Mercurial > repos > iuc > umi_tools_extract

annotate umi-tools_extract.xml @ 2:d1015c2516b7 draft

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planemo upload commit eea727c3bdfe36d9d16036d5ab79fb8b27c4e82e
author iuc
date Wed, 10 Jan 2018 19:10:01 -0500
parents 79436b3019e9
children e73a22ff585c
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1 <tool id="umi_tools_extract" name="UMI-tools extract" version="@VERSION@.0">
0
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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 #set $gz = False
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9 #if $input_type.type == 'single':
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10 #if $input_type.input_single.is_of_type("fastq.gz", "fastqsanger.gz"):
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11 ln -s '$input_type.input_single' input_single.gz &&
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12 #set $gz = True
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13 #end if
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14 #else
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15 #if $input_type.input_read1.is_of_type("fastq.gz", "fastqsanger.gz"):
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16 ln -s '$input_type.input_read1' input_read1.gz &&
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17 ln -s '$input_type.input_read2' input_read2.gz &&
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18 #set $gz = True
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19 #end if
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20 #end if
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21 umi_tools extract
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22 --bc-pattern='$bc_pattern'
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23 #if $input_type.type == 'single':
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24 #if $gz:
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25 --stdin=input_single.gz
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26 --stdout out.gz
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27 #else
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28 --stdin='$input_type.input_single'
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29 --stdout '$out'
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30 #end if
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31 #else:
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32 #if $gz:
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33 --stdin=input_read1.gz
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34 --read2-in=input_read2.gz
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35 --stdout out1.gz
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36 --read2-out=out2.gz
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37 #else:
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38 --stdin='$input_type.input_read1'
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39 --read2-in='$input_type.input_read2'
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40 --stdout '$out1'
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41 --read2-out='$out2'
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42 #end if
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43 #if $input_type.barcode.split == "1":
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44 --split-barcode
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45 --bc-pattern2='$input_type.barcode.bc_pattern2'
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46 #end if
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47 #end if
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48 #if not $prime3:
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49 --3prime
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50 #end if
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51 #if $quality.quality_selector =='true':
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52 --quality-filter-threshold '$quality.quality_filter_threshold'
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53 --quality-encoding '$quality.quality_encoding'
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54 #end if
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55 #if $print_log == "1":
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56 --log='$out_log'
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57 #else
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58 --supress-stats
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59 #end if
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60 #if $gz:
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61 #if $input_type.type == 'single':
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62 && mv out.gz '$out'
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63 #else
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64 && mv out1.gz '$out1'
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65 && mv out2.gz '$out2'
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66 #end if
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67 #end if
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68 ]]></command>
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69 <inputs>
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70 <conditional name="input_type">
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71 <param name="type" type="select" label="Library type">
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72 <option value="single">Single-end</option>
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73 <option value="paired">Paired-end</option>
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74 </param>
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75 <when value="single">
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76 <param name="input_single" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />
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77 </when>
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78 <when value="paired">
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79 <param name="input_read1" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />
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80 <param name="input_read2" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />
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81 <conditional name="barcode">
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82 <param name="split" argument="--split-barcode" type="select" label="Barcode on both reads?">
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83 <option value="0">Barcode on first read only</option>
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84 <option value="1">Barcode on both reads</option>
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85 </param>
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86 <when value="0">
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87 </when>
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88 <when value="1">
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89 <param name="bc_pattern2" argument="--bc-pattern2" type="text" value="" label="Barcode pattern for second read"
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90 help="Use this option to specify the format of the UMI/barcode for
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91 the second read pair if required.">
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92 </param>
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93 </when>
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94 </conditional>
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95 </when>
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96 </conditional>
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97 <param name="bc_pattern" argument="--bc-pattern" type="text" label="Barcode pattern for first read"
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98 help="Use this option to specify the format of the UMI/barcode. Use Ns to
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99 represent the random positions and Xs to indicate the bc positions.
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100 Bases with Ns will be extracted and added to the read name. Remaining
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101 bases, marked with an X will be reattached to the read.">
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102 </param>
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103 <param name="prime3" argument="--3prime" type="boolean" label="Is the barcode at the 5' end?"
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104 truevalue="1" falsevalue="0" checked="true"
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105 help="By default the barcode is assumed to be on the 5' end of the read, but
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106 use this option to sepecify that it is on the 3' end instead." />
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107 <param name="print_log" argument="-L" type="boolean" label="Output log?"
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108 truevalue="1" falsevalue="0" checked="true"
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109 help="Choose if you want to generate a text file containing logging information." />
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110 <conditional name="quality">
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111 <param name="quality_selector" type="select" label="Enable quality filter?" >
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112 <option value="false">No</option>
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113 <option value="true">Yes</option>
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114 </param>
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115 <when value="false">
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116 </when>
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117 <when value="true">
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118 <param name="quality_filter_threshold" label="Phred score threshold"
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119 type="integer" value="20" argument="--quality-filter-threshold"
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120 help="Remove reads where any UMI base quality score falls below this threshold." />
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121 <param name="quality_encoding" argument="--quality-encoding" type="select" label="Library type"
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122 help="Quality score encoding. Choose from phred33 [33-77], phred64 [64-106] or solexa [59-106].">
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123 <option value="phred33">phred33 [33-77]</option>
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124 <option value="phred64">phred64 [64-106]</option>
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125 <option value="solexa">solexa [59-106]</option>
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126 </param>
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127 </when>
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128 </conditional>
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129 </inputs>
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130 <outputs>
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131 <data name="out" format_source="input_single">
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132 <filter>input_type['type'] == "single"</filter>
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133 </data>
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134 <data name="out1" format_source="input_read1">
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135 <filter>input_type['type'] == "paired"</filter>
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136 </data>
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137 <data name="out2" format_source="input_read2">
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138 <filter>input_type['type'] == "paired"</filter>
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139 </data>
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140 <data name="out_log" format="txt">
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141 <filter>print_log == True</filter>
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142 </data>
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143 </outputs>
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144 <tests>
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145 <test>
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146 <param name="type" value="single" />
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147 <param name="input_single" value="t_R1.fastq" ftype="fastq" />
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148 <param name="bc_pattern" value="XXXNNN" />
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149 <param name="prime3" value="0" />
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150 <param name="quality_selector" value="true" />
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151 <param name="quality_filter_threshold" value="10" />
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152 <param name="quality_encoding" value="phred33" />
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153 <output name="out" file="out_SE.fastq" />
1
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154 <output name="out_log" file="out_single.log" lines_diff="22"/>
0
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155 </test>
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156 <test>
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157 <param name="type" value="paired" />
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158 <param name="input_read1" value="t_R1.fastq.gz" ftype="fastq.gz" />
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159 <param name="input_read2" value="t_R2.fastq.gz" ftype="fastq.gz" />
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160 <param name="bc_pattern" value="NNNXXX" />
1
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161 <output name="out1" file="out_R1.fastq.gz" decompress="true" lines_diff="2" />
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162 <output name="out2" file="out_R2.fastq.gz" decompress="true" lines_diff="2" />
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163 <output name="out_log" file="out_paired.log" lines_diff="16"/>
0
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164 </test>
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165 </tests>
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166 <help><![CDATA[
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167
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168
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169 UMI-tools extract.py - Extract UMI from fastq
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170 =============================================
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171
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172 Purpose
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173 -------
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174
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175 Extract UMI barcode from a read and add it to the read name, leaving
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176 any sample barcode in place. Can deal with paired end reads and UMIs
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177 split across the paired ends
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178
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179 Options
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180 -------
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181
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182 --split-barcode
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183 By default the UMI is assumed to be on the first read. Use this
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184 option if the UMI is contained on both reads and specify the
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185 pattern of the barcode/UMI on the second read using the option
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186 ``--bc-pattern2``
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187
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188 --bc-pattern
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189 Use this option to specify the format of the UMI/barcode. Use Ns to
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190 represent the random positions and Xs to indicate the bc positions.
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191 Bases with Ns will be extracted and added to the read name. Remaining
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192 bases, marked with an X will be reattached to the read.
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193
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194 E.g. If the pattern is NNXXNN,
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195 Then the read:
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196
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197 @HISEQ:87:00000000 read1
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198 AAGGTTGCTGATTGGATGGGCTAG
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199 DA1AEBFGGCG01DFH00B1FF0B
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200 +
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201
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202 will become:
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203 @HISEQ:87:00000000_AATT read1
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204 GGGCTGATTGGATGGGCTAG
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205 1AFGGCG01DFH00B1FF0B
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206 +
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207
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208 --bc-pattern2
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209 Use this option to specify the format of the UMI/barcode for
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210 the second read pair if required. If --bc-pattern2 is not
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211 supplied, this defaults to the same pattern as --bc-pattern
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212
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213 --3prime
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214 By default the barcode is assumed to be on the 5' end of the read, but
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215 use this option to sepecify that it is on the 3' end instead
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216
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217 -L
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218 Specify a log file to retain logging information and final statistics
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219
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220 --split-barcode
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221 barcode is split across read pair
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222
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223 --quality-filter-threshold=QUALITY_FILTER_THRESHOLD
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224 Remove reads where any UMI base quality score falls
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225 below this threshold
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226 --quality-encoding=QUALITY_ENCODING
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227 Quality score encoding. Choose from phred33[33-77]
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228 phred64 [64-106] or solexa [59-106]
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229
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230 Usage:
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231 ------
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232
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233 For single ended reads:
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234 umi_tools extract --bc-pattern=[PATTERN] -L extract.log [OPTIONS]
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235
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236 reads from stdin and outputs to stdout.
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237
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238 For paired end reads:
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239 umi_tools extract --bc-pattern=[PATTERN] --read2-in=[FASTQIN] --read2-out=[FASTQOUT] -L extract.log [OPTIONS]
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240
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241 reads end one from stdin and end two from FASTQIN and outputs end one to stdin
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242 and end two to FASTQOUT.
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243
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244 ]]></help>
1
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245 <expand macro="citations" />
0
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246 </tool>