--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/kc-align.xml	Tue Mar 17 15:24:15 2020 -0400
@@ -0,0 +1,85 @@
+<tool id="kc-align" name="Kc-Align" version="0.1.0" python_template_version="3.5">
+    <requirements>
+        <requirement type="package" version="0.5">kcalign</requirement>
+        <requirement type="package" version="2.04">kalign2</requirement>
+    </requirements>
+    <command detect_errors="exit_code">
+        <![CDATA[
+        kc-align
+            --mode $position.mode
+            --reference '$reference'
+            --reads '$reads'
+            #if $position.mode == "genome":
+                --start $position.start
+                --end $position.end
+            #end if
+    ]]></command>
+    <inputs>
+        <param name="reference" type="data" format="fasta" label="Reference Sequence" help="Single FASTA reference sequence to be aligned" />
+        <param name="reads" type="data" format="fasta" label="Reads" help="Single or multi-FASTA seqeunces to be aligned with the reference" />
+        <conditional name="position" >
+            <param name="mode" type="select" label="Mode" >
+                <option value="genome">Genome</option>
+                <option value="gene">Gene</option>
+                <option value="mixed">Mixed</option>
+            </param>
+            <when value="genome" >
+                <param name="start" type="integer" value="0" min="0" label="Start Position" help="The 1-indexed start position of the gene of interest in the reference sequence" />
+                <param name="end" type="integer" value="0" min="0" label="End Position" help="The 1-indexed end position of the gene of interest in the reference sequence" />
+            </when>
+            <when value="gene" >
+            </when>
+            <when value="mixed" >
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="fasta" format="fasta" from_work_dir="kc-align.fasta" label="out.fasta" />
+        <data name="clustal" format="txt" from_work_dir="kc-align.clustal" label="out.clustal" />
+    </outputs>
+<tests>
+    <test>
+        <param name="reference" ftype="fasta" value="MN908947.3.fasta" />
+        <param name="reads" ftype="fasta" value="corona.fasta" />
+        <param name="mode" value="genome" />
+        <param name="start" value="21563" />
+        <param name="end" value="25384" />
+        <output name="fasta" ftype="fasta" compare="diff" value="kc-align.fasta" />
+        <output name="clustal" ftype="txt" compare="diff" value="kc-align.clustal" />
+    </test>
+</tests>
+    <help><![CDATA[
+
+============
+Kc-Align
+============
+
+Kc-Algin is a codon-aware multiple aligner that uses Kalgin2 to produce in-frame gapped codon alignments for selection analysis of small genomes (mostly viral and some smaller bacterial genomes). Takes nucleotide seqeunces as inputs, converts them to their in-frame amino acid sequences, performs multiple alignment with Kalign, and then converts the alignments back to their original codon sequence while preserving the gaps. Produces two outputs: the gapped nucleotide alignments in FASTA format and in CLUSTAL format.
+
+Kc-Align will also attempt to detect any frameshift mutations in the input reads. If a frameshift is detected, that sequence will not be included in the multiple alignment and its ID will be printed to stdout.
+
+Modes:
+------
+        
+Kc-Align can be run in three different modes, depending on your input data.
+
+* In **genome** mode, the "reference" and "reads" input parameters are all full genome FASTA files. This mode also requires the 1-based start and end position numbers corresponding to the gene you are interested in aligning from the reference input.
+
+* If both the "reference" and "reads" inputs are already in-frame genes, the **gene** mode should be used. This mode does not require start and end position parameters as the reference is already in-frame.
+
+* For the case when your "reference" is an in-frame gene while the "reads" are whole genomes, the **mixed** mode can be used. Like gene mode, this mode does not require the start and end point position parameters.
+
+
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+        	@misc{githubkcalign,
+            author = {Nicholas Keener, Emil Bouvier},
+            year = {2020},
+            title = {Kc-Align},
+            publisher = {Github},
+            journal = {Github repository},
+            url = {https://github.com/davebx/kc-align},
+        }</citation>
+    </citations>
+</tool>