Mercurial > repos > iuc > umi_tools_extract

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bc1b362f6783d3fc0ed0f42c14687001d7ff5f7a
author iuc
date Sat, 05 Oct 2024 13:07:19 +0000
parents 7accf7407811
children
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27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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1 <tool id="umi_tools_extract" name="UMI-tools extract" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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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="bio_tools"/>
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 @COMMAND_LINK@
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11 umi_tools extract
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13 @FASTQ_BARCODE_EXTRACTION_OPTIONS@
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14 #if $input_type_cond.input_type == 'single':
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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15 #if $gz:
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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16 --stdin=input_single.gz
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17 --stdout out.gz
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18 #else
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19 --stdin=input_single.txt
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20 --stdout '$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 #if $input_type_cond.input_type == 'paired'
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32 --stdout '$out'
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33 --read2-out='$out2'
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34 #else
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35 --stdout '$out_paired_collection.forward'
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36 --read2-out='$out_paired_collection.reverse'
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37 #end if
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38 #end if
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39 $input_type_cond.reconcile_pairs
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40 #end if
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41
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42 #if $whitelist
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43 --whitelist='$whitelist'
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44 #end if
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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45 #if $blacklist
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46 --blacklist='$blacklist'
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47 #end if
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48 $error_correct_cell.value
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49
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50 #if $quality.quality_selector =='true':
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51 #if str($quality.quality_filter_threshold) != ''
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52 --quality-filter-threshold '$quality.quality_filter_threshold'
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53 #end if
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54 #if str($quality.quality_filter_mask) != ''
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55 --quality-filter-mask '$quality.quality_filter_mask'
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56 #end if
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57 #if $input_type_cond.input_type != 'paired_collection'
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58 #set input=$input_type_cond.input_read1
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59 #else
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60 #set input=$input_type_cond.input_readpair.forward
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61 #end if
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62 --quality-encoding
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63 #if $input.ext.startswith("fastqillumina")
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64 phred64
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65 #else if $input.ext.startswith("fastqsolexa")
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66 solexa
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67 #else
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68 phred33
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69 #end if
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70 #end if
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71 @LOG@
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72 #if $gz:
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73 #if $input_type_cond.input_type == 'single':
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74 && mv out.gz '$out'
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75 #else if $input_type_cond.input_type == 'paired'
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76 && mv out1.gz '$out'
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77 && mv out2.gz '$out2'
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78 #else
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79 && mv out1.gz '$out_paired_collection.forward'
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80 && mv out2.gz '$out_paired_collection.reverse'
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81 #end if
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82 #end if
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83 ]]></command>
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84 <inputs>
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85 <expand macro="input_types">
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86 <param argument="--reconcile-pairs" type="boolean" truevalue="--reconcile-pairs" falsevalue="" checked="false" label="Allow unpaired reads" help="Allow the presences of reads in read2 input that are not present in read1 input. This allows cell barcode filtering of read1s without considering read2s" />
27ac32a22ad2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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87 </expand>
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88 <expand macro="fastq_barcode_extraction_options_macro"/>
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89
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90 <param argument="--whitelist" type="data" optional="true" format="txt,tabular,tsv" label="Allowlist of accepted barcodes" />
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91 <param argument="--blacklist" type="data" optional="true" format="txt,tabular,tsv" label="Denylist of accepted barcodes" />
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92 <param 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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93
0
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94 <conditional name="quality">
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95 <param name="quality_selector" type="select" label="Enable quality filter?" >
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96 <option value="false">No</option>
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97 <option value="true">Yes</option>
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98 </param>
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99 <when value="false">
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100 </when>
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101 <when value="true">
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102 <param argument="--quality-filter-threshold" label="Phred score threshold"
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103 type="integer" value="" optional="true"
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104 help="Remove reads where any UMI base quality score falls below this threshold" />
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105 <param argument="--quality-filter-mask" label="Mask UMI bases below threshold"
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106 type="integer" value="" optional="true"
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107 help="If a UMI base has a quality below this threshold,
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108 replace the base with 'N'" />
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109 </when>
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110 </conditional>
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111 <expand macro="log_input_macro"/>
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112 </inputs>
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113 <outputs>
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114 <data name="out" format_source="input_read1" label="${tool.name} on ${on_string}: Forward reads" >
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115 <filter>input_type_cond['input_type'] in ['single', 'paired']</filter>
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116 </data>
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117 <data name="out2" format_source="input_read2" label="${tool.name} on ${on_string}: Reverse reads" >
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118 <filter>input_type_cond['input_type'] == 'paired'</filter>
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119 </data>
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120 <collection name="out_paired_collection" type="paired" label="${tool.name} on ${on_string}: Reads">
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121 <data name="forward" format_source="input_readpair" />
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122 <data name="reverse" format_source="input_readpair" />
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123 <filter>input_type_cond['input_type'] == 'paired_collection'</filter>
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124 </collection>
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125 <expand macro="log_output_macro"/>
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126 </outputs>
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127 <tests>
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128 <test expect_num_outputs="2">
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129 <conditional name="input_type_cond">
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130 <param name="input_type" value="single" />
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131 <param name="input_read1" value="t_R1.fastq" ftype="fastqsanger" />
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132 <param name="bc_pattern" value="XXXNNN" />
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133 </conditional>
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134 <conditional name="extract_method_cond">
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135 <param name="prime3" value="true" />
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136 </conditional>
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137 <param name="quality_selector" value="true" />
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138 <param name="quality_filter_threshold" value="10" />
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139 <param name="log" value="true"/>
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140 <output name="out" file="out_SE.fastq" ftype="fastqsanger" />
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141 <output name="out_log" >
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142 <assert_contents>
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143 <has_text text="Input Reads: 100" />
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144 <has_text text="umi quality: 28" />
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145 <has_text text="Reads output: 72" />
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146 </assert_contents>
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147 </output>
0
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148 </test>
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149 <test expect_num_outputs="3">
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150 <conditional name="input_type_cond">
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151 <param name="input_type" value="paired" />
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152 <param name="input_read1" value="t_R1.fastq.gz" ftype="fastqsanger.gz" />
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153 <param name="input_read2" value="t_R2.fastq.gz" ftype="fastqsanger.gz" />
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154 <param name="bc_pattern" value="NNNXXX" />
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155 </conditional>
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156 <param name="log" value="true"/>
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157 <output name="out" file="out_R1.fastq.gz" decompress="true" lines_diff="2" ftype="fastqsanger.gz" />
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158 <output name="out2" file="out_R2.fastq.gz" decompress="true" lines_diff="2" ftype="fastqsanger.gz" />
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159 <output name="out_log" >
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160 <assert_contents>
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161 <has_text text="Input Reads: 100" />
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162 <has_text text="Reads output: 100" />
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163 </assert_contents>
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164 </output>
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165 </test>
15
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166 <test expect_num_outputs="4">
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167 <conditional name="input_type_cond">
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168 <param name="input_type" value="paired_collection" /> <!-- same as before, but uncompressed -->
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169 <param name="paired_type" value="no" />
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170 <param name="input_readpair">
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171 <collection type="paired" >
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172 <element name="forward" ftype="fastqsanger" value="t_R1.fastq" />
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173 <element name="reverse" ftype="fastqsanger" value="t_R2.fastq" />
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174 </collection>
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175 </param>
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176 <param name="bc_pattern" value="NNNXXX" />
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177 </conditional>
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178 <param name="log" value="true"/>
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179 <output_collection name="out_paired_collection" type="paired">
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180 <element name="forward" file="out_R1.fastq" ftype="fastqsanger" />
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181 <element name="reverse" file="out_R2.fastq" ftype="fastqsanger" />
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182 </output_collection>
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183 <output name="out_log" >
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184 <assert_contents>
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185 <has_text text="Input Reads: 100" />
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186 <has_text text="Reads output: 100" />
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187 </assert_contents>
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188 </output>
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189 </test>
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190 <test expect_num_outputs="3">
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191 <conditional name="input_type_cond">
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192 <param name="input_type" value="paired" />
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193 <param name="input_read1" value="scrb_seq_fastq.1.gz" ftype="fastqsanger.gz" />
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194 <param name="input_read2" value="scrb_seq_fastq.2.gz" ftype="fastqsanger.gz" />
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195 <param name="bc_pattern" value="CCCCCCNNNNNNNNNN" />
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196 </conditional>
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197 <param name="extract_method" value="string" />
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198 <param name="whitelist" value="scrb_seq_barcodes" />
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199 <param name="log" value="true"/>
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200 <output name="out2" file="scrb_extract.fastq.gz" decompress="true" ftype="fastqsanger.gz" />
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201 </test>
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202 <test expect_num_outputs="3"><!-- same as above but with regex barcode-->
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203 <conditional name="input_type_cond">
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204 <param name="input_type" value="paired" />
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205 <param name="input_read1" value="scrb_seq_fastq.1.gz" ftype="fastqsanger.gz" />
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206 <param name="input_read2" value="scrb_seq_fastq.2.gz" ftype="fastqsanger.gz" />
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207 <param name="bc_pattern" value="^(?P&lt;cell_1&gt;.{6})(?P&lt;umi_1&gt;.{10})" />
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208 </conditional>
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209 <param name="extract_method" value="regex" />
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210 <param name="whitelist" value="scrb_seq_barcodes" />
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211 <param name="log" value="true"/>
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212 <output name="out2" file="scrb_extract.fastq.gz" decompress="true" ftype="fastqsanger.gz" />
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213 </test>
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214 <test expect_num_outputs="2"><!-- CelSeq2 example -->
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215 <conditional name="input_type_cond">
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216 <param name="input_type" value="paired" />
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217 <param name="input_read1" value="read_R1.200.gz" ftype="fastqsanger.gz" />
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218 <param name="input_read2" value="read_R2.200.gz" ftype="fastqsanger.gz" />
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219 <param name="bc_pattern" value="NNNNNNCCCCCC" />
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220 </conditional>
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221 <param name="extract_method" value="string" />
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222 <output name="out" file="read_R1.200_extracted.fastq.gz" ftype="fastqsanger.gz" decompress="true" lines_diff="1" />
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223 <output name="out2" file="read_R2.200_extracted.fastq.gz" ftype="fastqsanger.gz" decompress="true" lines_diff="1" />
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224 </test>
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225 </tests>
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226 <help><![CDATA[
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227
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228 extract - Extract UMI from fastq
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229 ================================
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230
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231 Extract UMI barcode from a read and add it to the read name, leaving
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232 any sample barcode in place
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233
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234 Can deal with paired end reads and UMIs
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235 split across the paired ends. Can also optionally extract cell
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236 barcodes and append these to the read name also. See the section below
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237 for an explanation for how to encode the barcode pattern(s) to
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238 specficy the position of the UMI +/- cell barcode.
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239
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240
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241 Filtering and correcting cell barcodes
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242 --------------------------------------
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243
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244 ``umi_tools extract`` can optionally filter cell barcodes against a user-supplied
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245 whitelist (``--whitelist``). If a whitelist is not available for your data,
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246 e.g
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247 if you have performed droplet-based scRNA-Seq, you can use the
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248 whitelist tool.
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249
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250 Cell barcodes which do not match the whitelist (user-generated or
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251 automatically generated) can also be optionally corrected using the
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252 ``--error-correct-cell`` option.
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253
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254 The whitelist should be in the following format (tab-separated)::
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255
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256 AAAAAA AGAAAA
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257 AAAATC
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258 AAACAT
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259 AAACTA AAACTN,GAACTA
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260 AAATAC
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261 AAATCA GAATCA
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262 AAATGT AAAGGT,CAATGT
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263
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264 Where column 1 is the whitelisted cell barcodes and column 2 is
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265 the list (comma-separated) of other cell barcodes which should be
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266 corrected to the barcode in column 1. If the ``--error-correct-cell``
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267 option is not used, this column will be ignored. Any additional columns
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268 in the whitelist input, such as the counts columns from the output of
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269 umi_tools whitelist, will be ignored.
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270
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271 @FASTQ_BARCODE_EXTRACTION_HELP@
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272
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273 ]]></help>
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274 <expand macro="citations" />
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275 </tool>