Mercurial > repos > iuc > umi_tools_group

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit 11a7415c7f8a44a3f990080533c1de43a41d1e2e
author iuc
date Fri, 28 Feb 2025 20:42:09 +0000
parents 428735be9764
children
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1 <tool id="umi_tools_group" name="UMI-tools group" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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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="bio_tools"/>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 @LINK_SAM_BAM_INPUT@
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10
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11 umi_tools group
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12 #if $group_output:
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13 --group-out '$group_out'
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14 #end if
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15 --output-bam
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16 @GROUPDEDUP_OPTIONS@
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17 @BARCODE_OPTIONS@
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18 @UMI_GROUPING_OPTIONS@
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19 @SAMBAM_OPTIONS@
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20 @FULLSC_OPTIONS@
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21 -I '$input_file' -S grouped.bam
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22 @ADVANCED_OPTIONS@
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23 @LOG@
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24 ## using samtools sort is a workaround, for the following error that appears when Galaxy
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25 ## compares the generated file with the one in test-data
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26 ## `Converting history BAM to SAM failed: 'samtools returned with error 1: stdout=None, stderr=[main_samview] fail to read the header from "/tmp/tmpd8o61jykdedup_out6.bam".\n'. Will compare BAM files`
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27 ## may be dropped in the future
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28 --no-sort-output
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29 && samtools sort --no-PG grouped.bam -@ \${GALAXY_SLOTS:-1} -T "\${TMPDIR:-.}" -o '$output' -O BAM
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30 ]]></command>
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31 <inputs>
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32 <param name="input" type="data" format="sam,bam" label="Reads to group in SAM or BAM format" />
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33 <param name="group_output" argument="--group-out" type="boolean" truevalue="--group-out" falsevalue="" label="Output a flatfile describing the read groups" />
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34 <expand macro="groupdedup_options_macro"/>
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35 <expand macro="barcode_options_macro"/>
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36 <expand macro="umi_grouping_options_macro"/>
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37 <expand macro="sambam_options_macro"/>
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38 <expand macro="fullsc_options_macro"/>
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39 <expand macro="advanced_options_macro"/>
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40 <expand macro="log_input_macro"/>
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41 </inputs>
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42 <outputs>
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43 <data format="bam" name="output" label="${tool.name} on ${on_string}: Tagged BAM"/>
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44 <data format="tabular" name="group_out" label="${tool.name} on ${on_string}: Read groups">
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45 <filter>group_output</filter>
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46 </data>
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47 <expand macro="log_output_macro"/>
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48 </outputs>
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49 <tests>
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50 <test expect_num_outputs="1">
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51 <param name="input" value="group_in2.sam" ftype="sam" />
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52 <section name="advanced">
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53 <param name="random_seed" value="0" />
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54 </section>
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55 <conditional name="bc">
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56 <param name="extract_umi_method" value="read_id" />
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57 </conditional>
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58 <section name="sambam">
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59 <param name="paired" value="true" />
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60 </section>
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61 <section name="umi">
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62 <param name="method" value="unique" />
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63 </section>
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64 <output name="output" file="group_out2.bam" ftype="bam" />
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65 </test>
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66 <test expect_num_outputs="2">
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67 <param name="input" value="group_in3.bam" ftype="bam" />
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68 <section name="advanced">
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69 <param name="random_seed" value="0" />
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70 </section>
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71 <conditional name="bc">
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72 <param name="extract_umi_method" value="read_id" />
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73 </conditional>
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74 <param name="group_output" value="true" />
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75 <section name="umi">
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76 <param name="method" value="unique" />
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77 </section>
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78 <output name="group_out" file="group_out3.tab" />
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79 <output name="output" file="group_out3.bam" ftype="bam" />
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80 </test>
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81 <test expect_num_outputs="2">
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82 <param name="input" value="group_in4.bam" ftype="bam" />
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83 <section name="advanced">
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84 <param name="random_seed" value="0" />
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85 </section>
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86 <conditional name="bc">
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87 <param name="extract_umi_method" value="tag" />
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88 <param name="umi_tag" value="BX" />
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89 </conditional>
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90 <param name="group_output" value="true" />
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91 <section name="umi">
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92 <param name="method" value="unique" />
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93 </section>
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94 <output name="group_out" file="group_out4.tab" />
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95 <output name="output" file="group_out4.bam" ftype="bam" />
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96 </test>
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97 <test expect_num_outputs="1">
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98 <param name="input" value="group_in5.bam" ftype="bam" />
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99 <section name="advanced">
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100 <param name="random_seed" value="0" />
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101 </section>
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102 <conditional name="bc">
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103 <param name="extract_umi_method" value="read_id" />
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104 </conditional>
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105 <section name="umi">
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106 <param name="method" value="cluster" />
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107 </section>
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108 <output name="output" file="group_out5.bam" ftype="bam"/>
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109 </test>
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110 <test expect_num_outputs="1">
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111 <param name="input" value="group_in6.bam" ftype="bam" />
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112 <section name="advanced">
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113 <param name="random_seed" value="0" />
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114 </section>
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115 <conditional name="bc">
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116 <param name="extract_umi_method" value="read_id" />
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117 </conditional>
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118 <section name="umi">
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119 <param name="method" value="directional" />
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120 </section>
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121 <output name="output" file="group_out6.bam" ftype="bam"/>
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122 </test>
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123 </tests>
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124 <help><![CDATA[
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125 umi_tools group - Group reads based on their UMI
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126 ================================================
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127
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128 Purpose
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129 -------
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130
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131 The purpose of this command is to identify groups of reads based on
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132 their genomic coordinate and UMI.
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133
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134 The group command can be used to create two types of outfile: a tagged
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135 BAM or a flatfile describing the read groups
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136
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137 To generate the tagged-BAM file, use the option --output-bam and
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138 provide a filename with the -S option. Alternatively, if you do not
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139 provide a filename, the bam file will be outputted to the stdout. If
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140 you have provided the --log/-L option to send the logging output
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141 elsewhere, you can pipe the output from the group command directly to
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142 e.g samtools sort like so:
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143
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144 ``umi_tools group -I inf.bam --group-out=grouped.tsv --output-bam --log=group.log --paired | samtools sort - -o grouped_sorted.bam``
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145
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146 The tagged-BAM file will have two tagged per read:
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147
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148 - UG = Unique_id.
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149 0-indexed unique id number for each group of reads with the same genomic position and UMI or UMIs inferred to be from the same true UMI + errors
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150
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151 - BX = Final UMI.
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152 The inferred true UMI for the group
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153
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154 To generate the flatfile describing the read groups, include the
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155 --group-out=<filename> option. The columns of the read groups file are
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156 below. The first five columns relate to the read. The final 3 columns
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157 relate to the group.
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158
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159 - read_id
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160 read identifier
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161
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162 - contig
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163 alignment contig
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164
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165 - position
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166 Alignment position. Note that this position is not the start position of the read in the BAM file but the start of the read taking into account the read strand and cigar
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167
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168 - umi
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169 The read UMI
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170
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171 - umi_count
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172 The number of times this UMI is observed for reads at the same position
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173
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174 - final_umi
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175 The inferred true UMI for the group
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176
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177 - final_umi_count
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178 The total number of reads within the group
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179
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180 - unique_id
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181 The unique id for the group
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182
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183 @BARCODE_HELP@
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184
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185 @UMI_GROUPING_HELP@
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186 ]]></help>
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187 <expand macro="citations" />
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188 </tool>