Mercurial > repos > iuc > umi_tools_dedup

annotate umi-tools_dedup.xml @ 16:b63f68b03f4a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bc1b362f6783d3fc0ed0f42c14687001d7ff5f7a
author iuc
date Sat, 05 Oct 2024 13:06:05 +0000
parents f76cf6b8c130
children 362719583a9f
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1 <tool id="umi_tools_dedup" name="UMI-tools deduplicate" 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 <requirement type="package" version="1.21">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 echo $input.ext &&
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14 umi_tools dedup
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15 #if $output_stats_bool
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16 --output-stats=stats_outputs
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17 #end if
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18 @GROUPDEDUP_OPTIONS@
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19 @BARCODE_OPTIONS@
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20 @UMI_GROUPING_OPTIONS@
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21 @SAMBAM_OPTIONS@
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22 @FULLSC_OPTIONS@
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23 @ADVANCED_OPTIONS@
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24 -I '$input_file' -S deduped.bam
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25 ## using samtools sort is a workaround, for the following error that appears when Galaxy
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26 ## compares the generated file with the one in test-data
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27 ## `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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28 ## problem seems to be the BAM file generated with pysam
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29 ## may be dropped in the future
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30 --no-sort-output
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31 @LOG@
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32 && samtools sort --no-PG deduped.bam -@ \${GALAXY_SLOTS:-1} -T "\${TMPDIR:-.}" -o '$output' -O BAM
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33
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34 ]]></command>
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35 <inputs>
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36 <param name="input" type="data" format="sam,bam" label="Reads to deduplicate in SAM or BAM format" />
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37 <param name="output_stats_bool" type="boolean" checked="false" label="Output UMI related statistics files?"/>
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38 <expand macro="groupdedup_options_macro"/>
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39 <expand macro="barcode_options_macro"/>
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40 <expand macro="umi_grouping_options_macro"/>
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41 <expand macro="sambam_options_macro"/>
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42 <expand macro="fullsc_options_macro"/>
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43 <expand macro="advanced_options_macro"/>
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44 <expand macro="log_input_macro"/>
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45 </inputs>
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46 <outputs>
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47 <data format="bam" name="output" />
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48 <collection name="output_stats" type="list" label="${tool.name} on ${on_string} stats">
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49 <filter>output_stats_bool</filter>
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50 <data name="edit_distance" format="tabular" from_work_dir="stats_outputs_edit_distance.tsv"/>
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51 <data name="per_umi" format="tabular" from_work_dir="stats_outputs_per_umi.tsv"/>
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52 <data name="per_umi_per_position" format="tabular" from_work_dir="stats_outputs_per_umi_per_position.tsv"/>
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53 </collection>
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54 <expand macro="log_output_macro"/>
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55 </outputs>
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56 <tests>
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57 <test expect_num_outputs="1">
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58 <param name="input" value="group_in1.sam" ftype="sam" />
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59 <section name="advanced">
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60 <param name="random_seed" value="0" />
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61 </section>
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62 <conditional name="bc">
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63 <param name="extract_umi_method" value="read_id" />
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64 </conditional>
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65 <section name="umi">
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66 <param name="method" value="unique" />
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67 </section>
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68 <output name="output" file="dedup_out1.bam" ftype="bam" lines_diff="2"/><!--lines_diff won't be needed in later versions since umitools use \-\-no-PG internally -->
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69 </test>
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70 <test expect_num_outputs="1">
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71 <param name="input" value="group_in2.sam" ftype="sam" />
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72 <section name="advanced">
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73 <param name="random_seed" value="0" />
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74 </section>
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75 <conditional name="bc">
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76 <param name="extract_umi_method" value="read_id" />
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77 </conditional>
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78 <section name="sambam">
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79 <param name="paired" value="true" />
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80 </section>
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81 <section name="umi">
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82 <param name="method" value="unique" />
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83 </section>
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84 <output name="output" file="dedup_out2.bam" ftype="bam" lines_diff="2" />
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85 </test>
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86 <test expect_num_outputs="1">
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87 <param name="input" value="group_in3.bam" ftype="bam" />
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88 <section name="advanced">
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89 <param name="random_seed" value="0" />
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90 </section>
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91 <conditional name="bc">
083c516d19a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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92 <param name="extract_umi_method" value="read_id" />
083c516d19a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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parents: 11
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93 </conditional>
083c516d19a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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94 <section name="umi">
083c516d19a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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95 <param name="method" value="unique" />
083c516d19a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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96 </section>
083c516d19a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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97 <output name="output" file="dedup_out3.bam" ftype="bam" lines_diff="2" />
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98 </test>
11
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99 <test expect_num_outputs="1">
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100 <param name="input" value="group_in4.bam" ftype="bam" />
12
083c516d19a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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101 <section name="advanced">
083c516d19a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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102 <param name="random_seed" value="0" />
083c516d19a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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103 </section>
083c516d19a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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104 <conditional name="bc">
083c516d19a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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105 <param name="extract_umi_method" value="tag" />
083c516d19a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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106 <param name="umi_tag" value="BX" />
083c516d19a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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107 </conditional>
083c516d19a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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108 <section name="umi">
083c516d19a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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109 <param name="method" value="unique" />
083c516d19a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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110 </section>
083c516d19a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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111 <output name="output" file="dedup_out4.bam" ftype="bam" lines_diff="2"/>
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112 </test>
11
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113 <test expect_num_outputs="1">
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114 <param name="input" value="group_in5.bam" ftype="bam" />
12
083c516d19a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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115 <section name="advanced">
083c516d19a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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116 <param name="random_seed" value="0" />
083c516d19a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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117 </section>
083c516d19a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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118 <conditional name="bc">
083c516d19a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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119 <param name="extract_umi_method" value="read_id" />
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120 <param name="umi_tag" value="BX" />
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121 </conditional>
083c516d19a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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122 <section name="umi">
083c516d19a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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123 <param name="method" value="cluster" />
083c516d19a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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124 </section>
083c516d19a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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125 <output name="output" file="dedup_out5.bam" ftype="bam" lines_diff="2"/>
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126 </test>
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127 <test expect_num_outputs="1">
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128 <param name="input" value="group_in6.bam" ftype="bam" />
12
083c516d19a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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129 <section name="advanced">
083c516d19a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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130 <param name="random_seed" value="0" />
083c516d19a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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131 </section>
083c516d19a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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132 <conditional name="bc">
083c516d19a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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133 <param name="extract_umi_method" value="read_id" />
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134 <param name="umi_tag" value="BX" />
083c516d19a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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135 </conditional>
083c516d19a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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136 <section name="umi">
083c516d19a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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137 <param name="method" value="directional" />
083c516d19a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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138 </section>
083c516d19a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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139 <output name="output" file="dedup_out6.bam" ftype="bam" lines_diff="2"/>
0
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140 </test>
11
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141 <test expect_num_outputs="5">
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142 <param name="input" value="group_in6.bam" ftype="bam" />
12
083c516d19a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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143 <section name="advanced">
083c516d19a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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144 <param name="random_seed" value="0" />
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145 </section>
083c516d19a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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146 <conditional name="bc">
083c516d19a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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147 <param name="extract_umi_method" value="read_id" />
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148 <param name="umi_tag" value="BX" />
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149 </conditional>
083c516d19a9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit bf6a3aa532e8f9d122da4c1e39f3e256ae587b79"
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150 <section name="umi">
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151 <param name="method" value="directional" />
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152 </section>
11
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153 <param name="output_stats_bool" value="true"/>
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154 <output name="output" file="dedup_out6.bam" ftype="bam" lines_diff="2"/>
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155 <output_collection name="output_stats">
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156 <element name="edit_distance" file="stats_outputs_edit_distance.tsv" />
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157 <element name="per_umi" file="stats_outputs_per_umi.tsv" />
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158 <element name="per_umi_per_position" file="stats_outputs_per_umi_per_position.tsv" />
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159 </output_collection>
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160 </test>
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161 </tests>
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162 <help><![CDATA[
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163 umi_tools dedup - Deduplicate reads based on their UMI and mapping coordinates
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164 ==============================================================================
0
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165
ec7b02a30ed3 planemo upload commit eea727c3bdfe36d9d16036d5ab79fb8b27c4e82e
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166 Purpose
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167 -------
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168
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169 The purpose of this command is to deduplicate BAM files based on the first
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170 mapping co-ordinate and the UMI attached to the read.
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171
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172 @BARCODE_HELP@
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173
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174 @UMI_GROUPING_HELP@
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175
12
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176 Selecting the representative read
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177 ---------------------------------
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178 For every group of duplicate reads, a single representative read is
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179 retained.The following criteria are applied to select the read that
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180 will be retained from a group of duplicated reads:
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181
12
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182 1. The read with the lowest number of mapping coordinates (see
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183 ``--multimapping-detection-method`` option)
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184
12
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185 2. The read with the highest mapping quality. Note that this is not
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186 the read sequencing quality and that if two reads have the same
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187 mapping quality then one will be picked at random regardless of the
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188 read quality.
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189
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190 Otherwise a read is chosen at random.
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191
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192 Optional statistics output
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193 --------------------------
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194
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195 One can use the edit distance between UMIs at the same position as an
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196 quality control for the deduplication process by comparing with
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197 a null expectation of random sampling. For the random sampling, the
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198 observed frequency of UMIs is used to more reasonably model the null
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199 expectation.
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200
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201 Use the option ``Output UMI related statistics files?`` generate stats outfiles:
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202
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203 edit_distance
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204 Reports the (binned) average edit distance between the UMIs at each
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205 position. Positions with a single UMI are reported seperately. The
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206 edit distances are reported pre- and post-deduplication alongside
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207 the null expectation from random sampling of UMIs from the UMIs
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208 observed across all positions. Note that separate null
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209 distributions are reported since the null depends on the observed
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210 frequency of each UMI which is different pre- and
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211 post-deduplication. The post-duplication values should be closer to
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212 their respective null than the pre-deduplication vs null comparison
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213
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214 In addition, this option will trigger reporting of further summary
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215 statistics for the UMIs which may be informative for selecting the
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216 optimal deduplication method or debugging.
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217
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218 Each unique UMI sequence may be observed [0-many] times at multiple
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219 positions in the BAM. The following files report the distribution for
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220 the frequencies of each UMI.
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221
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222 per_umi_per_position
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223 The `_stats_per_umi_per_position.tsv` file simply tabulates the
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224 counts for unique combinations of UMI and position. E.g if prior to
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225 deduplication, we have two positions in the BAM (POSa, POSb), at
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226 POSa we have observed 2*UMIa, 1*UMIb and at POSb: 1*UMIc, 3*UMId,
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227 then the stats file is populated thus:
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228
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229 ====== =============
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230 counts instances_pre
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231 ------ -------------
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232 1 2
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233 2 1
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234 3 1
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235 ====== =============
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236
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237 If post deduplication, UMIb is grouped with UMIa such that POSa:
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238 3*UMIa, then the `instances_post` column is populated thus:
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239
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240 ====== ============= ==============
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241 counts instances_pre instances_post
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242 ------ ------------- --------------
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243 1 2 1
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244 2 1 0
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245 3 1 2
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246 ====== ============= ==============
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247
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248 per_umi_per
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249 The `_stats_per_umi_per.tsv` table provides UMI-level summary
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250 statistics. Keeping in mind that each unique UMI sequence can be
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251 observed at [0-many] times across multiple positions in the BAM,
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252
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253 :times_observed: How many positions the UMI was observed at
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254 :total_counts: The total number of times the UMI was observed across all positions
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255 :median_counts: The median for the distribution of how often the UMI was observed at each position (excluding zeros)
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256
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257 Hence, whenever times_observed=1, total_counts==median_counts.]]></help>
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258 <expand macro="citations" />
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259 </tool>