Mercurial > repos > iuc > ivar_removereads

annotate ivar_removereads.xml @ 17:5dc33613c288 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 32fbe8a14173afe0b39f1483afaba958dc6cd027
author iuc
date Fri, 21 Jun 2024 15:19:51 +0000
parents 8c05afb547fa
children
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8c05afb547fa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 02d1d482bda9804c69d2d03c890151bc491e5c73
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1 <tool id="ivar_removereads" name="ivar removereads" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
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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>
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6 <expand macro="requirements"/>
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7 <expand macro="version_command"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 cp '$input_bed' binding_sites.bed &&
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10 python '$__tool_directory__/sanitize_bed.py' binding_sites.bed &&
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11 #if $amplicons.computed == "yes"
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12 python '$__tool_directory__/write_amplicon_info_file.py' binding_sites.bed amplicon_info.tsv &&
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13 #else
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14 ln -s '$amplicon_info' amplicon_info.tsv &&
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15 #end if
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16 ivar getmasked
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17 -i '$variants_tsv' -b binding_sites.bed -f amplicon_info.tsv -p masked_primers &&
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19 python '$__tool_directory__/completemask.py' masked_primers.txt amplicon_info.tsv &&
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20 ln -s '$input_bam' sorted.bam &&
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21 ln -s '${input_bam.metadata.bam_index}' sorted.bam.bai &&
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23 ivar removereads
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24 -i sorted.bam
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25 -b binding_sites.bed
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26 -p removed_reads.bam
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27 -t masked_primers.txt
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28 ]]></command>
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29 <inputs>
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30 <param name="input_bam" argument="-i" type="data" format="bam"
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31 label="Bam input"
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32 help="BAM dataset, preprocessed with ivar trim, to remove reads from"/>
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33 <param name="variants_tsv" type="data" format="tabular"
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34 label="Variants input"
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35 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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36 <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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37 help="The same six-column BED dataset that served as input to ivar trim"/>
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38 <conditional name="amplicons">
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39 <param name="computed" type="select" label="Compute amplicon info from BED file" help="For suitable primer binding site datasets amplicon info can be computed directly (see tool help below). For others you will need to provide an extra amplicon info dataset.">
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40 <option value="yes" selected="true">Yes</option>
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41 <option value="no">No</option>
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42 </param>
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43 <when value="yes" />
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44 <when value="no">
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45 <param name="amplicon_info" type="data" format="tabular"
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46 label="Primer to amplicon assignment info"
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47 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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48 </when>
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49 </conditional>
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50 </inputs>
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51 <outputs>
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52 <data name="output_bam" format="bam" label="${tool.name} on ${on_string}" from_work_dir="removed_reads.bam"/>
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53 </outputs>
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54 <tests>
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55 <test>
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56 <param name="input_bam" value="zika/Z52_a.trimmed.sorted.bam"/>
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57 <param name="variants_tsv" value="zika/primers_Z52_consensus.tsv"/>
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58 <param name="input_bed" value="zika/db/zika_primers_consensus.bed"/>
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59 <conditional name="amplicons">
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60 <param name="computed" value="no"/>
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61 <param name="amplicon_info" value="zika/db/pair_information.tsv"/>
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62 </conditional>
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63 <assert_stdout>
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64 <!-- check that primer pairs are picked up correctly
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65 from the amplicon info file -->
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66 <has_text text="400_18_out_L**&#009;400_18_out_R**&#009;400_23_out_L&#009;400_23_out_R&#009;400_32_out_L&#009;400_32_out_R"/>
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67 </assert_stdout>
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68 <output name="output_bam" ftype="bam">
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69 <assert_contents>
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70 <has_size value="3130923" delta="1000"/>
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71 </assert_contents>
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72 </output>
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73 </test>
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74 <test>
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75 <param name="input_bam" value="zika/Z52_a.trimmed.sorted.bam"/>
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76 <param name="variants_tsv" value="zika/primers_Z52_consensus.tsv"/>
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77 <param name="input_bed" value="zika/db/zika_primers_consensus.bed"/>
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78 <conditional name="amplicons">
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79 <param name="computed" value="yes"/>
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80 </conditional>
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81 <assert_stdout>
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82 <!-- check that primer pairs are picked up correctly
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83 from the autogenerated amplicon info file -->
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84 <has_text text="400_18_out_L**&#009;400_18_out_R**&#009;400_23_out_L&#009;400_23_out_R&#009;400_32_out_L&#009;400_32_out_R"/>
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85 </assert_stdout>
11
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86 <output name="output_bam" ftype="bam">
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87 <assert_contents>
12
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88 <has_size value="3130923" delta="1000"/>
11
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89 </assert_contents>
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90 </output>
0
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91 </test>
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92 </tests>
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93 <help><![CDATA[
4
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94 This Galaxy tool combines the functionality of ``ivar getmasked`` and
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95 ``ivar removereads``. No separate ``ivar getmasked`` step is required when
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96 using this tool.
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97
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98 The wrapper takes as input a BAM dataset of aligned and sorted reads, from
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99 which the primers listed in the primer binding sites BED input have been
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100 trimmed with ``ivar trim``.
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101
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102 From this input it will remove reads that come from amplicons that have been
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103 generated with one or more primers that may have been affected in their binding
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104 by variants listed in the variants input file.
9
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105 To do its job, the needs to know which primers work together to form an
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106 amplicon. The tool can try to deduce this info from the names of the primers
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107 found in the primer info dataset. This will require a primer naming scheme
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108 following the regex pattern::
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109
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110 .*_(?P<amplicon_number>\d+).*_(?P<primer_orientation>L(?:EFT)?|R(?:IGHT)?)
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111
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112 *i.e.*, the following schemes will work (and get parsed as):
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113
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114 - ``nCoV-2019_1_LEFT`` (forward primer of amplicon 1)
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115 - ``400_2_out_R`` (reverse primer of amplicon 2)
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116 - ``QIAseq_163-2_LEFT`` (forward primer of amplicon 163)
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117
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118 Alternatively, you can specify the amplicon information explicitly through a
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119 dataset that lists the names of primers that together form any given amplicon.
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120 In it, primer names (exactly matching those in the primer info dataset) need to
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121 be TAB-separated with one line per amplicon.
4
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122
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123 .. class:: Warning mark
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124
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125 Preprocessing of the BAM input with ivar trim is essential for this tool to
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126 work because only ``ivar trim`` can add required primer information to the
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127 BAM auxillary data of every read.
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128
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129 ivar documentation can be found at `<https://andersen-lab.github.io/ivar/html/manualpage.html>`__.
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130 ]]></help>
0
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131 <expand macro="citations" />
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132 </tool>