Mercurial > repos > iuc > umi_tools_whitelist

annotate umi-tools_whitelist.xml @ 8:b7f28330cb30 draft

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author iuc
date Mon, 16 Jul 2018 17:35:05 -0400
parents 095c349b4343
children 3adbf2fa0928
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1 <tool id="umi_tools_whitelist" name="UMI-tools whitelist" version="@VERSION@.1">
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2 <description>Extract cell barcodes 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
0
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10 umi_tools whitelist
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11 --bc-pattern='$bc_pattern'
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12 --subset-reads='$subset_reads'
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13 #if $input_type.type == 'single':
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14 #if $gz:
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15 --stdin=input_single.gz
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16 #else
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17 --stdin=input_single.txt
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18 #end if
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19 #else: ## equally valid for both 'paired' and 'paired_collection'
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20 #if $gz:
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21 --stdin=input_read1.gz
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22 --read2-in=input_read2.gz
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23 #else:
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24 --stdin=input_read1.txt
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25 --read2-in=input_read2.txt
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26 #end if
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27 #if $input_type.barcode.barcode_select == "both_reads":
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28 --bc-pattern2='$input_type.barcode.bc_pattern2'
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29 #end if
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30 #end if
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31 #if $celloptions.use_cell_opts == "advanced":
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32 #if $celloptions.set_cell_number != "0":
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33 --set-cell-number=$celloptions.set_cell_number
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34 #end if
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35 #if $celloptions.expect_cells != "0":
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36 --expect-cells=$celloptions.expect_cells
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37 #end if
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38 --error-correct-threshold=$celloptions.error_correct_thresh
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39 #end if
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40 --method=$method
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41 --plot-prefix=OUT
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42
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43 $prime3
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44
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45 #if $log:
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46 --log='$out_log'
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47 #end if
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48
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49 --log2stderr
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50
0
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51 > '$out_whitelist' &&
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52
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53 mkdir '${ out_html_report.files_path }' &&
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54 cp OUT_*.png '${ out_html_report.files_path }' &&
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55
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56 echo "<html>
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57 <head></head><body>
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58 <h1>Cell and Count Metrics</h1>
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59 <img src=\"OUT_cell_barcode_count_density.png\" ><br />
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60 <img src=\"OUT_cell_barcode_knee.png\" ><br />
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61 <img src=\"OUT_cell_barcode_counts.png\" ><br />
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62 </body></html>" > '$out_html_report'
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63 &&
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64 mv OUT_cell_thresholds.tsv '$out_thresh'
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65 ]]></command>
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66 <inputs>
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67 <expand macro="input_types" />
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68 <param name="bc_pattern" argument="--bc-pattern" type="text" label="Barcode pattern for first read"
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69 help="Use this option to specify the format of the UMI/barcode. Use Ns to
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70 represent the random positions and Xs to indicate the bc positions.
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71 Bases with Ns will be extracted and added to the read name. Remaining
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72 bases, marked with an X will be reattached to the read.">
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73 </param>
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74 <param name="method" argument="--method" type="select" label="Count reads or UMIs"
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75 help="Many published protocols rank CBs by the number of reads the CBs appear in. However you could also use the number of unique UMIs a CB is associated with. Note that this is still and approximation to the number of transcripts captured because the same UMI could be associated with two different transcripts and be counted as independent." >
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76 <option value="reads" selected="true" />
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77 <option value="umis" />
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78 </param>
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79
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80 <param argument="--3prime" name="prime3" type="boolean" label="Is barcode on 3' end of the read?"
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81 truevalue="--3prime" falsevalue=""
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82 help="By default the barcode is assumed to be on the 5' end of the read, but
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83 use this option to specify that it is on the 3' end instead." />
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84 <param name="subset_reads" argument="--subset-reads" type="integer" min="0" value="0" label="Use the first N reads to automatically identify the true cell barcodes." />
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85 <conditional name="celloptions" >
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86 <param name="use_cell_opts" type="select" label="Cell parameters" >
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87 <option value="defaults" selected="True">Use Defaults</option>
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88 <option value="advanced">Advanced Options</option>
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89 </param>
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90 <when value="defaults"/>
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91 <when value="advanced">
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92 <param name="set_cell_number" type="integer" min="0" value="0" label="Specify the number of cell barcodes to accept" />
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93 <param name="expect_cells" type="integer" min="0" value="0" label="Prior expectation on the upper limit on the number of cells sequenced" />
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94 <param name="error_correct_thresh" type="integer" min="0" value="0" label="Hamming distance for correction of barcodes to whilelist barcodes. Set to zero to generate no error correcting metrics." />
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95 </when>
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96 </conditional>
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97 <param argument="--log" type="boolean" label="Output log?" truevalue="--log" falsevalue=""
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98 help="Choose if you want to generate a text file containing logging information." />
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99
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100 </inputs>
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101 <outputs>
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102 <data name="out_whitelist" format="tabular" label="${tool.name} on ${on_string}: Whitelist"/>
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103 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: logfile" >
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104 <filter>log</filter>
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105 </data>
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106 <data name="out_html_report" format="html" label="${tool.name} on ${on_string}: Webpage" />
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107 <data name="out_thresh" format="tabular" label="${tool.name} on ${on_string}: TSV Cell Thresholds" />
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108 </outputs>
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109 <tests>
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110 <test expect_num_outputs="3">
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111 <param name="type" value="single" />
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112 <param name="input_single" value="t_R2.fastq.gz" ftype="fastq" />
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113 <param name="bc_pattern" value="CCCCCCCCNNNNNNNN" />
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114 <param name="method" value="reads" />
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115 <param name="prime3" value="true" />
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116 <output name="out_whitelist" file="out_wl_single.txt" lines_diff="40" />
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117 <output name="out_thresh" file="out_wl_single.tresh.tab" />
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118 <output name="out_html_report" file="out_wl_single.html" />
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119 </test>
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120 <test expect_num_outputs="4">
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121 <param name="type" value="paired" />
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122 <param name="input_read1" value="t_R1.fastq.gz" ftype="fastq" />
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123 <param name="input_read2" value="t_R2.fastq.gz" ftype="fastq" />
4
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124 <param name="barcode_select" value="first_read_only" />
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125 <param name="bc_pattern" value="CCCNNNNNNNNXXXXX" />
0
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126 <param name="bc_pattern2" value="CCCCCCCCNNNNNNNN" />
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127 <param name="method" value="reads" />
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128 <param name="prime3" value="false" />
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129 <param name="use_cell_opts" value="advanced" />
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130 <param name="expect_cells" value="5" />
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131 <param name="error_correct_thresh" value="3" />
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132 <param name="log" value="true" />
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133 <output name="out_whitelist" file="out_wl_paired.txt" />
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134 <output name="out_log" file="out_wl_paired.log" lines_diff="40" />
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135 <output name="out_html_report" file="out_wl_paired.html" />
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136 <output name="out_thresh" file="out_wl_paired.tresh.tab" />
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137 </test>
2
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138 <test expect_num_outputs="4"> <!-- As previous, identical outputs but paired collection input -->
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139 <param name="type" value="paired_collection" />
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140 <param name="input_readpair" >
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141 <collection type="paired">
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142 <element name="forward" ftype="fastq.gz" value="t_R1.fastq.gz" />
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143 <element name="reverse" ftype="fastq.gz" value="t_R2.fastq.gz" />
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144 </collection>
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145 </param>
4
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146 <param name="barcode_select" value="first_read_only" />
2
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147 <param name="bc_pattern" value="CCCNNNNNNNNXXXXX" />
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148 <param name="bc_pattern2" value="CCCCCCCCNNNNNNNN" />
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149 <param name="method" value="reads" />
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150 <param name="prime3" value="false" />
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151 <param name="use_cell_opts" value="advanced" />
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152 <param name="expect_cells" value="5" />
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153 <param name="error_correct_thresh" value="3" />
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154 <param name="log" value="true" />
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155 <output name="out_whitelist" file="out_wl_paired.txt" />
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156 <output name="out_log" file="out_wl_paired.log" lines_diff="40" />
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157 <output name="out_html_report" file="out_wl_paired.html" />
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158 <output name="out_thresh" file="out_wl_paired.tresh.tab" />
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159 </test>
0
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160 </tests>
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161 <help><![CDATA[
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162
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163
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164 UMI-tools whitelist - Extract barcodes from fastq
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165 ==================================================
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166
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167 Purpose
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168 -------
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169
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170 Extract cell barcodes and identify the most likely true barcodes using
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171 the 'knee' method.
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172
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173 Options
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174 -------
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175
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176 --bc-pattern
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177 This should be used where the barcodes are always in the same
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178 place in the read.
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179
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180 - N = UMI position (required)
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181 - C = cell barcode position (optional)
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182 - X = sample position (optional)
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183
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184 Bases with Ns and Cs will be extracted and added to the read
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185 name. The corresponding sequence qualities will be removed from
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186 the read. Bases with an X will be reattached to the read.
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187
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188 E.g. If the pattern is NNNNCC,
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189 Then the read:
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190 @HISEQ:87:00000000 read1
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191 AAGGTTGCTGATTGGATGGGCTAG
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192 DA1AEBFGGCG01DFH00B1FF0B
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193 +
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194 will become:
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195 @HISEQ:87:00000000_TT_AAGG read1
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196 GCTGATTGGATGGGCTAG
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197 1AFGGCG01DFH00B1FF0B
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198 +
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199
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200 where 'TT' is the cell barcode and 'AAGG' is the UMI.
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201
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202
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203 --set-cell-number
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204 Use this option to explicity set the number of cell barcodes
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205 which should be accepted. Note that the exact number of cell
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206 barcodes in the outputted whitelist may be slightly less than
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207 this if there are multiple cells observed with the same
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208 frequency at the threshold between accepted and rejected cell
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209 barcodes.
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210
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211 --expect-cells=[EXPECTED_CELLS]
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212 An upper limit estimate for the number of inputted cells. The knee
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213 method will now select the first threshold (order ascendingly)
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214 which results in the number of cell barcodes accepted being <=
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215 EXPECTED_CELLS and > EXPECTED_CELLS * 0.1.
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216
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217
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218 --bc-pattern2
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219 Use this option to specify the format of the UMI/barcode for
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220 the second read pair if required. If --bc-pattern2 is not
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221 supplied, this defaults to the same pattern as --bc-pattern
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222
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223 --3prime
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224 By default the barcode is assumed to be on the 5' end of the read, but
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225 use this option to sepecify that it is on the 3' end instead
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226
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227 Usage:
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228 ------
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229
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230 For single ended reads:
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231 umi_tools whitelist --bc-pattern=[PATTERN] -L extract.log
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232 [OPTIONS]
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233
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234 reads from stdin and outputs to stdout.
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235
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236 For paired end reads where the cell barcodes is split across the read pairs:
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237 umi_tools whitelist --bc-pattern=[PATTERN]
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238 --bc-pattern2=[PATTERN] --read2-in=[FASTQIN] -L extract.log
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239 [OPTIONS]
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240
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241 reads end one from stdin and end two from FASTQIN and outputs to stdin
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242
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243
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244 Output:
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245 -------
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246
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247 The whitelist is outputted as 4 tab-separated columns:
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248
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249 1. whitelisted cell barcode
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250 2. Other cell barcode(s) (comma-separated) to correct to the
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251 whitelisted barcode
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252 3. Count for whitelisted cell barcodes
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253 4. Count(s) for the other cell barcode(s) (comma-separated)
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254
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255 example output:
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256
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257 AAAAAA AGAAAA 146 1
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258 AAAATC 22
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259 AAACAT 21
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260 AAACTA AAACTN,GAACTA 27 1,1
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261 AAATAC 72
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262 AAATCA GAATCA 37 3
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263 AAATGT AAAGGT,CAATGT 41 1,1
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264 AAATTG CAATTG 36 1
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265 AACAAT 18
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266 AACATA 24
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267
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268 If --error-correct-threshold is set to 0, columns 2 and 4 will be empty.
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269
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270
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271 ]]></help>
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272 <expand macro="citations" />
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273 </tool>