Mercurial > repos > iuc > umi_tools_extract

annotate umi-tools_extract.xml @ 6:6417d5ed05c6 draft

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author iuc
date Thu, 21 Jun 2018 15:20:02 -0400
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children 3cfd8e1073d7
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1 <tool id="umi_tools_extract" name="UMI-tools extract" version="@VERSION@.1">
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2 <description>Extract UMI 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 <command detect_errors="exit_code"><![CDATA[
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8 @COMMAND_LINK@
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9
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10 umi_tools extract
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11 --extract-method='$extract_method.value'
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12 --bc-pattern='$bc_pattern'
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13
0
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14 #if $input_type.type == 'single':
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15 #if $gz:
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16 --stdin=input_single.gz
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17 --stdout out.gz
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18 #else
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19 --stdin=input_single.txt
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20 --stdout '$out'
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21 #end if
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22 #else:
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23 #if $gz:
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24 --stdin=input_read1.gz
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25 --read2-in=input_read2.gz
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26 --stdout out1.gz
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27 --read2-out=out2.gz
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28 #else:
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29 --stdin=input_read1.txt
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30 --read2-in=input_read2.txt
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31 --stdout '$out1'
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32 --read2-out='$out2'
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33 #end if
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34 #if $input_type.barcode.barcode_select == "both_reads":
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35 --split-barcode
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36 --bc-pattern2='$input_type.barcode.bc_pattern2'
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37 #end if
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38 #end if
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39
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40 #if $barcodes.use_barcodes.value == 'yes':
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41 --filter-cell-barcode
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42 --whitelist='$barcodes.filter_barcode_file'
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43 '$barcodes.filter_correct.value'
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44 #end if
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45
0
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46 #if not $prime3:
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47 --3prime
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48 #end if
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49 #if $quality.quality_selector =='true':
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50 --quality-filter-threshold '$quality.quality_filter_threshold'
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51 --quality-encoding '$quality.quality_encoding'
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52 #end if
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53 #if $print_log == "1":
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54 --log='$out_log'
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55 #else
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56 --supress-stats
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57 #end if
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58 #if $gz:
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59 #if $input_type.type == 'single':
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60 && mv out.gz '$out'
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61 #else
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62 && mv out1.gz '$out1'
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63 && mv out2.gz '$out2'
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64 #end if
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65 #end if
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66 ]]></command>
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67 <inputs>
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68 <expand macro="input_types" />
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69
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70 <conditional name="barcodes" >
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71 <param name="use_barcodes" argument="--filter-cell-barcode" type="select" label="Use Known Barcodes?" >
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72 <option value="yes">Yes</option>
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73 <option value="no" selected="true" >No</option>
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74 </param>
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75 <when value="no" />
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76 <when value="yes" >
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77 <param name="filter_barcode_file" type="data" format="tsv" label="Barcode File" />
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78 <param name="filter_correct" argument="--error-correct-cell" type="boolean" truevalue="--error-correct-cell" falsevalue="" checked="false" label="Apply correction to cell barcodes?" help="This only applies if your barcode file has two columns output from the umi_tools whitelist command." />
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79 </when>
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80 </conditional>
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81
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82 <param name="extract_method" type="select" label="Method to extract barcodes" >
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83 <option value="regex">Regular Expressions</option>
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84 <option value="string" selected="true">String</option>
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85 </param>
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86
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87 <param name="bc_pattern" argument="--bc-pattern" type="text" label="Barcode pattern for first read"
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88 help="Use this option to specify the format of the UMI/barcode. Use Ns to
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89 represent the random positions and Xs to indicate the bc positions.
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90 Bases with Ns will be extracted and added to the read name. Remaining
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91 bases, marked with an X will be reattached to the read.">
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92 <sanitizer invalid_char="">
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93 <valid initial="string.letters,string.digits">
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94 <add value="!="/>
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95 <add value="-"/>
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96 <add value="_"/>
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97 <add value="."/>
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98 <add value="?"/>
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99 <add value="&lt;"/><!-- left triangle bracket -->
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100 <add value="&gt;"/><!-- right triangle bracket -->
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101 <add value="&#91;"/> <!-- left square bracket -->
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102 <add value="&#93;"/> <!-- right square bracket -->
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103 <add value="&#94;"/> <!-- caret -->
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104 <add value="&#123;"/> <!-- left curly -->
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105 <add value="&#125;"/> <!-- right curly -->
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106 <add value="&#40;"/> <!-- left parenthesis -->
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107 <add value="&#41;"/> <!-- right parenthesis -->
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108 </valid>
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109 </sanitizer>
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110 </param>
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111
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112 <param name="prime3" argument="--3prime" type="boolean" label="Is the barcode at the 5' end?"
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113 truevalue="1" falsevalue="0" checked="true"
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114 help="By default the barcode is assumed to be on the 5' end of the read, but
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115 use this option to sepecify that it is on the 3' end instead." />
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116 <param name="print_log" argument="-L" type="boolean" label="Output log?"
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117 truevalue="1" falsevalue="0" checked="true"
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118 help="Choose if you want to generate a text file containing logging information." />
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119 <conditional name="quality">
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120 <param name="quality_selector" type="select" label="Enable quality filter?" >
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121 <option value="false">No</option>
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122 <option value="true">Yes</option>
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123 </param>
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124 <when value="false">
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125 </when>
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126 <when value="true">
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127 <param name="quality_filter_threshold" label="Phred score threshold"
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128 type="integer" value="20" argument="--quality-filter-threshold"
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129 help="Remove reads where any UMI base quality score falls below this threshold." />
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130 <param name="quality_encoding" argument="--quality-encoding" type="select" label="Library type"
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131 help="Quality score encoding. Choose from phred33 [33-77], phred64 [64-106] or solexa [59-106].">
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132 <option value="phred33">phred33 [33-77]</option>
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133 <option value="phred64">phred64 [64-106]</option>
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134 <option value="solexa">solexa [59-106]</option>
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135 </param>
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136 </when>
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137 </conditional>
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138 </inputs>
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139 <outputs>
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140 <data name="out" format_source="input_single">
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141 <filter>input_type['type'] == "single"</filter>
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142 </data>
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143 <data name="out1" format_source="input_read1">
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144 <filter>input_type['type'] !== "single"</filter>
0
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145 </data>
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146 <data name="out2" format_source="input_read2">
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147 <filter>input_type['type'] !== "single"</filter>
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148 </data>
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149 <data name="out_log" format="txt">
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150 <filter>print_log == True</filter>
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151 </data>
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152 </outputs>
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153 <tests>
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154 <test>
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155 <param name="type" value="single" />
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156 <param name="input_single" value="t_R1.fastq" ftype="fastq" />
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157 <param name="bc_pattern" value="XXXNNN" />
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158 <param name="prime3" value="0" />
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159 <param name="quality_selector" value="true" />
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160 <param name="quality_filter_threshold" value="10" />
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161 <param name="quality_encoding" value="phred33" />
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162 <output name="out" file="out_SE.fastq" />
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163 <output name="out_log" file="out_single.log" lines_diff="22"/>
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164 </test>
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165 <test>
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166 <param name="type" value="paired" />
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167 <param name="input_read1" value="t_R1.fastq.gz" ftype="fastq.gz" />
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168 <param name="input_read2" value="t_R2.fastq.gz" ftype="fastq.gz" />
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169 <param name="bc_pattern" value="NNNXXX" />
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170 <output name="out1" file="out_R1.fastq.gz" decompress="true" lines_diff="2" />
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171 <output name="out2" file="out_R2.fastq.gz" decompress="true" lines_diff="2" />
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172 <output name="out_log" file="out_paired.log" lines_diff="16"/>
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173 </test>
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174 <test>
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175 <param name="type" value="paired_collection" /> <!-- same as before, but uncompressed -->
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176 <param name="input_readpair" >
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177 <collection type="paired">
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178 <element name="forward" ftype="fastq" value="t_R1.fastq" />
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179 <element name="reverse" ftype="fastq" value="t_R2.fastq" />
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180 </collection>
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181 </param>
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182 <param name="bc_pattern" value="NNNXXX" />
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183 <output name="out1" file="out_R1.fastq.gz" decompress="true" lines_diff="2" />
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184 <output name="out2" file="out_R2.fastq.gz" decompress="true" lines_diff="2" />
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185 <output name="out_log" file="out_paired.log" lines_diff="25" />
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186 </test>
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187 <test>
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188 <param name="type" value="paired" />
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189 <param name="input_read1" value="scrb_seq_fastq.1.gz" ftype="fastq.gz" />
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190 <param name="input_read2" value="scrb_seq_fastq.2.gz" ftype="fastq.gz" />
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191 <param name="extract_method" value="string" />
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192 <param name="bc_pattern" value="CCCCCCNNNNNNNNNN" />
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193 <param name="use_barcodes" value="yes" />
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194 <param name="filter_barcode_file" value="scrb_seq_barcodes" />
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195 <output name="out2" file="scrb_extract.fastq.gz" decompress="true" />
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196 </test>
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197 <test><!-- same as above but with regex barcode-->
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198 <param name="type" value="paired" />
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199 <param name="input_read1" value="scrb_seq_fastq.1.gz" ftype="fastq.gz" />
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200 <param name="input_read2" value="scrb_seq_fastq.2.gz" ftype="fastq.gz" />
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201 <param name="extract_method" value="regex" />
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202 <param name="bc_pattern" value="^(?P&lt;cell_1&gt;.{6})(?P&lt;umi_1&gt;.{10})" />
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203 <param name="use_barcodes" value="yes" />
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204 <param name="filter_barcode_file" value="scrb_seq_barcodes" />
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205 <output name="out2" file="scrb_extract.fastq.gz" decompress="true" />
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206 </test>
0
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207 </tests>
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208 <help><![CDATA[
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209
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210
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211 UMI-tools extract.py - Extract UMI from fastq
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212 =============================================
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213
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214 Purpose
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215 -------
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216
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217 Extract UMI barcode from a read and add it to the read name, leaving
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218 any sample barcode in place. Can deal with paired end reads and UMIs
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219 split across the paired ends
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220
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221 Options
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222 -------
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223
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224 --split-barcode
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225 By default the UMI is assumed to be on the first read. Use this
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226 option if the UMI is contained on both reads and specify the
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227 pattern of the barcode/UMI on the second read using the option
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228 ``--bc-pattern2``
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229
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230 --bc-pattern
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231 Use this option to specify the format of the UMI/barcode. Use Ns to
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232 represent the random positions and Xs to indicate the bc positions.
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233 Bases with Ns will be extracted and added to the read name. Remaining
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234 bases, marked 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 NNXXNN,
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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 DA1AEBFGGCG01DFH00B1FF0B
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242 +
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243
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244 will become:
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245 @HISEQ:87:00000000_AATT read1
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246 GGGCTGATTGGATGGGCTAG
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247 1AFGGCG01DFH00B1FF0B
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248 +
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249
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250 --bc-pattern2
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251 Use this option to specify the format of the UMI/barcode for
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252 the second read pair if required. If --bc-pattern2 is not
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253 supplied, this defaults to the same pattern as --bc-pattern
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254
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255 --3prime
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256 By default the barcode is assumed to be on the 5' end of the read, but
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257 use this option to sepecify that it is on the 3' end instead
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258
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259 -L
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260 Specify a log file to retain logging information and final statistics
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261
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262 --split-barcode
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263 barcode is split across read pair
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264
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265 --quality-filter-threshold=QUALITY_FILTER_THRESHOLD
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266 Remove reads where any UMI base quality score falls
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267 below this threshold
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268 --quality-encoding=QUALITY_ENCODING
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269 Quality score encoding. Choose from phred33[33-77]
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270 phred64 [64-106] or solexa [59-106]
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271
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272 Usage:
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273 ------
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274
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275 For single ended reads:
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276 umi_tools extract --bc-pattern=[PATTERN] -L extract.log [OPTIONS]
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277
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278 reads from stdin and outputs to stdout.
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279
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280 For paired end reads:
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281 umi_tools extract --bc-pattern=[PATTERN] --read2-in=[FASTQIN] --read2-out=[FASTQOUT] -L extract.log [OPTIONS]
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282
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283 reads end one from stdin and end two from FASTQIN and outputs end one to stdin
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284 and end two to FASTQOUT.
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285
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286 ]]></help>
1
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287 <expand macro="citations" />
0
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288 </tool>