Mercurial > repos > iuc > umi_tools_dedup

annotate umi-tools_dedup.xml @ 3:4f2c970cdb02 draft

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author iuc
date Tue, 05 Jun 2018 19:42:51 -0400
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1 <tool id="umi_tools_dedup" name="UMI-tools deduplicate" version="@VERSION@.0">
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2 <description>Extract UMI 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 <requirement type="package" version="1.6">samtools</requirement>
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8 </expand>
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9 <command detect_errors="exit_code"><![CDATA[
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10 #if $input.is_of_type("sam"):
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11 #set $input_file = $input
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12 #else:
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13 ln -sf '${input}' 'input.bam' &&
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14 ln -sf '$input.metadata.bam_index' 'input.bam.bai' &&
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15 #set $input_file = 'input.bam'
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16 #end if
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17
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18 umi_tools dedup
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19 --random-seed 0
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20 --extract-umi-method $extract_umi_method
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21 #if str($extract_umi_method) != 'read_id':
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22 --umi-separator '$umi_separator' --umi-tag '$umi_tag'
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23 #end if
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24 --method $method --edit-distance-threshold $edit_distance_threshold
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25 $paired $spliced_is_unique --soft-clip-threshold $soft_clip_threshold
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26 $read_length $whole_contig --subset $subset $per_contig $per_gene
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27 #if $gene_transcript_map:
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28 --gene-transcript-map '$gene_transcript_map'
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29 #end if
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30 #if len(str($gene_tag)) > 0:
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31 --gene-tag '$gene_tag'
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32 #end if
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33 #if $input.is_of_type("sam"):
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34 --in-sam
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35 #end if
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36 -I '$input_file' -S deduped.bam &&
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37 samtools sort deduped.bam -@ \${GALAXY_SLOTS:-1} -o '$output' -O BAM
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38 ]]></command>
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39 <inputs>
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40 <param name="input" type="data" format="sam,bam" label="Reads to deduplicate in SAM or BAM format" />
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41 <param name="extract_umi_method" argument="--extract-umi-method" type="select">
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42 <option value="read_id" selected="True">Read ID</option>
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43 <option value="tag">Tag</option>
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44 </param>
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45 <param name="umi_separator" argument="--umi-separator" type="text" label="Separator between read id and UMI." help="Ignored unless extracting by tag" />
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46 <param name="umi_tag" argument="--umi-tag" type="text" label="Tag which contains UMI." />
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47 <param argument="--method" type="select" label="Method used to identify PCR duplicates within reads." help="All methods start by identifying the reads with the same mapping position">
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48 <option value="unique">Reads group share the exact same UMI</option>
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49 <option value="percentile">Reads group share the exact same UMI. UMIs with counts less than 1% of the median counts for UMIs at the same position are ignored</option>
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50 <option value="cluster">Identify clusters based on hamming distance</option>
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51 <option value="adjacency">Identify clusters based on hamming distance and resolve networks by using the node counts</option>
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52 <option value="directional">Identify clusters based on distance and counts, restrict network expansion by threshold</option>
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53 </param>
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54 <param name="edit_distance_threshold" argument="--edit-distance-threshold" type="integer" value="1" label="Edit distance threshold" help="For the adjacency and cluster methods the threshold for the edit distance to connect two UMIs in the network can be increased. The default value of 1 works best unless the UMI is very long (&gt;14bp)" />
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55 <param argument="--paired" type="boolean" truevalue="--paired" falsevalue="" label="BAM is paired end" help="This will also force the use of the template length to determine reads with the same mapping coordinates." />
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56 <param name="spliced_is_unique" argument="--spliced-is-unique" type="boolean" truevalue="--spliced-is-unique" falsevalue="" label="Spliced reads are unique" help="Causes two reads that start in the same position on the same strand and having the same UMI to be considered unique if one is spliced and the other is not. (Uses the 'N' cigar operation to test for splicing)" />
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57 <param name="soft_clip_threshold" argument="--soft-clip-threshold" type="integer" value="4" label="Soft clip threshold" help="Mappers that soft clip, will sometimes do so rather than mapping a spliced read if there is only a small overhang over the exon junction. By setting this option, you can treat reads with at least this many bases soft-clipped at the 3' end as spliced." />
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58 <param name="read_length" argument="--read-length" type="boolean" truevalue="--read-length" falsevalue="" label="Use the read length as as a criterion when deduping" />
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59 <param name="whole_contig" argument="--whole-contig" type="boolean" truevalue="--whole-contig" falsevalue="" label="Consider all alignments to a single contig together" help="This is useful if you have aligned to a transcriptome multi-fasta" />
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60 <param argument="--subset" type="float" min="0.0" max="1.0" value="1.0" label="Only consider a random selection of the reads" />
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61 <param argument="--chrom" type="boolean" truevalue="--chrom" falsevalue="" label="Only consider a single chromosome" />
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62 <param name="per_contig" argument="--per-contig" type="boolean" truevalue="--per-contig" falsevalue="" label="Deduplicate per contig" help="Field 3 in BAM; RNAME. All reads with the same contig will be considered to have the same alignment position. This is useful if your library prep generates PCR duplicates with non identical alignment positions such as CEL-Seq. In this case, you would align to a reference transcriptome with one transcript per gene" />
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63 <param name="per_gene" argument="--per-gene" type="boolean" truevalue="--per-gene" falsevalue="" label="Deduplicate per gene" help="As above except with this option you can align to a reference transcriptome with more than one transcript per gene. You need to also provide a map of genes to transcripts. This will also add a metacontig ('MC') tag to the output BAM file." />
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64 <param name="gene_transcript_map" argument="--gene-transcript-map" type="data" format="tabular" optional="True" label="Tabular file mapping genes to transripts" />
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65 <param name="gene_tag" argument="--gene-tag" type="text" optional="True" label="Deduplicate by this gene tag" help="As --per-gene except here the gene information is encoded in the bam read tag specified so you do not need to supply the mapping file." />
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66 </inputs>
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67 <outputs>
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68 <data format="bam" name="output" />
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69 </outputs>
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70 <tests>
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71 <test>
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72 <param name="input" value="group_in1.sam" ftype="sam" />
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73 <param name="extract_umi_method" value="read_id" />
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74 <param name="method" value="unique" />
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75 <output name="output" file="dedup_out1.bam" ftype="bam" sort="True"/>
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76 </test>
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77 <test>
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78 <param name="input" value="group_in2.bam" ftype="bam" />
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79 <param name="extract_umi_method" value="read_id" />
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80 <param name="paired" value="True" />
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81 <param name="method" value="unique" />
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82 <output name="output" file="dedup_out2.bam" ftype="bam" sort="True" />
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83 </test>
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84 <test>
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85 <param name="input" value="group_in3.bam" ftype="bam" />
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86 <param name="extract_umi_method" value="read_id" />
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87 <param name="method" value="unique" />
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88 <output name="output" file="dedup_out3.bam" ftype="bam" sort="True" />
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89 </test>
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90 <test>
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91 <param name="input" value="group_in4.bam" ftype="bam" />
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92 <param name="extract_umi_method" value="tag" />
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93 <param name="umi_tag" value="BX" />
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94 <param name="method" value="unique" />
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95 <output name="output" file="dedup_out4.bam" ftype="bam" sort="True" />
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96 </test>
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97 <test>
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98 <param name="input" value="group_in5.bam" ftype="bam" />
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99 <param name="extract_umi_method" value="read_id" />
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100 <param name="umi_tag" value="BX" />
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101 <param name="method" value="cluster" />
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102 <output name="output" file="dedup_out5.bam" ftype="bam" sort="True" />
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103 </test>
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104 <test>
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105 <param name="input" value="group_in6.bam" ftype="bam" />
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106 <param name="extract_umi_method" value="read_id" />
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107 <param name="umi_tag" value="BX" />
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108 <param name="method" value="directional" />
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109 <output name="output" file="dedup_out6.bam" ftype="bam" sort="True" />
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110 </test>
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111 </tests>
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112 <help><![CDATA[
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113 umi_tools dedup - Deduplicate reads based on their UMI
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114 ======================================================
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115
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116 Purpose
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117 -------
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118
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119 The purpose of this command is to deduplicate BAM files based on the first
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120 mapping co-ordinate and the UMI attached to the read. It is assumed that the
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121 FASTQ files were processed with extract_umi.py before mapping and thus the UMI
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122 is the last word of the read name. e.g:
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123
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124 @HISEQ:87:00000000_AATT
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125
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126 where AATT is the UMI sequeuence.
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127
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128 If you have used an alternative method which does not separate the
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129 read id and UMI with a "_", such as bcl2fastq which uses ":", you can
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130 specify the separator with the option "--umi-separator=<sep>",
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131 replacing <sep> with e.g ":".
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132
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133 Alternatively, if your UMIs are encoded in a tag, you can specify this
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134 by setting the option --extract-umi-method=tag and set the tag name
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135 with the --umi-tag option. For example, if your UMIs are encoded in
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136 the 'UM' tag, provide the following options:
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137 "--extract-umi-method=tag --umi-tag=UM"
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138
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139 The start postion of a read is considered to be the start of its alignment
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140 minus any soft clipped bases. A read aligned at position 500 with
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141 cigar 2S98M will be assumed to start at postion 498.
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142
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143
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144 Methods
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145 -------
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146
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147 dedup can be run with multiple methods to identify groups of reads with
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148 the same (or similar) UMI(s). All methods start by identifying the
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149 reads with the same mapping position.
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150
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151 The simpliest method, "unique", groups reads with the exact same
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152 UMI. The network-based methods, "cluster", "adjacency" and
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153 "directional", build networks where nodes are UMIs and edges connect
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154 UMIs with an edit distance <= threshold (usually 1). The groups of
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155 reads are then defined from the network in a method-specific manner.
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156
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157 "unique"
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158 Reads group share the exact same UMI
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159
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160 "percentile"
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161 Reads group share the exact same UMI. UMIs with counts < 1% of the
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162 median counts for UMIs at the same position are ignored.
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163
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164 "cluster"
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165 Identify clusters of connected UMIs (based on hamming distance
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166 threshold). Each network is a read group
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167
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168 "adjacency"
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169 Cluster UMIs as above. For each cluster, select the node(UMI)
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170 with the highest counts. Visit all nodes one edge away. If all
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171 nodes have been visted, stop. Otherise, repeat with remaining
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172 nodes until all nodes have been visted. Each step
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173 defines a read group.
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174
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175 "directional" (default)
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176 Identify clusters of connected UMIs (based on hamming distance
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177 threshold) and umi A counts >= (2* umi B counts) - 1. Each
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178 network is a read group.
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179
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180 Options
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181 -------
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182
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183 --extract-umi-method (choice)
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184 How are the UMIs encoded in the read?
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185
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186 Options are:
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187
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188 - "read_id" (default)
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189 UMIs contained at the end of the read separated as
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190 specified with --umi-separator option
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191
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192 - "tag"
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193 UMIs contained in a tag, see --umi-tag option
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194
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195 --umi-separator (string)
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196 Separator between read id and UMI. See --extract-umi-method above
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197
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198 --umi-tag (string)
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199 Tag which contains UMI. See --extract-umi-method above
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200
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201 --edit-distance-threshold (int)
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202 For the adjacency and cluster methods the threshold for the
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203 edit distance to connect two UMIs in the network can be
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204 increased. The default value of 1 works best unless the UMI is
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205 very long (>14bp)
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206
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207 --paired
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208 BAM is paired end - output both read pairs. This will also
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209 force the use of the template length to determine reads with
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210 the same mapping coordinates.
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211
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212 --spliced-is-unique
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213 Causes two reads that start in the same position on the same
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214 strand and having the same UMI to be considered unique if one is
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215 spliced and the other is not. (Uses the 'N' cigar operation to test
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216 for splicing)
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217
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218 --soft-clip-threshold (int)
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219 Mappers that soft clip, will sometimes do so rather than mapping a
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220 spliced read if there is only a small overhang over the exon
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221 junction. By setting this option, you can treat reads with at least
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222 this many bases soft-clipped at the 3' end as spliced.
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223
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224 --multimapping-detection-method (string, choice)
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225 If the sam/bam contains tags to identify multimapping reads, you can
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226 specify for use when selecting the best read at a given loci.
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227 Supported tags are "NH", "X0" and "XT". If not specified, the read
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228 with the highest mapping quality will be selected
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229
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230 --read-length
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231 Use the read length as as a criteria when deduping, for e.g sRNA-Seq
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232
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233 --whole-contig
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234 Consider all alignments to a single contig together. This is useful if
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235 you have aligned to a transcriptome multi-fasta
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236
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237 --subset (float, [0-1])
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238 Only consider a fraction of the reads, chosen at random. This is useful
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239 for doing saturation analyses.
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240
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241 --chrom
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242 Only consider a single chromosome. This is useful for debugging purposes
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243
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244 --per-contig (string)
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245 Deduplicate per contig (field 3 in BAM; RNAME).
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246 All reads with the same contig will be
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247 considered to have the same alignment position. This is useful
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248 if your library prep generates PCR duplicates with non identical
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249 alignment positions such as CEL-Seq. In this case, you would
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250 align to a reference transcriptome with one transcript per gene
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251
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252 --per-gene (string)
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253 Deduplicate per gene. As above except with this option you can
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254 align to a reference transcriptome with more than one transcript
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255 per gene. You need to also provide --gene-transcript-map option.
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256 This will also add a metacontig ('MC') tag to the reads if used
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257 in conjunction with --output-bam
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258
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259 --gene-transcript-map (string)
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260 File mapping genes to transripts (tab separated), e.g:
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261
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262 gene1 transcript1
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263 gene1 transcript2
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264 gene2 transcript3
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265
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266 --gene-tag (string)
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267 Deduplicate per gene. As per --per-gene except here the gene
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268 information is encoded in the bam read tag specified so you do
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269 not need to supply --gene-transcript-map
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270
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271 --output-bam (string, filename)
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272 Output a tagged bam file to stdout or -S <filename>
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273
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274 -i, --in-sam/-o, --out-sam
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275 By default, inputs are assumed to be in BAM format and output are output
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276 in BAM format. Use these options to specify the use of SAM format for
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277 inputs or outputs.
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278
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279 -I (string, filename) input file name
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280 The input file must be sorted and indexed.
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281
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282 -S (string, filename) output file name
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283
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284 -L (string, filename) log file name
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285
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286 Usage
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287 -----
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288 umi_tools dedup -I infile.bam -S grouped.bam --
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289
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290 ]]></help>
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291 <expand macro="citations" />
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292 </tool>