comparison quast.xml @ 8:ebb0dcdb621a draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit e24f6cb40f19bad167b440e119e0300f15e04a78"

7:59db8ea8c845

<tool id="quast" name="Quast" version="@TOOL_VERSION@+galaxy0" >
    <description>Genome assembly Quality</description>
    <macros>
        <token name="@TOOL_VERSION@">5.0.2</token>
        <xml name="gene_thresholds">
            <param name="gene_thresholds" argument="--gene-thresholds" type="text" value="0,300,1500,3000" label="Comma-separated list of thresholds (in bp) for gene lengths to find with a finding tool"/>

<![CDATA[
**What it does**

QUAST = QUality ASsessment Tool. The tool evaluates genome assemblies by computing various metrics.

If you have one or multiple genome assemblies, you can assess their quality with Quast. It works with or without reference genome. If you are new to Quast, start by reading its `manual page <http://quast.bioinf.spbau.ru/manual.html>`_.

**Using Quast without reference**

Without reference Quast can calculate a number of assembly related-metrics but cannot provide any information about potential misassemblies, inversions, translocations, etc. Suppose you have three assemblies produced by Unicycler corresponding to three different antibiotic treatments *car*, *pit*, and *cef* (these stand for carbenicillin, piperacillin, and cefsulodin, respectively). Evaluating them without reference will produce the following Quast outputs:
 
 * Quast report in HTML format
 * `Contig viewer <http://quast.bioinf.spbau.ru/manual.html#sec3.4>`_ (an HTML file)
 * `Quast report <http://quast.bioinf.spbau.ru/manual.html#sec3.1.1>`_ in Tab-delimited format
 * Quast log (a file technical information about Quast tool execution)

The **tab delimited Quast report** will contain the following information::

 Assembly                  pit_fna cef_fna car_fna

 N75                        136321  136321  146521
 L50                             7       7       8
 L75                            15      15      16
 # N's per 100 kbp            0.00    0.00    0.00

where values are defined as specified in `Quast manual <http://quast.bioinf.spbau.ru/manual.html#sec3.1.1>`_

**Quast report in HTML format** contains graphs in addition to the above metrics, while **Contig viewer** draws contigs ordered from longest to shortest. This ordering is suitable for comparing only largest contigs or number of contigs longer than a specific threshold. The viewer shows N50 and N75 with color and textual indication. If the reference genome is available or at least approximate genome length is known (see `--est-ref-size`), NG50 and NG75 are also shown. You can also tone down contigs shorter than a specified threshold using Icarus control panel:

.. image:: $PATH_TO_IMAGES/contig_view_noR.png
   :width: 558
   :height: 412

Also see `Plot description <http://quast.bioinf.spbau.ru/manual.html#sec3.2>`_ section of the manual. 

**Using Quast with reference**

Car, pit, and cef are in fact assemblies of *Pseudomonas aeruginosa* UCBPP-PA14, so we can use its genome as a reference (by supplying a Fasta file containing *P. aeruginosa* pa14 genome to **Reference genome** input box). The following outputs will be produced (note the alignment viewer):

 * Quast report in HTML format
 * `Contig viewer <http://quast.bioinf.spbau.ru/manual.html#sec3.4>`_ (an HTML file)
 * `Alignment viewer <http://quast.bioinf.spbau.ru/manual.html#sec3.4>`_ (an HTML file)
 * `Quast report <http://quast.bioinf.spbau.ru/manual.html#sec3.1.1>`_ in Tab-delimited format
 * Summary of `misassemblies <http://quast.bioinf.spbau.ru/manual.html#sec3.1.2>`_
 * Summary of `unaligned contigs <http://quast.bioinf.spbau.ru/manual.html#sec3.1.3>`_
 * Quast log (a file technical information about Quast tool execution)

With the reference Quast produces a much more comprehensive set of results::

 Assembly                  pit_fna cef_fna car_fna

 NA75                       136321  136321  146521
 NGA75                      136321  136321  136321
 LA50                            7       7       8
 LGA50                           7       7       8
 LA75                           15      15      16
 LGA75                          15      15      17 

where, again, values are defined as specified in `Quast manual <http://quast.bioinf.spbau.ru/manual.html#sec3.1.1>`_. You can see that this report includes a variety of data that can only be computer against a reference assembly. 

 Using reference also produces an **Alignment viewer**:

.. image:: $PATH_TO_IMAGES/Align_view.png
   :width: 515
   :height: 395

Alignment viewer highlights regions of interest as, in this case, missassemblies that can potentially point to genome rearrangements (see more `here <http://quast.bioinf.spbau.ru/manual.html#sec3.4>`_).

    ]]>
    </help>

    <citations>
        <citation type="bibtex">@ARTICLE{a1,
            author = {Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi, Glenn Tesler},
            title = {QUAST: quality assessment tool for genomce assemblies, Bioinformatics (2013) 29 (8): 1072-1075}
        }</citation>
        <citation type="bibtex">@misc{quast41,
            title = {{Quast} v4.1},
            howpublished = {http://bioinf.spbau.ru/quast},
            note = {Released May 2016}}
        }</citation>
    </citations>
</tool>

8:ebb0dcdb621a

<tool id="quast" name="Quast" version="@TOOL_VERSION@+galaxy1" profile="18.01">
    <description>Genome assembly Quality</description>
    <macros>
        <token name="@TOOL_VERSION@">5.0.2</token>
        <xml name="gene_thresholds">
            <param name="gene_thresholds" argument="--gene-thresholds" type="text" value="0,300,1500,3000" label="Comma-separated list of thresholds (in bp) for gene lengths to find with a finding tool"/>

<![CDATA[
**What it does**

QUAST = QUality ASsessment Tool. The tool evaluates genome assemblies by computing various metrics.

If you have one or multiple genome assemblies, you can assess their quality with Quast. It works with or without reference genome. If you are new to Quast, start by reading its `manual page <http://quast.sourceforge.net/docs/manual.html>`_.

**Using Quast without reference**

Without reference Quast can calculate a number of assembly related-metrics but cannot provide any information about potential misassemblies, inversions, translocations, etc. Suppose you have three assemblies produced by Unicycler corresponding to three different antibiotic treatments *car*, *pit*, and *cef* (these stand for carbenicillin, piperacillin, and cefsulodin, respectively). Evaluating them without reference will produce the following Quast outputs:
 
 * Quast report in HTML format
 * `Contig viewer <http://quast.sourceforge.net/docs/manual.html#sec3.4>`_ (an HTML file)
 * `Quast report <http://quast.sourceforge.net/docs/manual.html#sec3.1.1>`_ in Tab-delimited format
 * Quast log (a file technical information about Quast tool execution)

The **tab delimited Quast report** will contain the following information::

 Assembly                  pit_fna cef_fna car_fna

 N75                        136321  136321  146521
 L50                             7       7       8
 L75                            15      15      16
 # N's per 100 kbp            0.00    0.00    0.00

where values are defined as specified in `Quast manual <http://quast.sourceforge.net/docs/manual.html#sec3.1.1>`_

**Quast report in HTML format** contains graphs in addition to the above metrics, while **Contig viewer** draws contigs ordered from longest to shortest. This ordering is suitable for comparing only largest contigs or number of contigs longer than a specific threshold. The viewer shows N50 and N75 with color and textual indication. If the reference genome is available or at least approximate genome length is known (see `--est-ref-size`), NG50 and NG75 are also shown. You can also tone down contigs shorter than a specified threshold using Icarus control panel:

.. image:: $PATH_TO_IMAGES/contig_view_noR.png
   :width: 558
   :height: 412

Also see `Plot description <http://quast.sourceforge.net/docs/manual.html#sec2>`_ section of the manual.

**Using Quast with reference**

Car, pit, and cef are in fact assemblies of *Pseudomonas aeruginosa* UCBPP-PA14, so we can use its genome as a reference (by supplying a Fasta file containing *P. aeruginosa* pa14 genome to **Reference genome** input box). The following outputs will be produced (note the alignment viewer):

 * Quast report in HTML format
 * `Contig viewer <http://quast.sourceforge.net/docs/manual.html#sec3.4>`_ (an HTML file)
 * `Alignment viewer <http://quast.sourceforge.net/docs/manual.html#sec3.4>`_ (an HTML file)
 * `Quast report <http://quast.sourceforge.net/docs/manual.html#sec3.1.1>`_ in Tab-delimited format
 * Summary of `misassemblies <http://quast.sourceforge.net/docs/manual.html#sec3.1.2>`_
 * Summary of `unaligned contigs <http://quast.sourceforge.net/docs/manual.html#sec3.1.3>`_
 * Quast log (a file technical information about Quast tool execution)

With the reference Quast produces a much more comprehensive set of results::

 Assembly                  pit_fna cef_fna car_fna

 NA75                       136321  136321  146521
 NGA75                      136321  136321  136321
 LA50                            7       7       8
 LGA50                           7       7       8
 LA75                           15      15      16
 LGA75                          15      15      17

where, again, values are defined as specified in `Quast manual <http://quast.sourceforge.net/docs/manual.html#sec3.1.1>`_. You can see that this report includes a variety of data that can only be computer against a reference assembly.

 Using reference also produces an **Alignment viewer**:

.. image:: $PATH_TO_IMAGES/Align_view.png
   :width: 515
   :height: 395

Alignment viewer highlights regions of interest as, in this case, missassemblies that can potentially point to genome rearrangements (see more `here <http://quast.sourceforge.net/docs/manual.html#sec3.4>`_).

    ]]>
    </help>

    <citations>
        <citation type="doi">10.1093/bioinformatics/bty266</citation>
        <citation type="doi">10.1093/bioinformatics/btw379</citation>
        <citation type="doi">10.1093/bioinformatics/btv697</citation>
        <citation type="doi">10.1093/bioinformatics/btt086</citation>
    </citations>
</tool>