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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,
            author = {Ardin et al},
            keywords = {Galaxy, Mutation signatures, Mutation spectra, Single base substitutions},
            title = {{MutSpec}: a Galaxy toolbox for streamlined analyses of somatic mutation spectra in human and mouse cancer genomes},
            url = {http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1011-z}
        }
    </citation>
</citations>

</tool>