view classification.xml @ 6:3c50a937d7c1 draft

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<tool id="PHYLO_classification" name="Output classifications" version="2.1.0">
  <description>in tabular format</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <requirements>
    <requirement type="package">yapp_env</requirement>
  </requirements>
  <stdio>
    <expand macro="basic_errors"/>
  </stdio>
  <version_command>echo "pplacer $(pplacer --version)"</version_command>
  <command interpreter="bash">
    classification-wrapper.sh ${config}
  </command>
  <inputs>
    <param name="split_map" type="data" format="csv" label="Read-to-specimen map"/>
    <param name="label_map" type="data" format="csv" label="Specimen-to-label map"/>
    <param name="class_db" type="data" format="sqlite3" label="Placement database"/>
    <param name="want_rank" type="select" label="Desired classification rank">
      <option value="species" selected="true">Species</option>
      <option value="genus">Genus</option>
      <option value="family">Family</option>
      <option value="order">Order</option>
      <option value="class">Class</option>
      <option value="phylum">Phylum</option>
    </param>
  </inputs>
  <outputs>
    <data name="by_taxon" format="csv" label="By-taxon classification"/>
    <data name="by_specimen" format="csv" label="By-specimen classification"/>
    <data name="tallies_wide" format="csv" label="Tallies-wide classification"/>
  </outputs>
  <configfiles>
    <configfile name="config">
SPLIT_MAP="${split_map}"
LABEL_MAP="${label_map}"
CLASS_DB="${class_db}"
WANT_RANK="${want_rank}"

BY_TAXON="${by_taxon}"
BY_SPECIMEN="${by_specimen}"
TALLIES_WIDE="${tallies_wide}"
    </configfile>
  </configfiles>
  <!-- The contents of the help tag is parsed as reStructuredText. Please see
       help-template.rst for examples of commonly-used sections in other Galaxy
       tools. -->
  <help>

.. class:: infomark

**What it does**

This tool outputs the classifications made by ``pplacer`` to a tabular format
appropriate for use with R.

-----

**Example**

The classifications are simply done by containment. Say clade A of the
reference tree is the smallest such that contains a given placement. The most
specific classification for that read will be the lowest common ancestor of the
taxonomic classifications for the leaves of A. If the desired classification is
more specific than that, then we get a disconnect between the desired and the
actual classification. For example, if we try to classify at the species level
and the clade LCA is a genus, then we will get a genus name. If there is
uncertainty in read placement, then there is uncertainty in classification.

For example, here is a classification list made for one read using the tabular
output. The columns are as follows: read name, attempted rank for
classification, actual rank for classification, taxonomic identifier, and
confidence. You can see that in this example, there is some uncertainty at and
below species, but only one classification at the genus level::

    GLKT0ZE01CQ2BU                      root          root       1          1
    GLKT0ZE01CQ2BU                below_root    below_root  131567          1
    GLKT0ZE01CQ2BU              superkingdom  superkingdom       2          1
    GLKT0ZE01CQ2BU        below_superkingdom  superkingdom       2          1
    GLKT0ZE01CQ2BU  below_below_superkingdom  superkingdom       2          1
    GLKT0ZE01CQ2BU               superphylum  superkingdom       2          1
    GLKT0ZE01CQ2BU                    phylum        phylum    1239          1
    GLKT0ZE01CQ2BU                 subphylum        phylum    1239          1
    GLKT0ZE01CQ2BU                     class         class  186801          1
    GLKT0ZE01CQ2BU                  subclass         class  186801          1
    GLKT0ZE01CQ2BU                     order         order  186802          1
    GLKT0ZE01CQ2BU               below_order         order  186802          1
    GLKT0ZE01CQ2BU         below_below_order         order  186802          1
    GLKT0ZE01CQ2BU                  suborder         order  186802          1
    GLKT0ZE01CQ2BU                    family        family  186804          1
    GLKT0ZE01CQ2BU              below_family        family  186804          1
    GLKT0ZE01CQ2BU                     genus         genus    1257          1
    GLKT0ZE01CQ2BU             species_group         genus    1257          1
    GLKT0ZE01CQ2BU          species_subgroup         genus    1257          1
    GLKT0ZE01CQ2BU                   species         genus    1257  0.0732247
    GLKT0ZE01CQ2BU                   species       species    1261   0.853561
    GLKT0ZE01CQ2BU                   species       species  341694   0.073214
    GLKT0ZE01CQ2BU             below_species         genus    1257  0.0732247
    GLKT0ZE01CQ2BU             below_species       species    1261   0.853561
    GLKT0ZE01CQ2BU             below_species       species  341694   0.073214

  </help>
  <citations>
    <expand macro="cite_pplacer"/>
  </citations>
</tool>