--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Oct 12 14:21:34 2021 +0000
@@ -0,0 +1,79 @@
+<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>