Mercurial > repos > iuc > umi_tools_dedup

annotate umi-tools_dedup.xml @ 11:7fa28eb10fed draft

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"planemo upload commit 2da1197aac6a18df9252e5da096645d2ecaece88"
author iuc
date Wed, 10 Feb 2021 19:30:35 +0000
parents c6567483aa1e
children 4098ab380097
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1 <tool id="umi_tools_dedup" name="UMI-tools deduplicate" version="@VERSION@+galaxy1">
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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="1.9">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 $input_file = 'input.bam'
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16 #end if
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17
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18 umi_tools dedup
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19 '$output_stats_bool'
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20 --random-seed 0
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21 --extract-umi-method $extract_umi_method
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22 #if str($extract_umi_method) != 'read_id':
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23 --umi-separator '$umi_separator' --umi-tag '$umi_tag'
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24 #end if
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25 --method $method --edit-distance-threshold $edit_distance_threshold
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26 $paired $spliced_is_unique --soft-clip-threshold $soft_clip_threshold
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27 $read_length $whole_contig --subset $subset $per_contig $per_gene
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28 #if $gene_transcript_map:
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29 --gene-transcript-map '$gene_transcript_map'
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30 #end if
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31 #if len(str($gene_tag)) > 0:
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32 --gene-tag '$gene_tag'
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33 #end if
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34 #if $input.is_of_type("sam"):
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35 --in-sam
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36 #end if
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37 -I '$input_file' -S deduped.bam &&
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38 samtools sort deduped.bam -@ \${GALAXY_SLOTS:-1} -T "\${TMPDIR:-.}" -o '$output' -O BAM
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39 ]]></command>
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40 <inputs>
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41 <param name="input" type="data" format="sam,bam" label="Reads to deduplicate in SAM or BAM format" />
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42 <param name="extract_umi_method" argument="--extract-umi-method" type="select">
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43 <option value="read_id" selected="True">Read ID</option>
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44 <option value="tag">Tag</option>
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45 </param>
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46 <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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47 <param name="umi_tag" argument="--umi-tag" type="text" label="Tag which contains UMI." />
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48 <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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49 <option value="unique">Reads group share the exact same UMI</option>
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50 <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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51 <option value="cluster">Identify clusters based on hamming distance</option>
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52 <option value="adjacency">Identify clusters based on hamming distance and resolve networks by using the node counts</option>
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53 <option value="directional">Identify clusters based on distance and counts, restrict network expansion by threshold</option>
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54 </param>
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55 <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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56 <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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57 <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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58 <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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59 <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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60 <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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61 <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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62 <param argument="--chrom" type="boolean" truevalue="--chrom" falsevalue="" label="Only consider a single chromosome" />
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63 <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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64 <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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65 <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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66 <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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67 <param name="output_stats_bool" type="boolean" truevalue="--output-stats=stats_outputs" falsevalue="" checked="false" label="Output UMI related statistics files?"/>
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68 </inputs>
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69 <outputs>
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70 <data format="bam" name="output" />
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71 <collection name="output_stats" type="list" label="UMI_tools dedup stats">
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72 <filter>output_stats_bool</filter>
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73 <data name="edit_distance" format="tabular" from_work_dir="stats_outputs_edit_distance.tsv"/>
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74 <data name="per_umi" format="tabular" from_work_dir="stats_outputs_per_umi.tsv"/>
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75 <data name="per_umi_per_position" format="tabular" from_work_dir="stats_outputs_per_umi_per_position.tsv"/>
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76 </collection>
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77 </outputs>
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78 <tests>
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79 <test expect_num_outputs="1">
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80 <param name="input" value="group_in1.sam" ftype="sam" />
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81 <param name="extract_umi_method" value="read_id" />
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82 <param name="method" value="unique" />
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83 <output name="output" file="dedup_out1.bam" ftype="bam" sort="True"/>
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84 </test>
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85 <test expect_num_outputs="1">
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86 <param name="input" value="group_in2.bam" ftype="bam" />
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87 <param name="extract_umi_method" value="read_id" />
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88 <param name="paired" value="True" />
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89 <param name="method" value="unique" />
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90 <output name="output" file="dedup_out2.bam" ftype="bam" sort="True" />
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91 </test>
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92 <test expect_num_outputs="1">
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93 <param name="input" value="group_in3.bam" ftype="bam" />
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94 <param name="extract_umi_method" value="read_id" />
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95 <param name="method" value="unique" />
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96 <output name="output" file="dedup_out3.bam" ftype="bam" sort="True" />
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97 </test>
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98 <test expect_num_outputs="1">
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99 <param name="input" value="group_in4.bam" ftype="bam" />
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100 <param name="extract_umi_method" value="tag" />
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101 <param name="umi_tag" value="BX" />
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102 <param name="method" value="unique" />
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103 <output name="output" file="dedup_out4.bam" ftype="bam" sort="True" />
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104 </test>
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105 <test expect_num_outputs="1">
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106 <param name="input" value="group_in5.bam" ftype="bam" />
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107 <param name="extract_umi_method" value="read_id" />
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108 <param name="umi_tag" value="BX" />
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109 <param name="method" value="cluster" />
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110 <output name="output" file="dedup_out5.bam" ftype="bam" sort="True" />
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111 </test>
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112 <test expect_num_outputs="1">
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113 <param name="input" value="group_in6.bam" ftype="bam" />
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114 <param name="extract_umi_method" value="read_id" />
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115 <param name="umi_tag" value="BX" />
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116 <param name="method" value="directional" />
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117 <output name="output" file="dedup_out6.bam" ftype="bam" sort="True" />
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118 </test>
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119 <test expect_num_outputs="5">
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120 <param name="input" value="group_in6.bam" ftype="bam" />
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121 <param name="extract_umi_method" value="read_id" />
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122 <param name="umi_tag" value="BX" />
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123 <param name="method" value="directional" />
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124 <param name="output_stats_bool" value="true"/>
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125 <output name="output" file="dedup_out6.bam" ftype="bam" sort="True" />
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126 <output_collection name="output_stats">
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127 <element name="edit_distance" file="stats_outputs_edit_distance.tsv" />
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128 <element name="per_umi" file="stats_outputs_per_umi.tsv" />
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129 <element name="per_umi_per_position" file="stats_outputs_per_umi_per_position.tsv" />
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130 </output_collection>
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131 </test>
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132 </tests>
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133 <help><![CDATA[
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134 umi_tools dedup - Deduplicate reads based on their UMI
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135 ======================================================
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136
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137 Purpose
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138 -------
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139
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140 The purpose of this command is to deduplicate BAM files based on the first
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141 mapping co-ordinate and the UMI attached to the read. It is assumed that the
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142 FASTQ files were processed with extract_umi.py before mapping and thus the UMI
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143 is the last word of the read name. e.g:
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144
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145 @HISEQ:87:00000000_AATT
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146
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147 where AATT is the UMI sequeuence.
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148
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149 If you have used an alternative method which does not separate the
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150 read id and UMI with a "_", such as bcl2fastq which uses ":", you can
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151 specify the separator with the option "--umi-separator=<sep>",
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152 replacing <sep> with e.g ":".
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153
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154 Alternatively, if your UMIs are encoded in a tag, you can specify this
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155 by setting the option --extract-umi-method=tag and set the tag name
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156 with the --umi-tag option. For example, if your UMIs are encoded in
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157 the 'UM' tag, provide the following options:
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158 "--extract-umi-method=tag --umi-tag=UM"
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159
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160 The start postion of a read is considered to be the start of its alignment
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161 minus any soft clipped bases. A read aligned at position 500 with
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162 cigar 2S98M will be assumed to start at postion 498.
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163
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164
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165 Methods
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166 -------
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167
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168 dedup can be run with multiple methods to identify groups of reads with
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169 the same (or similar) UMI(s). All methods start by identifying the
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170 reads with the same mapping position.
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171
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172 The simpliest method, "unique", groups reads with the exact same
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173 UMI. The network-based methods, "cluster", "adjacency" and
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174 "directional", build networks where nodes are UMIs and edges connect
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175 UMIs with an edit distance <= threshold (usually 1). The groups of
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176 reads are then defined from the network in a method-specific manner.
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177
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178 "unique"
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179 Reads group share the exact same UMI
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180
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181 "percentile"
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182 Reads group share the exact same UMI. UMIs with counts < 1% of the
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183 median counts for UMIs at the same position are ignored.
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184
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185 "cluster"
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186 Identify clusters of connected UMIs (based on hamming distance
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187 threshold). Each network is a read group
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188
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189 "adjacency"
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190 Cluster UMIs as above. For each cluster, select the node(UMI)
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191 with the highest counts. Visit all nodes one edge away. If all
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192 nodes have been visted, stop. Otherise, repeat with remaining
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193 nodes until all nodes have been visted. Each step
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194 defines a read group.
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195
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196 "directional" (default)
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197 Identify clusters of connected UMIs (based on hamming distance
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198 threshold) and umi A counts >= (2* umi B counts) - 1. Each
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199 network is a read group.
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200
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201 Options
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202 -------
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203
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204 --extract-umi-method (choice)
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205 How are the UMIs encoded in the read?
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206
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207 Options are:
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208
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209 - "read_id" (default)
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210 UMIs contained at the end of the read separated as
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211 specified with --umi-separator option
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212
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213 - "tag"
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214 UMIs contained in a tag, see --umi-tag option
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215
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216 --umi-separator (string)
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217 Separator between read id and UMI. See --extract-umi-method above
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218
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219 --umi-tag (string)
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220 Tag which contains UMI. See --extract-umi-method above
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221
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222 --edit-distance-threshold (int)
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223 For the adjacency and cluster methods the threshold for the
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224 edit distance to connect two UMIs in the network can be
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225 increased. The default value of 1 works best unless the UMI is
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226 very long (>14bp)
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227
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228 --paired
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229 BAM is paired end - output both read pairs. This will also
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230 force the use of the template length to determine reads with
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231 the same mapping coordinates.
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232
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233 --spliced-is-unique
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234 Causes two reads that start in the same position on the same
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235 strand and having the same UMI to be considered unique if one is
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236 spliced and the other is not. (Uses the 'N' cigar operation to test
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237 for splicing)
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238
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239 --soft-clip-threshold (int)
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240 Mappers that soft clip, will sometimes do so rather than mapping a
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241 spliced read if there is only a small overhang over the exon
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242 junction. By setting this option, you can treat reads with at least
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243 this many bases soft-clipped at the 3' end as spliced.
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244
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245 --multimapping-detection-method (string, choice)
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246 If the sam/bam contains tags to identify multimapping reads, you can
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247 specify for use when selecting the best read at a given loci.
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248 Supported tags are "NH", "X0" and "XT". If not specified, the read
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249 with the highest mapping quality will be selected
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250
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251 --read-length
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252 Use the read length as as a criteria when deduping, for e.g sRNA-Seq
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253
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254 --whole-contig
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255 Consider all alignments to a single contig together. This is useful if
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256 you have aligned to a transcriptome multi-fasta
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257
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258 --subset (float, [0-1])
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259 Only consider a fraction of the reads, chosen at random. This is useful
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260 for doing saturation analyses.
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261
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262 --chrom
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263 Only consider a single chromosome. This is useful for debugging purposes
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264
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265 --per-contig (string)
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266 Deduplicate per contig (field 3 in BAM; RNAME).
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267 All reads with the same contig will be
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268 considered to have the same alignment position. This is useful
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269 if your library prep generates PCR duplicates with non identical
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270 alignment positions such as CEL-Seq. In this case, you would
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271 align to a reference transcriptome with one transcript per gene
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272
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273 --per-gene (string)
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274 Deduplicate per gene. As above except with this option you can
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275 align to a reference transcriptome with more than one transcript
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276 per gene. You need to also provide --gene-transcript-map option.
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277 This will also add a metacontig ('MC') tag to the reads if used
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278 in conjunction with --output-bam
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279
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280 --gene-transcript-map (string)
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281 File mapping genes to transripts (tab separated), e.g:
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282
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283 gene1 transcript1
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284 gene1 transcript2
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285 gene2 transcript3
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286
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287 --gene-tag (string)
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288 Deduplicate per gene. As per --per-gene except here the gene
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289 information is encoded in the bam read tag specified so you do
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290 not need to supply --gene-transcript-map
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291
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292 --output-bam (string, filename)
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293 Output a tagged bam file to stdout or -S <filename>
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294
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295 -i, --in-sam/-o, --out-sam
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296 By default, inputs are assumed to be in BAM format and output are output
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297 in BAM format. Use these options to specify the use of SAM format for
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298 inputs or outputs.
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299
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300 -I (string, filename) input file name
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301 The input file must be sorted and indexed.
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302
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303 -S (string, filename) output file name
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304
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305 -L (string, filename) log file name
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306
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307 Usage
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308 -----
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309 umi_tools dedup -I infile.bam -S grouped.bam --
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310
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311 ]]></help>
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312 <expand macro="citations" />
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313 </tool>