Mercurial > repos > iuc > umi_tools_whitelist
annotate umi-tools_whitelist.xml @ 3:853f74e08009 draft
planemo upload commit d8f6e961cc9f14c5b39762f87e11352c0aadefc9
author | iuc |
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date | Sat, 31 Mar 2018 17:36:28 -0400 |
parents | c1743022a8cd |
children | 095c349b4343 |
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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 $gz = True |
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28 #else |
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29 ln -s '$input_type.input_single' input_single.txt && |
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30 #end if |
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31 #elif $input_type.type == 'paired': |
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32 #if $input_type.input_read1.is_of_type("fastq.gz", "fastqsanger.gz"): |
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33 ln -s '$input_type.input_read1' input_read1.gz && |
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34 ln -s '$input_type.input_read2' input_read2.gz && |
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35 #set $gz = True |
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36 #else |
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37 ln -s '$input_type.input_read1' input_read1.txt && |
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38 ln -s '$input_type.input_read2' input_read2.txt && |
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39 #end if |
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40 #else ## paired_collection |
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41 #if $input_type.input_readpair.forward.is_of_type("fastq.gz", "fastqsanger.gz"): |
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42 ln -s '$input_type.input_readpair.forward' input_read1.gz && |
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43 ln -s '$input_type.input_readpair.reverse' input_read2.gz && |
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44 #set $gz = True |
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45 #else |
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46 ln -s '$input_type.input_readpair.forward' input_read1.txt && |
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47 ln -s '$input_type.input_readpair.reverse' input_read2.txt && |
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48 #end if |
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49 #end if |
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50 |
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51 umi_tools whitelist |
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52 --bc-pattern='$bc_pattern' |
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53 --subset-reads='$subset_reads' |
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54 #if $input_type.type == 'single': |
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55 #if $gz: |
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56 --stdin=input_single.gz |
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57 #else |
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58 --stdin=input_single.txt |
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59 #end if |
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60 #else: ## equally valid for both 'paired' and 'paired_collection' |
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61 #if $gz: |
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62 --stdin=input_read1.gz |
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63 --read2-in=input_read2.gz |
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64 #else: |
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65 --stdin=input_read1.txt |
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66 --read2-in=input_read2.txt |
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67 #end if |
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68 #if $input_type.barcode.barcode_select == "1": |
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69 --bc-pattern2='$input_type.barcode.bc_pattern2' |
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70 #end if |
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71 #end if |
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72 #if $celloptions.use_cell_opts == "advanced": |
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73 #if $celloptions.set_cell_number != "0": |
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74 --set-cell-number=$celloptions.set_cell_number |
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75 #end if |
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76 #if $celloptions.expect_cells != "0": |
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77 --expect-cells=$celloptions.expect_cells |
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78 #end if |
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79 --error-correct-threshold=$celloptions.error_correct_thresh |
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80 #end if |
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81 --method=$method |
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82 --plot-prefix=OUT |
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83 |
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84 $prime3 |
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85 |
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86 #if $log: |
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87 --log='$out_log' |
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88 #end if |
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89 |
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90 --log2stderr |
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91 |
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92 > '$out_whitelist' && |
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93 |
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94 mkdir '${ out_html_report.files_path }' && |
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95 cp OUT_*.png '${ out_html_report.files_path }' && |
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96 |
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97 echo "<html> |
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98 <head></head><body> |
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99 <h1>Cell and Count Metrics</h1> |
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100 <img src=\"OUT_cell_barcode_count_density.png\" ><br /> |
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101 <img src=\"OUT_cell_barcode_knee.png\" ><br /> |
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102 <img src=\"OUT_cell_barcode_counts.png\" ><br /> |
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103 </body></html>" > '$out_html_report' |
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104 && |
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105 mv OUT_cell_thresholds.tsv '$out_thresh' |
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106 ]]></command> |
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107 <inputs> |
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108 <conditional name="input_type"> |
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109 <param name="type" type="select" label="Library type"> |
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110 <option value="single">Single-end</option> |
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111 <option value="paired">Paired-end</option> |
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112 <option value="paired_collection">Paired-end Dataset Collection</option> |
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113 </param> |
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114 <when value="single"> |
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115 <param name="input_single" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" /> |
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116 </when> |
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117 <when value="paired"> |
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118 <param name="input_read1" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" /> |
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119 <param name="input_read2" type="data" format="fastq,fastq.gz" label="Reads in FASTQ format" /> |
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120 <expand macro="barcode2_conditional" /> |
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121 </when> |
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122 <when value="paired_collection"> |
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123 <param name="input_readpair" type="data_collection" collection_type="paired" format="fastq,fastq.gz" label="Reads in FASTQ format" /> |
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124 <expand macro="barcode2_conditional" /> |
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125 </when> |
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126 </conditional> |
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127 <param name="bc_pattern" argument="--bc-pattern" type="text" label="Barcode pattern for first read" |
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128 help="Use this option to specify the format of the UMI/barcode. Use Ns to |
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129 represent the random positions and Xs to indicate the bc positions. |
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130 Bases with Ns will be extracted and added to the read name. Remaining |
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131 bases, marked with an X will be reattached to the read."> |
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132 </param> |
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133 <param name="method" argument="--method" type="select" label="Count reads or UMIs" |
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134 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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135 <option value="reads" selected="true" /> |
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136 <option value="umis" /> |
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137 </param> |
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138 |
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139 <param argument="--3prime" name="prime3" type="boolean" label="Is barcode on 3' end of the read?" |
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140 truevalue="--3prime" falsevalue="" |
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141 help="By default the barcode is assumed to be on the 5' end of the read, but |
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142 use this option to specify that it is on the 3' end instead." /> |
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143 <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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144 <conditional name="celloptions" > |
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145 <param name="use_cell_opts" type="select" label="Cell parameters" > |
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146 <option value="defaults" selected="True">Use Defaults</option> |
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147 <option value="advanced">Advanced Options</option> |
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148 </param> |
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149 <when value="defaults"/> |
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150 <when value="advanced"> |
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151 <param name="set_cell_number" type="integer" min="0" value="0" label="Specify the number of cell barcodes to accept" /> |
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152 <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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153 <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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154 </when> |
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155 </conditional> |
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156 <param argument="--log" type="boolean" label="Output log?" truevalue="--log" falsevalue="" |
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157 help="Choose if you want to generate a text file containing logging information." /> |
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158 |
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159 </inputs> |
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160 <outputs> |
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161 <data name="out_whitelist" format="tabular" label="${tool.name} on ${on_string}: Whitelist"/> |
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162 <data name="out_log" format="txt" label="${tool.name} on ${on_string}: logfile" > |
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163 <filter>log</filter> |
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164 </data> |
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165 <data name="out_html_report" format="html" label="${tool.name} on ${on_string}: Webpage" /> |
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166 <data name="out_thresh" format="tabular" label="${tool.name} on ${on_string}: TSV Cell Thresholds" /> |
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167 </outputs> |
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168 <tests> |
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169 <test expect_num_outputs="3"> |
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170 <param name="type" value="single" /> |
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171 <param name="input_single" value="t_R2.fastq.gz" ftype="fastq" /> |
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172 <param name="bc_pattern" value="CCCCCCCCNNNNNNNN" /> |
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173 <param name="method" value="reads" /> |
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174 <param name="prime3" value="true" /> |
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175 <output name="out_whitelist" file="out_wl_single.txt" lines_diff="40" /> |
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176 <output name="out_thresh" file="out_wl_single.tresh.tab" /> |
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177 <output name="out_html_report" file="out_wl_single.html" /> |
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178 </test> |
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179 <test expect_num_outputs="4"> |
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180 <param name="type" value="paired" /> |
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181 <param name="input_read1" value="t_R1.fastq.gz" ftype="fastq" /> |
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182 <param name="input_read2" value="t_R2.fastq.gz" ftype="fastq" /> |
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183 <param name="barcode_select" value="both_reads" /> |
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184 <param name="bc_pattern" value="CCCNNNNNNNNXXXXX" /> |
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185 <param name="bc_pattern2" value="CCCCCCCCNNNNNNNN" /> |
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186 <param name="method" value="reads" /> |
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187 <param name="prime3" value="false" /> |
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188 <param name="use_cell_opts" value="advanced" /> |
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189 <param name="expect_cells" value="5" /> |
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190 <param name="error_correct_thresh" value="3" /> |
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191 <param name="log" value="true" /> |
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192 <output name="out_whitelist" file="out_wl_paired.txt" /> |
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193 <output name="out_log" file="out_wl_paired.log" lines_diff="40" /> |
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194 <output name="out_html_report" file="out_wl_paired.html" /> |
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195 <output name="out_thresh" file="out_wl_paired.tresh.tab" /> |
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196 </test> |
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197 <test expect_num_outputs="4"> <!-- As previous, identical outputs but paired collection input --> |
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198 <param name="type" value="paired_collection" /> |
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199 <param name="input_readpair" > |
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200 <collection type="paired"> |
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201 <element name="forward" ftype="fastq.gz" value="t_R1.fastq.gz" /> |
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202 <element name="reverse" ftype="fastq.gz" value="t_R2.fastq.gz" /> |
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203 </collection> |
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204 </param> |
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205 <param name="barcode_select" value="both_reads" /> |
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206 <param name="bc_pattern" value="CCCNNNNNNNNXXXXX" /> |
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207 <param name="bc_pattern2" value="CCCCCCCCNNNNNNNN" /> |
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208 <param name="method" value="reads" /> |
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209 <param name="prime3" value="false" /> |
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210 <param name="use_cell_opts" value="advanced" /> |
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211 <param name="expect_cells" value="5" /> |
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212 <param name="error_correct_thresh" value="3" /> |
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213 <param name="log" value="true" /> |
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214 <output name="out_whitelist" file="out_wl_paired.txt" /> |
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215 <output name="out_log" file="out_wl_paired.log" lines_diff="40" /> |
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216 <output name="out_html_report" file="out_wl_paired.html" /> |
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217 <output name="out_thresh" file="out_wl_paired.tresh.tab" /> |
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218 </test> |
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219 </tests> |
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220 <help><![CDATA[ |
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221 |
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222 |
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223 UMI-tools whitelist - Extract barcodes from fastq |
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224 ================================================== |
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225 |
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226 Purpose |
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227 ------- |
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228 |
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229 Extract cell barcodes and identify the most likely true barcodes using |
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230 the 'knee' method. |
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231 |
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232 Options |
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233 ------- |
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234 |
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235 --bc-pattern |
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236 This should be used where the barcodes are always in the same |
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237 place in the read. |
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238 |
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239 - N = UMI position (required) |
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240 - C = cell barcode position (optional) |
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241 - X = sample position (optional) |
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242 |
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243 Bases with Ns and Cs will be extracted and added to the read |
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244 name. The corresponding sequence qualities will be removed from |
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245 the read. Bases with an X will be reattached to the read. |
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246 |
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247 E.g. If the pattern is NNNNCC, |
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248 Then the read: |
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249 @HISEQ:87:00000000 read1 |
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250 AAGGTTGCTGATTGGATGGGCTAG |
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251 DA1AEBFGGCG01DFH00B1FF0B |
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252 + |
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253 will become: |
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254 @HISEQ:87:00000000_TT_AAGG read1 |
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255 GCTGATTGGATGGGCTAG |
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256 1AFGGCG01DFH00B1FF0B |
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257 + |
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258 |
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259 where 'TT' is the cell barcode and 'AAGG' is the UMI. |
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260 |
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261 |
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262 --set-cell-number |
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263 Use this option to explicity set the number of cell barcodes |
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264 which should be accepted. Note that the exact number of cell |
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265 barcodes in the outputted whitelist may be slightly less than |
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266 this if there are multiple cells observed with the same |
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267 frequency at the threshold between accepted and rejected cell |
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268 barcodes. |
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269 |
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270 --expect-cells=[EXPECTED_CELLS] |
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271 An upper limit estimate for the number of inputted cells. The knee |
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272 method will now select the first threshold (order ascendingly) |
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273 which results in the number of cell barcodes accepted being <= |
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274 EXPECTED_CELLS and > EXPECTED_CELLS * 0.1. |
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275 |
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276 |
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277 --bc-pattern2 |
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278 Use this option to specify the format of the UMI/barcode for |
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279 the second read pair if required. If --bc-pattern2 is not |
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280 supplied, this defaults to the same pattern as --bc-pattern |
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281 |
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282 --3prime |
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283 By default the barcode is assumed to be on the 5' end of the read, but |
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284 use this option to sepecify that it is on the 3' end instead |
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285 |
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286 Usage: |
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287 ------ |
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288 |
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289 For single ended reads: |
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290 umi_tools whitelist --bc-pattern=[PATTERN] -L extract.log |
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291 [OPTIONS] |
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292 |
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293 reads from stdin and outputs to stdout. |
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294 |
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295 For paired end reads where the cell barcodes is split across the read pairs: |
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296 umi_tools whitelist --bc-pattern=[PATTERN] |
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297 --bc-pattern2=[PATTERN] --read2-in=[FASTQIN] -L extract.log |
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298 [OPTIONS] |
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299 |
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300 reads end one from stdin and end two from FASTQIN and outputs to stdin |
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301 |
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302 |
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303 Output: |
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304 ------- |
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305 |
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306 The whitelist is outputted as 4 tab-separated columns: |
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307 |
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308 1. whitelisted cell barcode |
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309 2. Other cell barcode(s) (comma-separated) to correct to the |
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310 whitelisted barcode |
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311 3. Count for whitelisted cell barcodes |
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312 4. Count(s) for the other cell barcode(s) (comma-separated) |
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313 |
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314 example output: |
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315 |
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316 AAAAAA AGAAAA 146 1 |
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317 AAAATC 22 |
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318 AAACAT 21 |
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319 AAACTA AAACTN,GAACTA 27 1,1 |
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320 AAATAC 72 |
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321 AAATCA GAATCA 37 3 |
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322 AAATGT AAAGGT,CAATGT 41 1,1 |
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323 AAATTG CAATTG 36 1 |
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324 AACAAT 18 |
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325 AACATA 24 |
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326 |
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327 If --error-correct-threshold is set to 0, columns 2 and 4 will be empty. |
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328 |
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329 |
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330 ]]></help> |
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331 <expand macro="citations" /> |
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332 </tool> |