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comparison ivar_removereads.xml @ 9:8d36959b000d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit f09d0bee3e957564beccb1bdb3610de02f639ec7"
author iuc
date Fri, 20 Aug 2021 20:34:11 +0000
parents 28a6f1908fcc
children ee29337f905c
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8:28a6f1908fcc 9:8d36959b000d
1 <tool id="ivar_removereads" name="ivar removereads" version="@VERSION@+galaxy1"> 1 <tool id="ivar_removereads" name="ivar removereads" version="@VERSION@+galaxy2">
2 <description>Remove reads from trimmed BAM file</description> 2 <description>Remove reads from trimmed BAM file</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"> 6 <expand macro="requirements">
36 label="Variants input" 36 label="Variants input"
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." /> 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." />
38 <param name="input_bed" argument="-b" type="data" format="bed" label="Primer binding sites information" 38 <param name="input_bed" argument="-b" type="data" format="bed" label="Primer binding sites information"
39 help="The same six-column BED dataset that served as input to ivar trim"/> 39 help="The same six-column BED dataset that served as input to ivar trim"/>
40 <conditional name="amplicons"> 40 <conditional name="amplicons">
41 <param name="computed" type="select" label="Compute amplicon info from BED file" help="Compute the amplicon info file from the primer BED file"> 41 <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.">
42 <option value="yes" selected="true">Yes</option> 42 <option value="yes" selected="true">Yes</option>
43 <option value="no">No</option> 43 <option value="no">No</option>
44 </param> 44 </param>
45 <when value="yes" /> 45 <when value="yes" />
46 <when value="no"> 46 <when value="no">
84 trimmed with ``ivar trim``. 84 trimmed with ``ivar trim``.
85 85
86 From this input it will remove reads that come from amplicons that have been 86 From this input it will remove reads that come from amplicons that have been
87 generated with one or more primers that may have been affected in their binding 87 generated with one or more primers that may have been affected in their binding
88 by variants listed in the variants input file. 88 by variants listed in the variants input file.
89 To do its job, the needs to know which primers work together to form an
90 amplicon. The tool can try to deduce this info from the names of the primers
91 found in the primer info dataset. This will require a primer naming scheme
92 following the regex pattern::
93
94 .*_(?P<amplicon_number>\d+).*_(?P<primer_orientation>L(?:EFT)?|R(?:IGHT)?)
95
96 *i.e.*, the following schemes will work (and get parsed as):
97
98 - ``nCoV-2019_1_LEFT`` (forward primer of amplicon 1)
99 - ``400_2_out_R`` (reverse primer of amplicon 2)
100 - ``QIAseq_163-2_LEFT`` (forward primer of amplicon 163)
101
102 Alternatively, you can specify the amplicon information explicitly through a
103 dataset that lists the names of primers that together form any given amplicon.
104 In it, primer names (exactly matching those in the primer info dataset) need to
105 be TAB-separated with one line per amplicon.
89 106
90 .. class:: Warning mark 107 .. class:: Warning mark
91 108
92 Preprocessing of the BAM input with ivar trim is essential for this tool to 109 Preprocessing of the BAM input with ivar trim is essential for this tool to
93 work because only ``ivar trim`` can add required primer information to the 110 work because only ``ivar trim`` can add required primer information to the