transcript per gene" />
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518 <param argument="--gene-transcript-map" type="data" format="tabular" optional="true" label="Tabular file mapping genes to transripts" />
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519 <param argument="--per-cell" name="per_cell" type="boolean" truevalue="--per-cell" falsevalue="" label="Group reads only if they have the same cell barcode" />
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 9
diff changeset
520 </section>
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 9
diff changeset
521 </xml>
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 9
diff changeset
522 <token name="@SC_OPTIONS@"><![CDATA[
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 9
diff changeset
523 #if str($sc.gene_tag) != "":
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
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diff changeset
524 --gene-tag '$sc.gene_tag'
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 9
diff changeset
525 #end if
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 9
diff changeset
526 #if str($sc.assigned_status_tag) != "":
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 9
diff changeset
527 --assigned-status-tag '$sc.assigned_status_tag'
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 9
diff changeset
528 #end if
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 9
diff changeset
529 #if str($sc.skip_tags_regex) != "":
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 9
diff changeset
530 --skip-tags-regex '$sc.skip_tags_regex'
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 9
diff changeset
531 #end if
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 9
diff changeset
532 $sc.per_contig
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 9
diff changeset
533 #if $sc.gene_transcript_map:
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 9
diff changeset
534 --gene-transcript-map '$sc.gene_transcript_map'
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 9
diff changeset
535 #end if
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 9
diff changeset
536 $sc.per_cell
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 9
diff changeset
537 ]]></token>
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 9
diff changeset
538
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 9
diff changeset
539 <xml name="groupdedup_options_macro">
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 9
diff changeset
540 <section name="gd" title="group/dedup specific options">
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 9
diff changeset
541 <param argument="--buffer-whole-contig" type="boolean" truevalue="--buffer-whole-contig" falsevalue="" label="Read whole contig before outputting bundles" help="Guarantees that no reads are missed, but increases memory usage" />
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 9
diff changeset
542 <!-- TODO this option is hidden on the CLI. Should we expose it? -->
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 9
diff changeset
543 <param argument="--whole-contig" type="boolean" truevalue="--whole-contig" falsevalue="" label="Consider all alignments to a single contig together" help="This is useful if you have aligned to a transcriptome multi-fasta" />
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 9
diff changeset
544 <param argument="--multimapping-detection-method" type="select" optional="true" label="BAM Tag indicating multimapping " help="Some aligners identify multimapping using bam tags. Setting this option to NH, X0 or XT will use these tags when selecting the best read amongst reads with the same position and umi">
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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diff changeset
545 <option value="NH">NH</option>
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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diff changeset
546 <option value="X0">X0</option>
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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diff changeset
547 <option value="XT">XT</option>
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 9
diff changeset
548 </param>
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 9
diff changeset
549 </section>
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 9
diff changeset
550 </xml>
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 9
diff changeset
551 <token name="@GROUPDEDUP_OPTIONS@"><![CDATA[
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 9
diff changeset
552 $gd.buffer_whole_contig
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 9
diff changeset
553 $gd.whole_contig
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 9
diff changeset
554 $gd.multimapping_detection_method
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 9
diff changeset
555 ]]></token>
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 9
diff changeset
556
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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diff changeset
557 <xml name="log_input_macro">
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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diff changeset
558 <param argument="--log" type="boolean" label="Output log?" truevalue="--log" falsevalue="" help="Choose if you want to generate a text file containing logging information" />
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 9
diff changeset
559 </xml>
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 9
diff changeset
560 <xml name="log_output_macro">
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 9
diff changeset
561 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: logfile" >
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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diff changeset
562 <filter>log</filter>
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 9
diff changeset
563 </data>
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 9
diff changeset
564 </xml>
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 9
diff changeset
565 <token name="@LOG@"><![CDATA[
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 9
diff changeset
566 #if $log:
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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diff changeset
567 --log='$out_log'
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 9
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568 #end if
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 9
diff changeset
569 --log2stderr
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 9
diff changeset
570 ]]></token>
4098ab380097 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
iuc
parents: 9
diff changeset
571
0
a6477bafd522 planemo upload commit eea727c3bdfe36d9d16036d5ab79fb8b27c4e82e
iuc
parents:
diff changeset
572 </macros>