Mercurial > repos > iuc > umi_tools_whitelist

annotate umi-tools_whitelist.xml @ 1:dac4e7dc837d draft

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planemo upload commit c69e558f5186d40896ee40a49bdb2275949faf9e
author iuc
date Tue, 27 Mar 2018 14:26:15 -0400
parents b911124762a8
children c1743022a8cd
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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 #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 $gz = True
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19 #end if
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20 #end if
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21 umi_tools whitelist
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22 --bc-pattern='$bc_pattern'
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23 --subset-reads='$subset_reads'
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24 #if $input_type.type == 'single':
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25 #if $gz:
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26 --stdin=input_single.gz
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27 #else
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28 --stdin='$input_type.input_single'
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29 #end if
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30 #else:
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31 #if $gz:
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32 --stdin=input_read1.gz
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33 --read2-in=input_read2.gz
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34 #else:
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35 --stdin='$input_type.input_read1'
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36 --read2-in='$input_type.input_read2'
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37 #end if
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38 #if $input_type.barcode.barcode_select == "1":
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39 --bc-pattern2='$input_type.barcode.bc_pattern2'
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40 #end if
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41 #end if
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42 #if $celloptions.use_cell_opts == "advanced":
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43 #if $celloptions.set_cell_number != "0":
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44 --set-cell-number=$celloptions.set_cell_number
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45 #end if
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46 #if $celloptions.expect_cells != "0":
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47 --expect-cells=$celloptions.expect_cells
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48 #end if
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49 --error-correct-threshold=$celloptions.error_correct_thresh
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50 #end if
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51 --method=$method
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52 --plot-prefix=OUT
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53
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54 $prime3
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55
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56 #if $log:
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57 --log='$out_log'
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58 #end if
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59
1
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60 --log2stderr
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61
0
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62 > '$out_whitelist' &&
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63
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64 mkdir '${ out_html_report.files_path }' &&
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65 cp OUT_*.png '${ out_html_report.files_path }' &&
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66
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67 echo "<html>
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68 <head></head><body>
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69 <h1>Cell and Count Metrics</h1>
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70 <img src=\"OUT_cell_barcode_count_density.png\" ><br />
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71 <img src=\"OUT_cell_barcode_knee.png\" ><br />
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72 <img src=\"OUT_cell_barcode_counts.png\" ><br />
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73 </body></html>" > '$out_html_report'
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74 &&
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75 mv OUT_cell_thresholds.tsv '$out_thresh'
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76 ]]></command>
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77 <inputs>
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78 <conditional name="input_type">
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79 <param name="type" type="select" label="Library type">
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80 <option value="single">Single-end</option>
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81 <option value="paired">Paired-end</option>
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82 </param>
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83 <when value="single">
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84 <param name="input_single" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />
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85 </when>
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86 <when value="paired">
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87 <param name="input_read1" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />
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88 <param name="input_read2" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />
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89 <conditional name="barcode">
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90 <param name="barcode_select" argument="--split-barcode" type="select" label="Barcode on both reads?">
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91 <option value="first_read_only">Barcode on first read only</option>
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92 <option value="both_reads">Barcode on both reads</option>
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93 </param>
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94 <when value="first_read_only"/>
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95 <when value="both_reads">
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96 <param name="bc_pattern2" argument="--bc-pattern2" type="text" value="" label="Barcode pattern for second read"
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97 help="Use this option to specify the format of the UMI/barcode for
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98 the second read pair if required.">
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99 </param>
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100 </when>
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101 </conditional>
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102 </when>
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103 </conditional>
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104 <param name="bc_pattern" argument="--bc-pattern" type="text" label="Barcode pattern for first read"
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105 help="Use this option to specify the format of the UMI/barcode. Use Ns to
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106 represent the random positions and Xs to indicate the bc positions.
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107 Bases with Ns will be extracted and added to the read name. Remaining
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108 bases, marked with an X will be reattached to the read.">
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109 </param>
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110 <param name="method" argument="--method" type="select" label="Count reads or UMIs"
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111 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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112 <option value="reads" selected="true" />
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113 <option value="umis" />
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114 </param>
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115
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116 <param argument="--3prime" name="prime3" type="boolean" label="Is barcode on 3' end of the read?"
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117 truevalue="--3prime" falsevalue=""
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118 help="By default the barcode is assumed to be on the 5' end of the read, but
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119 use this option to specify that it is on the 3' end instead." />
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120 <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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121 <conditional name="celloptions" >
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122 <param name="use_cell_opts" type="select" label="Cell parameters" >
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123 <option value="defaults" selected="True">Use Defaults</option>
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124 <option value="advanced">Advanced Options</option>
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125 </param>
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126 <when value="defaults"/>
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127 <when value="advanced">
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128 <param name="set_cell_number" type="integer" min="0" value="0" label="Specify the number of cell barcodes to accept" />
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129 <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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130 <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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131 </when>
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132 </conditional>
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133 <param argument="--log" type="boolean" label="Output log?" truevalue="--log" falsevalue=""
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134 help="Choose if you want to generate a text file containing logging information." />
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135
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136 </inputs>
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137 <outputs>
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138 <data name="out_whitelist" format="tabular" label="${tool.name} on ${on_string}: Whitelist"/>
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139 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: logfile" >
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140 <filter>log</filter>
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141 </data>
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142 <data name="out_html_report" format="html" label="${tool.name} on ${on_string}: Webpage" />
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143 <data name="out_thresh" format="tabular" label="${tool.name} on ${on_string}: TSV Cell Thresholds" />
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144 </outputs>
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145 <tests>
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146 <test expect_num_outputs="3">
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147 <param name="type" value="single" />
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148 <param name="input_single" value="t_R2.fastq.gz" ftype="fastq" />
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149 <param name="bc_pattern" value="CCCCCCCCNNNNNNNN" />
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150 <param name="method" value="reads" />
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151 <param name="prime3" value="true" />
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152 <output name="out_whitelist" file="out_wl_single.txt" lines_diff="40" />
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153 <output name="out_thresh" file="out_wl_single.tresh.tab" />
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154 <output name="out_html_report" file="out_wl_single.html" />
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155 </test>
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156 <test expect_num_outputs="4">
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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" />
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159 <param name="input_read2" value="t_R2.fastq.gz" ftype="fastq" />
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160 <param name="barcode_select" value="both_reads" />
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161 <param name="bc_pattern" value="CCCNNNNNNNNXXXXX" />
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162 <param name="bc_pattern2" value="CCCCCCCCNNNNNNNN" />
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163 <param name="method" value="reads" />
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164 <param name="prime3" value="false" />
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165 <param name="use_cell_opts" value="advanced" />
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166 <param name="expect_cells" value="5" />
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167 <param name="error_correct_thresh" value="3" />
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168 <param name="log" value="true" />
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169 <output name="out_whitelist" file="out_wl_paired.txt" />
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170 <output name="out_log" file="out_wl_paired.log" lines_diff="40" />
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171 <output name="out_html_report" file="out_wl_paired.html" />
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172 <output name="out_thresh" file="out_wl_paired.tresh.tab" />
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173 </test>
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174 </tests>
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175 <help><![CDATA[
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176
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177
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178 UMI-tools whitelist - Extract barcodes from fastq
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179 ==================================================
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180
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181 Purpose
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182 -------
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183
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184 Extract cell barcodes and identify the most likely true barcodes using
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185 the 'knee' method.
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186
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187 Options
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188 -------
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189
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190 --bc-pattern
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191 This should be used where the barcodes are always in the same
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192 place in the read.
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193
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194 - N = UMI position (required)
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195 - C = cell barcode position (optional)
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196 - X = sample position (optional)
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197
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198 Bases with Ns and Cs will be extracted and added to the read
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199 name. The corresponding sequence qualities will be removed from
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200 the read. Bases with an X will be reattached to the read.
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201
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202 E.g. If the pattern is NNNNCC,
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203 Then the read:
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204 @HISEQ:87:00000000 read1
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205 AAGGTTGCTGATTGGATGGGCTAG
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206 DA1AEBFGGCG01DFH00B1FF0B
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207 +
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208 will become:
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209 @HISEQ:87:00000000_TT_AAGG read1
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210 GCTGATTGGATGGGCTAG
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211 1AFGGCG01DFH00B1FF0B
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212 +
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213
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214 where 'TT' is the cell barcode and 'AAGG' is the UMI.
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215
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216
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217 --set-cell-number
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218 Use this option to explicity set the number of cell barcodes
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219 which should be accepted. Note that the exact number of cell
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220 barcodes in the outputted whitelist may be slightly less than
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221 this if there are multiple cells observed with the same
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222 frequency at the threshold between accepted and rejected cell
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223 barcodes.
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224
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225 --expect-cells=[EXPECTED_CELLS]
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226 An upper limit estimate for the number of inputted cells. The knee
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227 method will now select the first threshold (order ascendingly)
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228 which results in the number of cell barcodes accepted being <=
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229 EXPECTED_CELLS and > EXPECTED_CELLS * 0.1.
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230
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231
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232 --bc-pattern2
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233 Use this option to specify the format of the UMI/barcode for
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234 the second read pair if required. If --bc-pattern2 is not
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235 supplied, this defaults to the same pattern as --bc-pattern
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236
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237 --3prime
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238 By default the barcode is assumed to be on the 5' end of the read, but
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239 use this option to sepecify that it is on the 3' end instead
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240
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241 Usage:
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242 ------
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243
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244 For single ended reads:
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245 umi_tools whitelist --bc-pattern=[PATTERN] -L extract.log
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246 [OPTIONS]
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247
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248 reads from stdin and outputs to stdout.
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249
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250 For paired end reads where the cell barcodes is split across the read pairs:
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251 umi_tools whitelist --bc-pattern=[PATTERN]
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252 --bc-pattern2=[PATTERN] --read2-in=[FASTQIN] -L extract.log
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253 [OPTIONS]
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254
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255 reads end one from stdin and end two from FASTQIN and outputs to stdin
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256
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257
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258 Output:
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259 -------
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260
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261 The whitelist is outputted as 4 tab-separated columns:
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262
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263 1. whitelisted cell barcode
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264 2. Other cell barcode(s) (comma-separated) to correct to the
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265 whitelisted barcode
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266 3. Count for whitelisted cell barcodes
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267 4. Count(s) for the other cell barcode(s) (comma-separated)
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268
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269 example output:
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270
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271 AAAAAA AGAAAA 146 1
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272 AAAATC 22
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273 AAACAT 21
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274 AAACTA AAACTN,GAACTA 27 1,1
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275 AAATAC 72
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276 AAATCA GAATCA 37 3
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277 AAATGT AAAGGT,CAATGT 41 1,1
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278 AAATTG CAATTG 36 1
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279 AACAAT 18
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280 AACATA 24
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281
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282 If --error-correct-threshold is set to 0, columns 2 and 4 will be empty.
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283
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284
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285 ]]></help>
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286 <expand macro="citations" />
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287 </tool>