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<?xml version="1.0"?>
<tool id="mutSpeccompare" name="MutSpec Compare" version="0.0.1">
<description>Compare signatures with the cosine similarity method</description>

<requirements>
    <requirement type="set_environment">SCRIPT_PATH</requirement>
    <requirement type="package" version="3.1.2">R</requirement>
    <requirement type="package" version="0.1">mutspec</requirement>
</requirements>

<command interpreter="bash">
	mutspecCompare_wrapper.sh
	$newsign
	$output
	#if $refSignatureSource.source == "fromtable":
		\$SCRIPT_PATH/Frequency-COSMICv72-Hupki.txt
	#else
		${refSignatureSource.h_publish}
	#end if
</command>

<inputs>
	<conditional name="refSignatureSource">
		<param name="source" type="select" label="Reference signatures" help="You may select the provided file that includes published signatures (see details further below) or your own reference file">
			<option value="fromtable">Use COSMICv72_Hupki2014</option>
			<option value="history">Use one from my history</option>
		</param>
		<when value="fromtable">
			<options from_data_table="published_signature_matrice" />
		</when>
		<when value="history">
			<param name="h_publish" type="data" format="tabular" label="Select a file from my history" help="Matrix correctly formated (see details further below)"/>
		</when>
    </conditional>
    	
	<param name="newsign" type="data" format="html" label="Newly identified signature" help="Select an output of the tool MutSpec-NMF"/>
	
</inputs>

<outputs>
	<data name="output" format="html" label="Similarity_Matrix on dataset ${newsign.name}" />
</outputs> 


<help>

**What it does**

Compare two matrices containing published and newly identified mutation signatures using the `cosine similarity`__ method as already used by `Alexandrov et al. 2013`__, `Olivier et al. 2014`__ or `Schulze et al. 2015`__

.. __: http://en.wikipedia.org/wiki/Cosine_similarity

.. __: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3588146/

.. __: http://www.nature.com/srep/2014/140327/srep04482/full/srep04482.html

.. __: http://www.nature.com/ng/journal/v47/n5/fig_tab/ng.3252_SF3.html

--------------------------------------------------------------------------------------------------------------------------------------------------

**Output**

A HTML page displaying a heatmap representing the similarity between the new signatures and the published ones.

Values close to 1 (red) indicate a high similarity between the signatures.

--------------------------------------------------------------------------------------------------------------------------------------------------

**Published signatures**

The reference signatures matrix (COSMICv72-Hupki2014 matrix) includes

1. The 30 signatures published in `COSMIC database, v72`__

2. The 4 experimental signatures obtained in mouse cells for AA, MNNG, BaP and AID that were published in `Olivier et al. 2014`__


.. __: http://cancer.sanger.ac.uk/cosmic/signatures

.. __: http://www.nature.com/srep/2014/140327/srep04482/full/srep04482.html



--------------------------------------------------------------------------------------------------------------------------------------------------

**Example**

Matrix of known signatures

+-------------------+---------------+-----------------------+--------------+--------------+
| Substitution Type | Trinucleotide | Somatic Mutation Type |  Signature 1 |  Signature 2 |
+===================+===============+=======================+==============+==============+
|        C>A        |      ACA      |         A[C>A]A       | 0.0110983262 | 0.0006827082 +
+-------------------+---------------+-----------------------+--------------+--------------+
|        C>A        |      ACC      |         A[C>A]C       | 0.0091493407 | 0.0006191072 +
+-------------------+---------------+-----------------------+--------------+--------------+
|        C>A        |      ACG      |         A[C>A]G       | 0.0014900705 | 0.000099279  +
+-------------------+---------------+-----------------------+--------------+--------------+
|        C>A        |      ACT      |         A[C>A]T       | 0.0062338852 | 0.0003238914 +
+-------------------+---------------+-----------------------+--------------+--------------+
|        C>A        |      CCA      |         C[C>A]A       | 0.0065958701 | 0.000677445  +
+-------------------+---------------+-----------------------+--------------+--------------+
|        C>A        |      CCC      |         C[C>A]C       | 0.0073423678 | 0.000213681  +
+-------------------+---------------+-----------------------+--------------+--------------+


</help>


<citations>
    <citation type="bibtex">
        @article{ardin_mutspec:_2016,
            title = {{MutSpec}: a Galaxy toolbox for streamlined analyses of somatic mutation spectra in human and mouse cancer genomes},
            volume = {17},
            issn = {1471-2105},
            doi = {10.1186/s12859-016-1011-z},
            shorttitle = {{MutSpec}},
            abstract = {{BACKGROUND}: The nature of somatic mutations observed in human tumors at single gene or genome-wide levels can reveal information on past carcinogenic exposures and mutational processes contributing to tumor development. While large amounts of sequencing data are being generated, the associated analysis and interpretation of mutation patterns that may reveal clues about the natural history of cancer present complex and challenging tasks that require advanced bioinformatics skills. To make such analyses accessible to a wider community of researchers with no programming expertise, we have developed within the web-based user-friendly platform Galaxy a first-of-its-kind package called {MutSpec}.
        {RESULTS}: {MutSpec} includes a set of tools that perform variant annotation and use advanced statistics for the identification of mutation signatures present in cancer genomes and for comparing the obtained signatures with those published in the {COSMIC} database and other sources. {MutSpec} offers an accessible framework for building reproducible analysis pipelines, integrating existing methods and scripts developed in-house with publicly available R packages. {MutSpec} may be used to analyse data from whole-exome, whole-genome or targeted sequencing experiments performed on human or mouse genomes. Results are provided in various formats including rich graphical outputs. An example is presented to illustrate the package functionalities, the straightforward workflow analysis and the richness of the statistics and publication-grade graphics produced by the tool.
        {CONCLUSIONS}: {MutSpec} offers an easy-to-use graphical interface embedded in the popular Galaxy platform that can be used by researchers with limited programming or bioinformatics expertise to analyse mutation signatures present in cancer genomes. {MutSpec} can thus effectively assist in the discovery of complex mutational processes resulting from exogenous and endogenous carcinogenic insults.},
            pages = {170},
            number = {1},
            journaltitle = {{BMC} Bioinformatics},
            author = {Ardin, Maude and Cahais, Vincent and Castells, Xavier and Bouaoun, Liacine and Byrnes, Graham and Herceg, Zdenko and Zavadil, Jiri and Olivier, Magali},
            date = {2016},
            pmid = {27091472},
            keywords = {Galaxy, Mutation signatures, Mutation spectra, Single base substitutions}
        }
    </citation>
</citations>

</tool>