Mercurial > repos > iuc > umi_tools_group

annotate umi-tools_group.xml @ 14:1263189f6204 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit b5b83fd1cf0a44edcd9a6cc7562a3add2f47bd3f"
author iuc
date Sat, 23 Oct 2021 20:36:52 +0000
parents cf25b50eff0a
children 257be15474a7
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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 <expand macro="bio_tools"/>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements">
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8 <requirement type="package" version="1.12">samtools</requirement>
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9 </expand>
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10 <command detect_errors="exit_code"><![CDATA[
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11 @LINK_SAM_BAM_INPUT@
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12
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13 umi_tools group
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14 #if $group_output:
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15 --group-out '$group_out'
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16 #end if
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17 --output-bam
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18 @GROUPDEDUP_OPTIONS@
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19 @BARCODE_OPTIONS@
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20 @UMI_GROUPING_OPTIONS@
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21 @SAMBAM_OPTIONS@
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22 @FULLSC_OPTIONS@
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23 -I '$input_file' -S grouped.bam
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24 @ADVANCED_OPTIONS@
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25 @LOG@
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26 ## TODO using samtools sort is a workaround, for the following error that appears when Galaxy
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27 ## compares the generated file with the one in test-data
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28 ## `Converting history BAM to SAM failed: 'samtools returned with error 1: stdout=None, stderr=[main_samview] fail to read the header from "/tmp/tmpd8o61jykdedup_out6.bam".\n'. Will compare BAM files`
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29 ## may be dropped in the future
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30 --no-sort-output
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31 && samtools sort --no-PG grouped.bam -@ \${GALAXY_SLOTS:-1} -T "\${TMPDIR:-.}" -o '$output' -O BAM
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32 ]]></command>
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33 <inputs>
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34 <param name="input" type="data" format="sam,bam" label="Reads to group in SAM or BAM format" />
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35 <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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36 <expand macro="groupdedup_options_macro"/>
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37 <expand macro="barcode_options_macro"/>
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38 <expand macro="umi_grouping_options_macro"/>
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39 <expand macro="sambam_options_macro"/>
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40 <expand macro="fullsc_options_macro"/>
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41 <expand macro="advanced_options_macro"/>
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42 <expand macro="log_input_macro"/>
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43 </inputs>
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44 <outputs>
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45 <data format="bam" name="output" />
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46 <data format="tabular" name="group_out">
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47 <filter>group_output</filter>
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48 </data>
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49 <expand macro="log_output_macro"/>
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50 </outputs>
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51 <tests>
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52 <test expect_num_outputs="1">
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53 <param name="input" value="group_in2.sam" ftype="sam" />
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54 <section name="advanced">
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55 <param name="random_seed" value="0" />
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56 </section>
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57 <conditional name="bc">
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58 <param name="extract_umi_method" value="read_id" />
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59 </conditional>
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60 <section name="sambam">
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61 <param name="paired" value="true" />
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62 </section>
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63 <section name="umi">
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64 <param name="method" value="unique" />
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65 </section>
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66 <output name="output" file="group_out2.bam" ftype="bam" />
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67 </test>
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68 <test expect_num_outputs="2">
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69 <param name="input" value="group_in3.bam" ftype="bam" />
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70 <section name="advanced">
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71 <param name="random_seed" value="0" />
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72 </section>
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73 <conditional name="bc">
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74 <param name="extract_umi_method" value="read_id" />
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75 </conditional>
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76 <param name="group_output" value="true" />
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77 <section name="umi">
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78 <param name="method" value="unique" />
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79 </section>
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80 <output name="group_out" file="group_out3.tab" />
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81 <output name="output" file="group_out3.bam" ftype="bam" />
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82 </test>
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83 <test expect_num_outputs="2">
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84 <param name="input" value="group_in4.bam" ftype="bam" />
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85 <section name="advanced">
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86 <param name="random_seed" value="0" />
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87 </section>
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88 <conditional name="bc">
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89 <param name="extract_umi_method" value="tag" />
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90 <param name="umi_tag" value="BX" />
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91 </conditional>
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92 <param name="group_output" value="true" />
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93 <section name="umi">
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94 <param name="method" value="unique" />
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95 </section>
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96 <output name="group_out" file="group_out4.tab" />
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97 <output name="output" file="group_out4.bam" ftype="bam" />
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98 </test>
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99 <test expect_num_outputs="1">
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100 <param name="input" value="group_in5.bam" ftype="bam" />
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101 <section name="advanced">
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102 <param name="random_seed" value="0" />
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103 </section>
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104 <conditional name="bc">
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105 <param name="extract_umi_method" value="read_id" />
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106 </conditional>
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107 <section name="umi">
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108 <param name="method" value="cluster" />
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109 </section>
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110 <output name="output" file="group_out5.bam" ftype="bam"/>
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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 <section name="advanced">
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115 <param name="random_seed" value="0" />
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116 </section>
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117 <conditional name="bc">
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118 <param name="extract_umi_method" value="read_id" />
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119 </conditional>
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120 <section name="umi">
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121 <param name="method" value="directional" />
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122 </section>
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123 <output name="output" file="group_out6.bam" ftype="bam"/>
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124 </test>
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125 </tests>
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126 <help><![CDATA[
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127 umi_tools group - Group reads based on their UMI
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128 ================================================
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129
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130 Purpose
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131 -------
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132
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133 The purpose of this command is to identify groups of reads based on
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134 their genomic coordinate and UMI.
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135
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136 The group command can be used to create two types of outfile: a tagged
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137 BAM or a flatfile describing the read groups
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138
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139 To generate the tagged-BAM file, use the option --output-bam and
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140 provide a filename with the -S option. Alternatively, if you do not
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141 provide a filename, the bam file will be outputted to the stdout. If
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142 you have provided the --log/-L option to send the logging output
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143 elsewhere, you can pipe the output from the group command directly to
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144 e.g samtools sort like so:
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145
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146 ``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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147
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148 The tagged-BAM file will have two tagged per read:
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149
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150 - UG = Unique_id.
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151 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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152
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153 - BX = Final UMI.
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154 The inferred true UMI for the group
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155
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156 To generate the flatfile describing the read groups, include the
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157 --group-out=<filename> option. The columns of the read groups file are
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158 below. The first five columns relate to the read. The final 3 columns
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159 relate to the group.
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160
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161 - read_id
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162 read identifier
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163
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164 - contig
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165 alignment contig
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166
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167 - position
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168 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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169
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170 - umi
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171 The read UMI
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172
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173 - umi_count
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174 The number of times this UMI is observed for reads at the same position
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175
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176 - final_umi
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177 The inferred true UMI for the group
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178
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179 - final_umi_count
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180 The total number of reads within the group
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181
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182 - unique_id
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183 The unique id for the group
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184
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185 @BARCODE_HELP@
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186
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187 @UMI_GROUPING_HELP@
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188 ]]></help>
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189 <expand macro="citations" />
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190 </tool>