Mercurial > repos > iuc > umi_tools_whitelist

annotate umi-tools_whitelist.xml @ 10:3adbf2fa0928 draft

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"planemo upload commit 28e58376e1d70e38276873a7d5e2ab44db88c2c0"
author iuc
date Tue, 27 Aug 2019 17:11:52 -0400
parents 095c349b4343
children 262026eb36a5
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1 <tool id="umi_tools_whitelist" name="UMI-tools whitelist" version="@VERSION@.0">
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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='$bc_pattern'
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12 --extract-method='$extract_method'
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13 --subset-reads='$subset_reads'
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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 #else
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18 --stdin=input_single.txt
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19 #end if
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20 #else: ## equally valid for both 'paired' and 'paired_collection'
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21 #if $gz:
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22 --stdin=input_read1.gz
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23 --read2-in=input_read2.gz
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24 #else:
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25 --stdin=input_read1.txt
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26 --read2-in=input_read2.txt
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27 #end if
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28 #if $input_type.barcode.barcode_select == "both_reads":
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29 --bc-pattern2='$input_type.barcode.bc_pattern2'
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30 #end if
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31 #end if
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32 #if $celloptions.use_cell_opts == "advanced":
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33 #if $celloptions.set_cell_number != "0":
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34 --set-cell-number=$celloptions.set_cell_number
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35 #end if
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36 #if $celloptions.expect_cells != "0":
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37 --expect-cells=$celloptions.expect_cells
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38 #end if
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39 --error-correct-threshold=$celloptions.error_correct_thresh
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40 #end if
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41 --method=$method
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42 --plot-prefix=OUT
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43
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44 $prime3
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45
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46 #if $log:
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47 --log='$out_log'
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48 #end if
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49
2
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50 --log2stderr
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51
0
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52 > '$out_whitelist' &&
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53
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54 mkdir '${ out_html_report.files_path }' &&
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55 cp OUT_*.png '${ out_html_report.files_path }' &&
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56
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57 echo "<html>
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58 <head></head><body>
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59 <h1>Cell and Count Metrics</h1>
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60 <img src=\"OUT_cell_barcode_count_density.png\" ><br />
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61 <img src=\"OUT_cell_barcode_knee.png\" ><br />
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62 <img src=\"OUT_cell_barcode_counts.png\" ><br />
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63 </body></html>" > '$out_html_report'
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64 &&
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65 mv OUT_cell_thresholds.tsv '$out_thresh'
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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 <param name="bc_pattern" argument="--bc-pattern" type="text" label="Barcode pattern for first read"
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70 help="Use this option to specify the format of the UMI/barcode. Use Ns to
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71 represent the random positions and Xs to indicate the bc positions.
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72 Bases with Ns will be extracted and added to the read name. Remaining
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73 bases, marked with an X will be reattached to the read.">
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74 <expand macro="barcode_sanitizer" />
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75 </param>
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76 <param name="extract_method" argument="--extract-method" type="select" label="Barcode Extraction Method"
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77 help="If bracketed expressions are used in the above barcode pattern, then set this to 'regex'. Otherwise leave as 'string'" >
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78 <option value="string" selected="true" />
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79 <option value="regex" />
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80 </param>
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81 <param name="method" argument="--method" type="select" label="Count reads or UMIs"
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82 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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83 <option value="reads" selected="true" />
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84 <option value="umis" />
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85 </param>
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86 <param argument="--3prime" name="prime3" type="boolean" label="Is barcode on 3' end of the read?"
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87 truevalue="--3prime" falsevalue=""
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88 help="By default the barcode is assumed to be on the 5' end of the read, but
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89 use this option to specify that it is on the 3' end instead." />
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90 <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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91 <conditional name="celloptions" >
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92 <param name="use_cell_opts" type="select" label="Cell parameters" >
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93 <option value="defaults" selected="True">Use Defaults</option>
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94 <option value="advanced">Advanced Options</option>
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95 </param>
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96 <when value="defaults"/>
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97 <when value="advanced">
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98 <param name="set_cell_number" type="integer" min="0" value="0" label="Specify the number of cell barcodes to accept" />
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99 <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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100 <param name="error_correct_thresh" type="integer" min="0" value="0" label="Hamming distance for correction of barcodes to whitelist barcodes. Set to zero to generate no error correcting metrics." />
0
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101 </when>
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102 </conditional>
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103 <param argument="--log" type="boolean" label="Output log?" truevalue="--log" falsevalue=""
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104 help="Choose if you want to generate a text file containing logging information." />
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105 </inputs>
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106 <outputs>
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107 <data name="out_whitelist" format="tabular" label="${tool.name} on ${on_string}: Whitelist"/>
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108 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: logfile" >
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109 <filter>log</filter>
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110 </data>
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111 <data name="out_html_report" format="html" label="${tool.name} on ${on_string}: Webpage" />
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112 <data name="out_thresh" format="tabular" label="${tool.name} on ${on_string}: TSV Cell Thresholds" />
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113 </outputs>
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114 <tests>
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115 <test expect_num_outputs="3">
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116 <conditional name="input_type" >
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117 <param name="type" value="single" />
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118 <param name="input_single" value="t_R2.fastq.gz" ftype="fastq.gz" />
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119 </conditional>
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120 <param name="bc_pattern" value="CCCCCCCCNNNNNNNN" />
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121 <param name="method" value="reads" />
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122 <param name="prime3" value="true" />
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123 <output name="out_whitelist" file="out_wl_single.txt" lines_diff="40" />
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124 <output name="out_thresh" file="out_wl_single.tresh.tab" />
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125 <output name="out_html_report" file="out_wl_single.html" />
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126 </test>
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127 <test expect_num_outputs="4">
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128 <conditional name="input_type" >
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129 <param name="type" value="paired" />
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130 <param name="input_read1" value="t_R1.fastq.gz" ftype="fastq.gz" />
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131 <param name="input_read2" value="t_R2.fastq.gz" ftype="fastq.gz" />
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132 </conditional>
4
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133 <param name="barcode_select" value="first_read_only" />
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134 <param name="bc_pattern" value="CCCNNNNNNNNXXXXX" />
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135 <param name="bc_pattern2" value="CCCCCCCCNNNNNNNN" />
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136 <param name="method" value="reads" />
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137 <param name="prime3" value="false" />
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138 <param name="use_cell_opts" value="advanced" />
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139 <param name="expect_cells" value="5" />
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140 <param name="error_correct_thresh" value="3" />
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141 <param name="log" value="true" />
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142 <output name="out_whitelist" file="out_wl_paired.txt" />
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143 <output name="out_log" file="out_wl_paired.log" lines_diff="40" />
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144 <output name="out_html_report" file="out_wl_paired.html" />
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145 <output name="out_thresh" file="out_wl_paired.tresh.tab" />
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146 </test>
2
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147 <test expect_num_outputs="4"> <!-- As previous, identical outputs but paired collection input -->
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148 <conditional name="input_type" >
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149 <param name="type" value="paired_collection" />
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150 <param name="input_readpair" >
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151 <collection type="paired">
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152 <element name="forward" ftype="fastq.gz" value="t_R1.fastq.gz" />
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153 <element name="reverse" ftype="fastq.gz" value="t_R2.fastq.gz" />
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154 </collection>
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155 </param>
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156 </conditional>
4
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157 <param name="barcode_select" value="first_read_only" />
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158 <param name="bc_pattern" value="CCCNNNNNNNNXXXXX" />
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159 <param name="bc_pattern2" value="CCCCCCCCNNNNNNNN" />
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160 <param name="method" value="reads" />
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161 <param name="prime3" value="false" />
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162 <param name="use_cell_opts" value="advanced" />
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163 <param name="expect_cells" value="5" />
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164 <param name="error_correct_thresh" value="3" />
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165 <param name="log" value="true" />
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166 <output name="out_whitelist" file="out_wl_paired.txt" />
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167 <output name="out_log" file="out_wl_paired.log" lines_diff="40" />
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168 <output name="out_html_report" file="out_wl_paired.html" />
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169 <output name="out_thresh" file="out_wl_paired.tresh.tab" />
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170 </test>
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171 <!-- Error report on not accepting regex and lt and gt symbols -->
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172 <test expect_num_outputs="3">
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173 <conditional name="input_type" >
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174 <param name="type" value="single" />
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175 <param name="input_single" value="testYYY.40k.fastq.gz" ftype="fastq.gz" />
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176 </conditional>
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177 <param name="bc_pattern" value="(?P&#60;cell_1&#62;.{8,10})(?P&#60;discard_1&#62;ACTGGCCTGCGA){s&#60;=3}(?P&#60;cell_2&#62;.{9})(?P&#60;discard_2&#62;GGTAGCGGTGACA){s&#60;=3}(?P&#60;cell_3&#62;.{9})(?P&#60;umi_1&#62;.{8})T{3}.*" />
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178 <param name="extract_method" value="regex" />
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179 <param name="method" value="umis" />
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180 <param name="prime3" value="true" />
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181 <output name="out_whitelist" file="out_wl_user.single.txt" />
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182 <output name="out_thresh" file="out_wl_user.single.tresh.tab" />
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183 <output name="out_html_report" file="out_wl_user.single.html" />
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184 </test>
0
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185 </tests>
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186 <help><![CDATA[
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187
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188
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189 UMI-tools whitelist - Extract barcodes from fastq
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190 ==================================================
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191
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192 Purpose
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193 -------
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194
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195 Extract cell barcodes and identify the most likely true barcodes using
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196 the 'knee' method.
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197
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198 Options
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199 -------
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200
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201 --bc-pattern
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202 This should be used where the barcodes are always in the same
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203 place in the read.
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204
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205 - N = UMI position (required)
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206 - C = cell barcode position (optional)
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207 - X = sample position (optional)
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208
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209 Bases with Ns and Cs will be extracted and added to the read
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210 name. The corresponding sequence qualities will be removed from
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211 the read. Bases with an X will be reattached to the read.
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212
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213 E.g. If the pattern is NNNNCC,
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214 Then the read:
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215 @HISEQ:87:00000000 read1
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216 AAGGTTGCTGATTGGATGGGCTAG
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217 DA1AEBFGGCG01DFH00B1FF0B
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218 +
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219 will become:
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220 @HISEQ:87:00000000_TT_AAGG read1
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221 GCTGATTGGATGGGCTAG
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222 1AFGGCG01DFH00B1FF0B
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223 +
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224
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225 where 'TT' is the cell barcode and 'AAGG' is the UMI.
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226
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227
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228 --set-cell-number
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229 Use this option to explicity set the number of cell barcodes
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230 which should be accepted. Note that the exact number of cell
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231 barcodes in the outputted whitelist may be slightly less than
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232 this if there are multiple cells observed with the same
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233 frequency at the threshold between accepted and rejected cell
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234 barcodes.
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235
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236 --expect-cells=[EXPECTED_CELLS]
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237 An upper limit estimate for the number of inputted cells. The knee
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238 method will now select the first threshold (order ascendingly)
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239 which results in the number of cell barcodes accepted being <=
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240 EXPECTED_CELLS and > EXPECTED_CELLS * 0.1.
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241
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242
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243 --bc-pattern2
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244 Use this option to specify the format of the UMI/barcode for
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245 the second read pair if required. If --bc-pattern2 is not
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246 supplied, this defaults to the same pattern as --bc-pattern
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247
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248 --3prime
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249 By default the barcode is assumed to be on the 5' end of the read, but
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250 use this option to sepecify that it is on the 3' end instead
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251
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252 Usage:
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253 ------
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254
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255 For single ended reads:
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256 umi_tools whitelist --bc-pattern=[PATTERN] -L extract.log
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257 [OPTIONS]
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258
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259 reads from stdin and outputs to stdout.
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260
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261 For paired end reads where the cell barcodes is split across the read pairs:
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262 umi_tools whitelist --bc-pattern=[PATTERN]
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263 --bc-pattern2=[PATTERN] --read2-in=[FASTQIN] -L extract.log
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264 [OPTIONS]
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265
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266 reads end one from stdin and end two from FASTQIN and outputs to stdin
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267
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268
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269 Output:
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270 -------
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271
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272 The whitelist is outputted as 4 tab-separated columns:
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273
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274 1. whitelisted cell barcode
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275 2. Other cell barcode(s) (comma-separated) to correct to the
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276 whitelisted barcode
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277 3. Count for whitelisted cell barcodes
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278 4. Count(s) for the other cell barcode(s) (comma-separated)
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279
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280 example output:
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281
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282 AAAAAA AGAAAA 146 1
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283 AAAATC 22
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284 AAACAT 21
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285 AAACTA AAACTN,GAACTA 27 1,1
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286 AAATAC 72
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287 AAATCA GAATCA 37 3
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288 AAATGT AAAGGT,CAATGT 41 1,1
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289 AAATTG CAATTG 36 1
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290 AACAAT 18
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291 AACATA 24
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292
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293 If --error-correct-threshold is set to 0, columns 2 and 4 will be empty.
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294
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295
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296 ]]></help>
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297 <expand macro="citations" />
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298 </tool>