Mercurial > repos > iuc > ivar_removereads

annotate ivar_removereads.xml @ 8:28a6f1908fcc draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
author iuc
date Thu, 05 Aug 2021 12:44:59 +0000
parents 75c279fa403a
children 8d36959b000d
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1 <tool id="ivar_removereads" name="ivar removereads" version="@VERSION@+galaxy1">
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2 <description>Remove reads from trimmed BAM file</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
4
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6 <expand macro="requirements">
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7 <requirement type="package" version="3.8.1">python</requirement>
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8 </expand>
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9 <expand macro="version_command" />
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10 <command detect_errors="exit_code"><![CDATA[
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11 cp '$input_bed' binding_sites.bed &&
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12 python '$__tool_directory__/sanitize_bed.py' binding_sites.bed &&
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13 #if $amplicons.computed == "yes"
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14 python '$__tool_directory__/write_amplicon_info_file.py' binding_sites.bed amplicon_info.tsv &&
28a6f1908fcc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 6dae6f97a45a61b1f10be4227d978584624c3b3d"
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15 #else
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16 ln -s '$amplicon_info' amplicon_info.tsv &&
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17 #end if
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18 ivar getmasked
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19 -i '$variants_tsv' -b binding_sites.bed -f amplicon_info.tsv -p masked_primers &&
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20
8
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21 python '$__tool_directory__/completemask.py' masked_primers.txt amplicon_info.tsv &&
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22 ln -s '$input_bam' sorted.bam &&
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23 ln -s '${input_bam.metadata.bam_index}' sorted.bam.bai &&
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24
0
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25 ivar removereads
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26 -i sorted.bam
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27 -b binding_sites.bed
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28 -p removed_reads.bam
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29 -t masked_primers.txt
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30 ]]></command>
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31 <inputs>
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32 <param name="input_bam" argument="-i" type="data" format="bam"
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33 label="Bam input"
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34 help="BAM dataset, preprocessed with ivar trim, to remove reads from" />
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35 <param name="variants_tsv" type="data" format="tabular"
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36 label="Variants input"
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37 help="This dataset will be scanned for variants that affect primer binding sites and needs to be in tabular format with affected chromosome names in the first, and positions in the second column. If there is a header line, the name of the second column should be POS." />
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38 <param name="input_bed" argument="-b" type="data" format="bed" label="Primer binding sites information"
ee2beb764a7b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 693df287d23b0fd9dfd134b41d401a438c3f5ad6"
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39 help="The same six-column BED dataset that served as input to ivar trim"/>
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40 <conditional name="amplicons">
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41 <param name="computed" type="select" label="Compute amplicon info from BED file" help="Compute the amplicon info file from the primer BED file">
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42 <option value="yes" selected="true">Yes</option>
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43 <option value="no">No</option>
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44 </param>
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45 <when value="yes" />
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46 <when value="no">
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47 <param name="amplicon_info" type="data" format="tabular"
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48 label="Primer to amplicon assignment info"
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49 help="This input should consist of one line per amplicon with the tab-separated names of all primers used to generate that amplicon."/>
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50 </when>
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51 </conditional>
0
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52 </inputs>
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53 <outputs>
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54 <data name="output_bam" format="bam" label="${tool.name} on ${on_string}" from_work_dir="removed_reads.bam"/>
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55 </outputs>
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56 <tests>
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57 <test>
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58 <param name="input_bam" value="zika/Z52_a.trimmed.sorted.bam"/>
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59 <param name="variants_tsv" value="zika/primers_Z52_consensus.tsv"/>
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60 <param name="input_bed" value="zika/db/zika_primers_consensus.bed"/>
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61 <conditional name="amplicons">
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62 <param name="computed" value="no" />
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63 <param name="amplicon_info" value="zika/db/pair_information.tsv"/>
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64 </conditional>
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65 <output name="output_bam" file="zika/Z52_a.masked.bam" compare="sim_size" delta="100000" />
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66 </test>
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67 <test>
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68 <param name="input_bam" value="zika/Z52_a.trimmed.sorted.bam"/>
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69 <param name="variants_tsv" value="zika/primers_Z52_consensus.tsv"/>
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70 <param name="input_bed" value="zika/db/zika_primers_consensus.bed"/>
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71 <conditional name="amplicons">
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72 <param name="computed" value="yes" />
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73 </conditional>
0
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74 <output name="output_bam" file="zika/Z52_a.masked.bam" compare="sim_size" delta="100000" />
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75 </test>
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76 </tests>
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77 <help><![CDATA[
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78 This Galaxy tool combines the functionality of ``ivar getmasked`` and
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79 ``ivar removereads``. No separate ``ivar getmasked`` step is required when
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80 using this tool.
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81
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82 The wrapper takes as input a BAM dataset of aligned and sorted reads, from
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83 which the primers listed in the primer binding sites BED input have been
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84 trimmed with ``ivar trim``.
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85
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86 From this input it will remove reads that come from amplicons that have been
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87 generated with one or more primers that may have been affected in their binding
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88 by variants listed in the variants input file.
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89
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90 .. class:: Warning mark
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91
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92 Preprocessing of the BAM input with ivar trim is essential for this tool to
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93 work because only ``ivar trim`` can add required primer information to the
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94 BAM auxillary data of every read.
0
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95
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96 ivar documentation can be found at `<https://andersen-lab.github.io/ivar/html/manualpage.html>`__.
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97 ]]></help>
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98 <expand macro="citations" />
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99 </tool>