<tool id="snp_dists" name="SNP distance matrix" version="@TOOL_VERSION@+galaxy0" python_template_version="3.5">
    <macros>
        <token name="@TOOL_VERSION@">0.6.3</token>
    </macros>
    <description>Compute distance in SNPs between all sequences in a FASTA file</description>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">snp-dists</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        snp-dists -q 
            $a
            $k
            $b
            '$input' > '$output'
    ]]></command>
    <inputs>
        <param name="input" type="data" format="fasta,fasta.gz" label="FASTA multiple sequence alignment" 
            help="Provide a multiple sequence alignment containing sequences of equal length" />
        <param argument="-a" type="boolean" truevalue="-a" falsevalue="" label="Count all differences, not just ACTG" />
        <param argument="-k" type="boolean" truevalue="-k" falsevalue="" label="Keep case, don't uppercase all letters" />
        <param argument="-b" type="boolean" truevalue="-b" falsevalue="" label="Blank top left corner cell" />
    </inputs>
    <outputs>
        <data format="tabular" name="output" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="input" ftype="fasta" value="input1.fasta" />
            <output name="output" value="output_default1.tabular" ftype="tabular" />
        </test>
        <test>
            <param name="input" ftype="fasta" value="input1.fasta" />
            <param name="a" value="True" />
            <output name="output" value="output_all_diffs1.tabular" ftype="tabular" />
        </test>
        <test>
            <param name="input" ftype="fasta" value="input1.fasta" />
            <param name="k" value="True" />
            <output name="output" value="output_keep_case1.tabular" ftype="tabular" />
        </test>
        <test>
            <param name="input" ftype="fasta" value="input1.fasta" />
            <param name="b" value="True" />
            <output name="output" value="output_blank_cell1.tabular" ftype="tabular" />
        </test>
    </tests>
    <help><![CDATA[
    **snp-dists**

    This tool computes a SNP distance matrix from a multiple sequence alignment (MSA) of
    sequences (all of the same length). Such distance matrices are often used as in
    studies of disease outbreaks.

    The output is a tabular file, for example this matrix describing four M. tuberculosis isolates
    and their relationship to the inferred ancestral reference sequence:

=============== ======= =========   =========   =========   =========
snp-dists 0.6.3	MTB_anc	ERR550641   ERR550671   ERR550691   ERR550703
--------------- ------- ---------   ---------   ---------   ---------
MTB_anc	        0       746         726         772         749
--------------- ------- ---------   ---------   ---------   ---------
ERR550641       746     0           26          44          13
--------------- ------- ---------   ---------   ---------   ---------
ERR550671       726     26          0           64          29
--------------- ------- ---------   ---------   ---------   ---------
ERR550691       772     44          64          0           39
--------------- ------- ---------   ---------   ---------   ---------
ERR550703       749     13          29          39          0
=============== ======= =========   =========   =========   =========

    ]]></help>
    <citations>
        <citation type="bibtex">
@misc{githubsnp-dists,
  author = {Seemann, Torsten},
  year = {2019},
  title = {snp-dists},
  publisher = {GitHub},
  journal = {GitHub repository},
  url = {https://github.com/tseemann/snp-dists},
}</citation>
    </citations>
</tool>