Mercurial > repos > iuc > umi_tools_whitelist

annotate umi-tools_whitelist.xml @ 2:c1743022a8cd draft

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planemo upload commit e274ffd67bede657f4f5a2c6524023ff57f0db87
author iuc
date Thu, 29 Mar 2018 18:24:04 -0400
parents dac4e7dc837d
children 853f74e08009
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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 <macro name="barcode2_conditional" >
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6 <conditional name="barcode">
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7 <param name="barcode_select" argument="--split-barcode" type="select" label="Barcode on both reads?">
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8 <option value="first_read_only">Barcode on first read only</option>
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9 <option value="both_reads">Barcode on both reads</option>
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10 </param>
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11 <when value="first_read_only"/>
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12 <when value="both_reads">
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13 <param name="bc_pattern2" argument="--bc-pattern2" type="text" value="" label="Barcode pattern for second read"
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14 help="Use this option to specify the format of the UMI/barcode for
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15 the second read pair if required.">
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16 </param>
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17 </when>
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18 </conditional>
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19 </macro>
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20 </macros>
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21 <expand macro="requirements" />
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22 <command detect_errors="exit_code"><![CDATA[
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23 #set $gz = False
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24 #if $input_type.type == 'single':
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25 #if $input_type.input_single.is_of_type("fastq.gz", "fastqsanger.gz"):
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26 ln -s '$input_type.input_single' input_single.gz &&
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27 #set $gz = True
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28 #end if
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29 #elif $input_type.type == 'paired':
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30 #if $input_type.input_read1.is_of_type("fastq.gz", "fastqsanger.gz"):
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31 ln -s '$input_type.input_read1' input_read1.gz &&
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32 ln -s '$input_type.input_read2' input_read2.gz &&
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33 #set $gz = True
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34 #end if
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35 #else ## paired_collection
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36 #if $input_type.input_readpair.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
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37 ln -s '$input_type.input_readpair.forward' input_read1.gz &&
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38 ln -s '$input_type.input_readpair.reverse' input_read2.gz &&
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39 #set $gz = True
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40 #end if
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41 #end if
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42 umi_tools whitelist
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43 --bc-pattern='$bc_pattern'
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44 --subset-reads='$subset_reads'
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45 #if $input_type.type == 'single':
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46 #if $gz:
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47 --stdin=input_single.gz
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48 #else
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49 --stdin='$input_type.input_single'
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50 #end if
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51 #else: ## equally valid for both 'paired' and 'paired_collection'
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52 #if $gz:
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53 --stdin=input_read1.gz
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54 --read2-in=input_read2.gz
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55 #else:
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56 --stdin='$input_type.input_read1'
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57 --read2-in='$input_type.input_read2'
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58 #end if
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59 #if $input_type.barcode.barcode_select == "1":
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60 --bc-pattern2='$input_type.barcode.bc_pattern2'
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61 #end if
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62 #end if
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63 #if $celloptions.use_cell_opts == "advanced":
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64 #if $celloptions.set_cell_number != "0":
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65 --set-cell-number=$celloptions.set_cell_number
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66 #end if
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67 #if $celloptions.expect_cells != "0":
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68 --expect-cells=$celloptions.expect_cells
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69 #end if
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70 --error-correct-threshold=$celloptions.error_correct_thresh
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71 #end if
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72 --method=$method
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73 --plot-prefix=OUT
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74
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75 $prime3
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76
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77 #if $log:
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78 --log='$out_log'
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79 #end if
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80
2
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81 --log2stderr
1
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82
0
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83 > '$out_whitelist' &&
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84
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85 mkdir '${ out_html_report.files_path }' &&
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86 cp OUT_*.png '${ out_html_report.files_path }' &&
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87
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88 echo "<html>
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89 <head></head><body>
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90 <h1>Cell and Count Metrics</h1>
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91 <img src=\"OUT_cell_barcode_count_density.png\" ><br />
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92 <img src=\"OUT_cell_barcode_knee.png\" ><br />
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93 <img src=\"OUT_cell_barcode_counts.png\" ><br />
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94 </body></html>" > '$out_html_report'
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95 &&
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96 mv OUT_cell_thresholds.tsv '$out_thresh'
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97 ]]></command>
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98 <inputs>
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99 <conditional name="input_type">
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100 <param name="type" type="select" label="Library type">
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101 <option value="single">Single-end</option>
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102 <option value="paired">Paired-end</option>
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103 <option value="paired_collection">Paired-end Dataset Collection</option>
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104 </param>
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105 <when value="single">
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106 <param name="input_single" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />
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107 </when>
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108 <when value="paired">
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109 <param name="input_read1" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />
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110 <param name="input_read2" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" />
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111 <expand macro="barcode2_conditional" />
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112 </when>
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113 <when value="paired_collection">
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114 <param name="input_readpair" type="data_collection" collection_type="paired" format="fastq,fastq.gz" label="Reads in FASTQ format" />
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115 <expand macro="barcode2_conditional" />
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116 </when>
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117 </conditional>
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118 <param name="bc_pattern" argument="--bc-pattern" type="text" label="Barcode pattern for first read"
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119 help="Use this option to specify the format of the UMI/barcode. Use Ns to
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120 represent the random positions and Xs to indicate the bc positions.
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121 Bases with Ns will be extracted and added to the read name. Remaining
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122 bases, marked with an X will be reattached to the read.">
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123 </param>
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124 <param name="method" argument="--method" type="select" label="Count reads or UMIs"
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125 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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126 <option value="reads" selected="true" />
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127 <option value="umis" />
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128 </param>
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129
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130 <param argument="--3prime" name="prime3" type="boolean" label="Is barcode on 3' end of the read?"
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131 truevalue="--3prime" falsevalue=""
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132 help="By default the barcode is assumed to be on the 5' end of the read, but
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133 use this option to specify that it is on the 3' end instead." />
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134 <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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135 <conditional name="celloptions" >
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136 <param name="use_cell_opts" type="select" label="Cell parameters" >
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137 <option value="defaults" selected="True">Use Defaults</option>
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138 <option value="advanced">Advanced Options</option>
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139 </param>
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140 <when value="defaults"/>
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141 <when value="advanced">
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142 <param name="set_cell_number" type="integer" min="0" value="0" label="Specify the number of cell barcodes to accept" />
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143 <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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144 <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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145 </when>
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146 </conditional>
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147 <param argument="--log" type="boolean" label="Output log?" truevalue="--log" falsevalue=""
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148 help="Choose if you want to generate a text file containing logging information." />
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149
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150 </inputs>
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151 <outputs>
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152 <data name="out_whitelist" format="tabular" label="${tool.name} on ${on_string}: Whitelist"/>
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153 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: logfile" >
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154 <filter>log</filter>
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155 </data>
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156 <data name="out_html_report" format="html" label="${tool.name} on ${on_string}: Webpage" />
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157 <data name="out_thresh" format="tabular" label="${tool.name} on ${on_string}: TSV Cell Thresholds" />
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158 </outputs>
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159 <tests>
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160 <test expect_num_outputs="3">
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161 <param name="type" value="single" />
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162 <param name="input_single" value="t_R2.fastq.gz" ftype="fastq" />
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163 <param name="bc_pattern" value="CCCCCCCCNNNNNNNN" />
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164 <param name="method" value="reads" />
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165 <param name="prime3" value="true" />
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166 <output name="out_whitelist" file="out_wl_single.txt" lines_diff="40" />
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167 <output name="out_thresh" file="out_wl_single.tresh.tab" />
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168 <output name="out_html_report" file="out_wl_single.html" />
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169 </test>
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170 <test expect_num_outputs="4">
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171 <param name="type" value="paired" />
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172 <param name="input_read1" value="t_R1.fastq.gz" ftype="fastq" />
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173 <param name="input_read2" value="t_R2.fastq.gz" ftype="fastq" />
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174 <param name="barcode_select" value="both_reads" />
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175 <param name="bc_pattern" value="CCCNNNNNNNNXXXXX" />
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176 <param name="bc_pattern2" value="CCCCCCCCNNNNNNNN" />
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177 <param name="method" value="reads" />
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178 <param name="prime3" value="false" />
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179 <param name="use_cell_opts" value="advanced" />
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180 <param name="expect_cells" value="5" />
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181 <param name="error_correct_thresh" value="3" />
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182 <param name="log" value="true" />
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183 <output name="out_whitelist" file="out_wl_paired.txt" />
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184 <output name="out_log" file="out_wl_paired.log" lines_diff="40" />
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185 <output name="out_html_report" file="out_wl_paired.html" />
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186 <output name="out_thresh" file="out_wl_paired.tresh.tab" />
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187 </test>
2
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188 <test expect_num_outputs="4"> <!-- As previous, identical outputs but paired collection input -->
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189 <param name="type" value="paired_collection" />
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190 <param name="input_readpair" >
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191 <collection type="paired">
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192 <element name="forward" ftype="fastq.gz" value="t_R1.fastq.gz" />
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193 <element name="reverse" ftype="fastq.gz" value="t_R2.fastq.gz" />
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194 </collection>
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195 </param>
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196 <param name="barcode_select" value="both_reads" />
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197 <param name="bc_pattern" value="CCCNNNNNNNNXXXXX" />
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198 <param name="bc_pattern2" value="CCCCCCCCNNNNNNNN" />
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199 <param name="method" value="reads" />
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200 <param name="prime3" value="false" />
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201 <param name="use_cell_opts" value="advanced" />
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202 <param name="expect_cells" value="5" />
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203 <param name="error_correct_thresh" value="3" />
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204 <param name="log" value="true" />
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205 <output name="out_whitelist" file="out_wl_paired.txt" />
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206 <output name="out_log" file="out_wl_paired.log" lines_diff="40" />
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207 <output name="out_html_report" file="out_wl_paired.html" />
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208 <output name="out_thresh" file="out_wl_paired.tresh.tab" />
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209 </test>
0
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210 </tests>
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211 <help><![CDATA[
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212
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213
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214 UMI-tools whitelist - Extract barcodes from fastq
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215 ==================================================
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216
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217 Purpose
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218 -------
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219
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220 Extract cell barcodes and identify the most likely true barcodes using
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221 the 'knee' method.
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222
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223 Options
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224 -------
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225
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226 --bc-pattern
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227 This should be used where the barcodes are always in the same
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228 place in the read.
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229
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230 - N = UMI position (required)
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231 - C = cell barcode position (optional)
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232 - X = sample position (optional)
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233
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234 Bases with Ns and Cs will be extracted and added to the read
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235 name. The corresponding sequence qualities will be removed from
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236 the read. Bases with an X will be reattached to the read.
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237
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238 E.g. If the pattern is NNNNCC,
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239 Then the read:
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240 @HISEQ:87:00000000 read1
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241 AAGGTTGCTGATTGGATGGGCTAG
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242 DA1AEBFGGCG01DFH00B1FF0B
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243 +
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244 will become:
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245 @HISEQ:87:00000000_TT_AAGG read1
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246 GCTGATTGGATGGGCTAG
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247 1AFGGCG01DFH00B1FF0B
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248 +
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249
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250 where 'TT' is the cell barcode and 'AAGG' is the UMI.
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251
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252
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253 --set-cell-number
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254 Use this option to explicity set the number of cell barcodes
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255 which should be accepted. Note that the exact number of cell
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256 barcodes in the outputted whitelist may be slightly less than
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257 this if there are multiple cells observed with the same
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258 frequency at the threshold between accepted and rejected cell
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259 barcodes.
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260
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261 --expect-cells=[EXPECTED_CELLS]
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262 An upper limit estimate for the number of inputted cells. The knee
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263 method will now select the first threshold (order ascendingly)
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264 which results in the number of cell barcodes accepted being <=
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265 EXPECTED_CELLS and > EXPECTED_CELLS * 0.1.
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266
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267
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268 --bc-pattern2
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269 Use this option to specify the format of the UMI/barcode for
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270 the second read pair if required. If --bc-pattern2 is not
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271 supplied, this defaults to the same pattern as --bc-pattern
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272
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273 --3prime
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274 By default the barcode is assumed to be on the 5' end of the read, but
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275 use this option to sepecify that it is on the 3' end instead
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276
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277 Usage:
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278 ------
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279
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280 For single ended reads:
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281 umi_tools whitelist --bc-pattern=[PATTERN] -L extract.log
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282 [OPTIONS]
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283
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284 reads from stdin and outputs to stdout.
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285
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286 For paired end reads where the cell barcodes is split across the read pairs:
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287 umi_tools whitelist --bc-pattern=[PATTERN]
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288 --bc-pattern2=[PATTERN] --read2-in=[FASTQIN] -L extract.log
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289 [OPTIONS]
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290
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291 reads end one from stdin and end two from FASTQIN and outputs to stdin
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292
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293
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294 Output:
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295 -------
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296
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297 The whitelist is outputted as 4 tab-separated columns:
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298
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299 1. whitelisted cell barcode
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300 2. Other cell barcode(s) (comma-separated) to correct to the
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301 whitelisted barcode
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302 3. Count for whitelisted cell barcodes
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303 4. Count(s) for the other cell barcode(s) (comma-separated)
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304
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305 example output:
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306
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307 AAAAAA AGAAAA 146 1
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308 AAAATC 22
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309 AAACAT 21
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310 AAACTA AAACTN,GAACTA 27 1,1
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311 AAATAC 72
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312 AAATCA GAATCA 37 3
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313 AAATGT AAAGGT,CAATGT 41 1,1
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314 AAATTG CAATTG 36 1
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315 AACAAT 18
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316 AACATA 24
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317
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318 If --error-correct-threshold is set to 0, columns 2 and 4 will be empty.
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319
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320
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321 ]]></help>
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322 <expand macro="citations" />
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323 </tool>