<macros>
    <token name="@TOOL_VERSION@">0.6.1</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">tracy</requirement>
            <yield/>
        </requirements>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1186/s12864-020-6635-8</citation>
            <yield />
        </citations>
    </xml>
    <xml name="version_command">
        <version_command>tracy --version</version_command>
    </xml>
    <xml name="common_options">
        <param argument="--pratio" type="float" value="0.33" label="Peak ratio to call base" />
        <param argument="--maxindel" type="integer" value="1000" label="Maximum indel size in Sanger trace" min="1" />
        <param argument="--linelimit" type="integer" value="60" label="Alignment line length" min="1" />
    </xml>
    <xml name="kmer_options">
        <section name="kmer" title="Kmer options">
            <param argument="--kmer" type="integer" value="15" label="Kmer size to anchor trace" min="1" />
            <param argument="--support" type="integer" value="3" label="Minimum kmer support" min="1" />
        </section>
    </xml>
    <xml name="trim_options">
        <section name="trim" title="Trimming options">
            <param argument="--trim" type="integer" value="0" label="Trimming stringency (0: use trimLeft and trimRight)" />
            <param argument="--trimLeft" type="integer" value="50" label="Trim size left" min="0" />
            <param argument="--trimRight" type="integer" value="50" label="Trim size right" min="0" />
        </section>
    </xml>
    <xml name="alignment_options">
        <section name="alignment" title="Alignment options">
            <param argument="--gapopen" type="integer" value="-10" max="0" label="Gap open penalty" />
            <param argument="--gapext" type="integer" value="-4" max="0" label="Gap extension penalty" />
            <param argument="--match" type="integer" value="3" min="0" label="Match score" />
            <param argument="--mismatch" type="integer" value="-5" max="0" label="Mismatch penalty" />
        </section>
    </xml>
    <token name="@pratio@"><![CDATA[
The *pratio* parameter is a floating point value expressing the minimum proportion of the maximum trace value that will still be
called as a base. For example, if the maximum value found in the trace file is 10, and pratio is 0.3, a peak needs to be
higher than 3 to be called as a base.        
    ]]></token>
    <token name="@trim_options@"><![CDATA[
Prior to alignment the trace file is trimmed. Either a fixed number of bases can be trimmed from the left or right sides of
the trace, or trimming points (on the left or right or the trace) can be automatically found using an algorithm that works
outwards from the best 10% of the trace and uses a sliding window (of size 10 bases) to find the point where the trace
quality falls below a computed threshold. This automated trimming algorithm can be tuned using a *trimming stringency* (higher
values mean stricter trimming).
    ]]></token>
    <token name="@alignment@"><![CDATA[
The dynamic programming step of the alignment uses the `Gotoh's algorithm <http://rna.informatik.uni-freiburg.de/Teaching/index.jsp?toolName=Gotoh>`_ 
which can be tuned using scores for nucleotide matches, mismatches, gap opening and gap extension.
    ]]></token>
    <xml name="optional_outputs">
        <param name="optional_outputs" type="select" multiple="true" label="Optional outputs">
            <option value="json">JSON</option>
            <option value="tabular">tabular statistics report</option>
        </param>
    </xml>
    <xml name="json_output" token_toolname="">
        <data name="out_json" format="json" from_work_dir="out.json" label="tracy @TOOLNAME@ JSON on ${on_string}">
            <filter>optional_outputs and 'json' in optional_outputs</filter>
        </data>    
    </xml>
    <xml name="tabular_output" token_toolname="">
        <data name="out_stats" format="tabular" from_work_dir="out.abif" label="tracy @TOOLNAME@ stats on ${on_string}">
            <actions>
                <action name="column_names" type="metadata" default="pos,peakA,peakC,peakG,peakT,basenum,primary,secondary,consensus,qual,trim" />
            </actions>
            <filter>optional_outputs and 'tabular' in optional_outputs</filter>
        </data>
    </xml>
</macros>