comparison ivar_removereads.xml @ 9:8d36959b000d draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit f09d0bee3e957564beccb1bdb3610de02f639ec7"

8:28a6f1908fcc

<tool id="ivar_removereads" name="ivar removereads" version="@VERSION@+galaxy1">
    <description>Remove reads from trimmed BAM file</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">

        label="Variants input"
        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." />
        <param name="input_bed" argument="-b" type="data" format="bed" label="Primer binding sites information"
        help="The same six-column BED dataset that served as input to ivar trim"/>
        <conditional name="amplicons">
            <param name="computed" type="select" label="Compute amplicon info from BED file" help="Compute the amplicon info file from the primer BED file">
                <option value="yes" selected="true">Yes</option>
                <option value="no">No</option>
            </param>
            <when value="yes" />
            <when value="no">

trimmed with ``ivar trim``.

From this input it will remove reads that come from amplicons that have been
generated with one or more primers that may have been affected in their binding
by variants listed in the variants input file.

.. class:: Warning mark

   Preprocessing of the BAM input with ivar trim is essential for this tool to
   work because only ``ivar trim`` can add required primer information to the

9:8d36959b000d

<tool id="ivar_removereads" name="ivar removereads" version="@VERSION@+galaxy2">
    <description>Remove reads from trimmed BAM file</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">

        label="Variants input"
        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." />
        <param name="input_bed" argument="-b" type="data" format="bed" label="Primer binding sites information"
        help="The same six-column BED dataset that served as input to ivar trim"/>
        <conditional name="amplicons">
            <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.">
                <option value="yes" selected="true">Yes</option>
                <option value="no">No</option>
            </param>
            <when value="yes" />
            <when value="no">

trimmed with ``ivar trim``.

From this input it will remove reads that come from amplicons that have been
generated with one or more primers that may have been affected in their binding
by variants listed in the variants input file.
To do its job, the needs to know which primers work together to form an
amplicon. The tool can try to deduce this info from the names of the primers
found in the primer info dataset. This will require a primer naming scheme
following the regex pattern::

  .*_(?P<amplicon_number>\d+).*_(?P<primer_orientation>L(?:EFT)?|R(?:IGHT)?)

*i.e.*, the following schemes will work (and get parsed as):

- ``nCoV-2019_1_LEFT`` (forward primer of amplicon 1)
- ``400_2_out_R`` (reverse primer of amplicon 2)
- ``QIAseq_163-2_LEFT`` (forward primer of amplicon 163)

Alternatively, you can specify the amplicon information explicitly through a
dataset that lists the names of primers that together form any given amplicon.
In it, primer names (exactly matching those in the primer info dataset) need to
be TAB-separated with one line per amplicon.

.. class:: Warning mark

   Preprocessing of the BAM input with ivar trim is essential for this tool to
   work because only ``ivar trim`` can add required primer information to the