--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tracy_assemble.xml	Tue Oct 12 14:20:41 2021 +0000
@@ -0,0 +1,120 @@
+<tool id="tracy_assemble" name="tracy Assemble" version="@TOOL_VERSION@+galaxy0" profile="20.09">
+    <description>genomic region from tiled, overlapping Sanger Chromatogram trace files</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>    
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <command detect_errors="exit_code"><![CDATA[
+        tracy assemble 
+          #if $ref.useref == 'yes':
+            --reference '$ref.reference'
+            $ref.incref
+          #end if
+          --pratio $pratio 
+          --trim $trim 
+          --fracmatch $fracmatch
+          --called $called
+          --format $format
+          $inccons
+          --gapopen $alignment.gapopen
+          --gapext $alignment.gapext
+          --match $alignment.match
+          --mismatch $alignment.mismatch
+          #for tracefile in $tracefiles
+            '$tracefile'
+          #end for
+          &&
+          #if $format == 'fastq'
+            mv out.cons.fq '$out_consensus'
+          #else
+            mv out.cons.fa '$out_consensus'
+          #end if
+    ]]></command>
+    <inputs>
+        <param name="tracefiles" type="data" format="ab1,scf" multiple="true" optional="false" label="Sanger chromatogram tracefiles to assemble" />
+        <param argument="--pratio" type="float" value="0.33" label="Peak ratio to call base" />
+        <param argument="--trim" type="integer" value="4" min="1" label="Trimming stringency" />
+        <param argument="--fracmatch" type="float" value="0.5" min="0" max="1" label="Minimum fraction of matches [0:1]" />
+        <param argument="--called" type="float" value="0.1" min="0" label="Fraction of traces required for consensus" />
+        <param argument="--format" type="select" label="Output format">
+            <option value="fasta" selected="true">FASTA</option>
+            <option value="fastq">FASTQ</option>
+        </param>
+        <param argument="--inccons" type="boolean" truevalue="--inccons" falsevalue="" label="Include consensus in FASTA alignment" />
+        <conditional name="ref" label="Reference guided assembly options">
+            <param type="select" name="useref" label="Use reference to guide assembly">
+                <option value="yes">Yes</option>
+                <option value="no" selected="true">No</option>
+            </param>
+            <when value="yes">
+                <param argument="--reference" type="data" format="fasta" label="FASTA or ABI format genome" />
+                <param argument="--incref" type="boolean" truevalue="--incref" falsevalue="" label="Include reference in consensus" />
+            </when>
+            <when value="no">
+            </when>
+        </conditional>
+        <expand macro="alignment_options" />
+        <param name="json_output" type="boolean" label="Produce JSON output" />
+    </inputs>
+    <outputs>
+        <data name="out_json" format="json" from_work_dir="out.json" label="tracy assemble JSON on ${on_string}">
+            <filter>json_output</filter>
+        </data>
+        <data name="out_consensus" format="fasta" label="tracy assemble consensus on ${on_string}">
+            <change_format>
+                <when input="format" value="fasta" format="fasta" />
+                <when input="format" value="fastq" format="fastq" />
+            </change_format>
+        </data>
+        <data name="out_alignment" format="fasta" from_work_dir="out.align.fa" label="tracy assemble alignment on ${on_string}" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="2">
+            <param name="tracefiles" value="input1.ab1,input1.ab1" ftype="ab1" />
+            <output name="out_consensus" value="out1.consensus.fasta" ftype="fasta" />    
+            <output name="out_alignment" value="out1.alignment.fasta" ftype="fasta" lines_diff="4" />    
+        </test>
+        <test expect_num_outputs="2">
+            <param name="tracefiles" value="input1.ab1,input1.ab1" ftype="ab1" />
+            <conditional name="ref">
+                <param name="useref" value="yes" />
+                <param name="reference" value="reference1.fasta" />
+            </conditional>
+            <output name="out_consensus" value="out1.consensus.fasta" ftype="fasta" />    
+            <output name="out_alignment" value="out2.alignment.fasta" ftype="fasta" lines_diff="4" />    
+        </test>
+        <test expect_num_outputs="3">
+            <param name="tracefiles" value="input1.ab1,input1.ab1" ftype="ab1" />
+            <param name="json_output" value="true" />
+            <output name="out_json" ftype="json">
+                <assert_contents>
+                    <has_text text='"peakA": [5, 5, 5, 5, 5, 4' />
+                </assert_contents>
+            </output>
+            <output name="out_consensus" value="out1.consensus.fasta" ftype="fasta" />    
+            <output name="out_alignment" value="out1.alignment.fasta" ftype="fasta" lines_diff="4" />    
+        </test>
+    </tests>
+    <help><![CDATA[
+**What this does**
+
+This tool assembles trace files that are from overlapping regions (using tracy_), optionally using a reference genome.
+The assembled sequence is output either as FASTQ or FASTA.
+
+@pratio@
+
+Prior to assembling the traces, they are trimmed using an algorithm that automatically finds left and right trimming
+positions. This algorithm can be tuned using the *trimming stringency* (higher values mean stricter trimmer).
+
+Trace files have to match (either each other or, when using reference guided assembly, the reference sequence) 
+at at least *fracmatch* positions (by default 10%) to be considered as part of the assembly.
+
+Read more here_.
+
+.. _tracy: https://github.com/gear-genomics/tracy
+.. _here: https://www.gear-genomics.com/docs/tracy/cli/#trace-assembly
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>
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