Mercurial > repos > iuc > fgbio_findswitchbackreads

annotate fgbio_findswitchbackreads.xml @ 1:62f157ab67d1 draft default tip

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author iuc
date Tue, 04 Nov 2025 18:39:24 +0000
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1 <tool id="fgbio_findswitchbackreads" name="fgbio FindSwitchbackReads" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>identifies reads derived from a template switch during library construction</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 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
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10 @PREPARE_FASTA_IDX@
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11
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12 ## Link input BAM file
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13 ln -s '$input' input.bam &&
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14
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15 fgbio FindSwitchbackReads
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16 --input input.bam
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17 --output output.bam
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18 --ref \$reffa
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19 --sort-order Coordinate
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20 #if str($max_offset) != '':
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21 --max-offset $max_offset
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22 #end if
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23 #if str($max_gap) != '':
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24 --max-gap $max_gap
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25 #end if
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26 #if str($min_length) != '':
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27 --min-length $min_length
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28 #end if
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29 #if str($max_error_rate) != '':
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30 --max-error-rate $max_error_rate
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31 #end if
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32 $dont_unmap
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33 $metrics
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34 ]]></command>
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35 <inputs>
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36 <param argument="--input" type="data" format="bam,sam" label="Input BAM/SAM file"/>
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37 <expand macro="mandatory_reference" argument="--ref" help="Reference genome fasta file"/>
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38 <param argument="--max-offset" type="integer" optional="true" min="0" value="35" label="Maximum offset" help="Maximum offset between end the two segments of the read on the reference. Set to 0 to disable read-based checks."/>
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39 <param argument="--max-gap" type="integer" optional="true" min="0" value="500" label="Maximum gap" help="Maximum gap between R1 and R2 of tandem reads to call a template a switchback. Set to 0 to disable tandem-based checks."/>
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40 <param argument="--min-length" type="integer" optional="true" min="1" value="6" label="Minimum match length" help="Minimum match length of the switched back segment."/>
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41 <param argument="--max-error-rate" type="float" optional="true" min="0.0" max="1.0" value="0.1" label="Maximum error rate" help="Maximum mismatch error rate of switchback match to genome."/>
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42 <param argument="--dont-unmap" type="boolean" truevalue="--dont-unmap" falsevalue="" checked="false" label="Don't unmap reads" help="IF true, do NOT unmap reads from switchback templates."/>
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43 <param argument="--metrics" type="boolean" truevalue="--metrics metrics" falsevalue="" checked="false" label="Output metrics" help="Generate metrics files."/>
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44 </inputs>
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45 <outputs>
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46 <data name="output" format="bam" from_work_dir="output.bam" label="${tool.name} on ${on_string}: output"/>
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47 <collection name="metrics_collection" type="list" label="${tool.name} on ${on_string}: metrics">
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48 <filter>metrics</filter>
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49 <discover_datasets pattern="metrics\.(?P&lt;designation&gt;.+)\.txt" format="txt"/>
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50 </collection>
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51 <data name="metrics_plots" format="pdf" from_work_dir="metrics.plots.pdf" label="${tool.name} on ${on_string}: plots">
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52 <filter>metrics</filter>
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53 </data>
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54 </outputs>
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55 <tests>
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56 <test expect_num_outputs="1">
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57 <param name="input" value="test1_in.bam"/>
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58 <conditional name="addref_cond">
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59 <param name="addref_select" value="history"/>
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60 <param name="ref" value="test1.fa"/>
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61 </conditional>
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62 <output name="output" file="test1_out.bam"/>
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63 </test>
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64 <test expect_num_outputs="1">
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65 <param name="input" value="test1_in.bam"/>
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66 <conditional name="addref_cond">
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67 <param name="addref_select" value="history"/>
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68 <param name="ref" value="test1.fa"/>
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69 </conditional>
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70 <param name="max_gap" value="0"/>
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71 <output name="output" file="test2_out.bam"/>
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72 </test>
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73 </tests>
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74 <help><![CDATA[
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75 **What it does**
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76
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77 FindSwitchbackReads finds reads where a template switch occurred during library construction. Some library construction methods, notably ultra-low-input shotgun methods, are prone to template switching events that create molecules (templates, inserts) that instead of being a linear copy of a segment of genomic DNA, instead are chimeras formed by starting on one strand of DNA and then switching to the opposite strand.
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78
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79 **Algorithm**
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80
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81 Templates that contain strand switch events (switch-backs) are found by this tool in two different ways:
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82
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83 1. By looking at reads that contain soft-clipped bases at their 5' end that, when reverse complemented, matches the genome proximal to the 5'-most mapped base of the read (read-based switchbacks).
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84
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85 2. By identifying templates with 'FF' or 'RR' (aka tandem) orientation where it is surmised that the template switch occurred in the un-sequenced region of the template between R1 and R2 (tandem-based switchbacks).
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86
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87 **Input and Output**
fe8744fd4198 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fgbio commit 88711b338e90adc003a90930a43df3315b2ece70
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88
fe8744fd4198 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fgbio commit 88711b338e90adc003a90930a43df3315b2ece70
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89 The tool takes as input a SAM or BAM file and produces a filtered BAM file where switchback templates are identified and optionally unmapped. All reads from a switch-back template are tagged with an 'sb' tag that describes the nature of the switchback.
fe8744fd4198 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fgbio commit 88711b338e90adc003a90930a43df3315b2ece70
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90
fe8744fd4198 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fgbio commit 88711b338e90adc003a90930a43df3315b2ece70
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91 **Parameters**
fe8744fd4198 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fgbio commit 88711b338e90adc003a90930a43df3315b2ece70
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92
fe8744fd4198 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fgbio commit 88711b338e90adc003a90930a43df3315b2ece70
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93 - **Maximum offset**: Controls how far away to search for the reverse-complemented sequence
fe8744fd4198 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fgbio commit 88711b338e90adc003a90930a43df3315b2ece70
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94 - **Maximum gap**: Maximum gap between R1 and R2 of tandem reads to call a template a switchback
fe8744fd4198 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fgbio commit 88711b338e90adc003a90930a43df3315b2ece70
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95 - **Minimum match length**: Minimum number of soft-clipped bases that must exist to trigger the search
fe8744fd4198 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fgbio commit 88711b338e90adc003a90930a43df3315b2ece70
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96 - **Maximum error rate**: Allows for some mismatches between the soft-clipped sequence and the genome
fe8744fd4198 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fgbio commit 88711b338e90adc003a90930a43df3315b2ece70
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97 - **Don't unmap reads**: By default, switchback reads are made unmapped. This option prevents that behavior
fe8744fd4198 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fgbio commit 88711b338e90adc003a90930a43df3315b2ece70
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98 - **Output metrics**: Generate summary metrics, length distributions, and plots
fe8744fd4198 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fgbio commit 88711b338e90adc003a90930a43df3315b2ece70
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99
fe8744fd4198 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fgbio commit 88711b338e90adc003a90930a43df3315b2ece70
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100 ]]></help>
fe8744fd4198 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fgbio commit 88711b338e90adc003a90930a43df3315b2ece70
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101 <expand macro="citations"/>
fe8744fd4198 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fgbio commit 88711b338e90adc003a90930a43df3315b2ece70
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102 </tool>