--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sarscov2formatter.xml	Mon May 04 05:39:35 2020 -0400
@@ -0,0 +1,66 @@
+<tool id="sarscov2formatter" name="sarscov2formatter" version="0.1" profile="18.01">
+    <requirements>
+        <requirement type="package" version="0.5.2">sarscov2formatter</requirement>
+    </requirements>
+    <command><![CDATA[
+sarscov2formatter
+-a $align
+#if $source.source_choice == 'ncbi':
+    -m ncbi
+#else:
+    -m '$source.meta'
+#end if
+    ]]></command>
+    <inputs>
+        <param name="align" type="data" format="fasta" label="Multiple Sequence Alignment (MSA)" help='MSA to be used in HyPhy analysis' />
+        <conditional name="source" >
+            <param name="source_choice" type="select" label="NCBI datasource or other?" >
+                <option value="ncbi">NCBI</option>
+                <option value="other">Other</option>
+            </param>
+            <when value="ncbi" />
+            <when value="other" >
+                 <param name="meta" type="data" format='tabular' label="Metadata source" help="Tabular file with metadata with the correct columns (see below)" />
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="msa" format="fasta" from_work_dir="msa.fasta" label="${tool.name}: MSA" />
+        <data name="dups" format="json" from_work_dir="duplicates.json" label="${tool.name}: Duplicates" />
+        <data name="outmeta" format="json" from_work_dir="meta.json" label="${tool.name}: Metadata" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="align" ftype="fasta" value="align.fasta" />
+            <param name="source_choice" value="ncbi" />
+            <output name="msa" ftype="fasta" compare="diff" value="msa.fasta" />
+            <output name="dups" ftype="json" compare="diff" value="dups.json" />
+            <output name="outmeta" ftype="json" compare="diff" value="meta.json" />
+        </test>
+    </tests>
+        <help><![CDATA[
+
+=================
+sarscov2formatter
+=================
+
+Custom sript that performs necessary formatting operations for the SARS-CoV2 Selection Analysis workflow.
+
+If using non-NCBI data, the metadata input file must be tabular with the following columns: ID, collection_date, country, state (optional), and locality (optional). Optional columns should still be created even if they are not used.
+
+Dates should be of the format: YYMMDD (example: May 1 2020 = 20200501).
+
+
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+            @misc{githubsarscov2formatter,
+            author = {Nicholas Keener},
+            year = {2020},
+            title = {sarscov2formatter},
+            publisher = {Github},
+            journal = {Github repository},
+            url = {https://github.com/nickeener/sarscov2formatter},
+        }</citation>
+    </citations>
+</tool>