--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/7_smp_matrix.xml	Wed Jan 24 14:18:21 2018 -0500
@@ -0,0 +1,71 @@
+<tool id="snp_matrix" name="7. Create a SNP matrix" version="1.0.1" profile="16.10">
+    <description>and associated distance metrics</description>
+    <requirements>
+        <requirement type="package" version="1.0.1">snp-pipeline</requirement>
+        <requirement type="package">tabix</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        $__tool_directory__/snp-wind.py ./ -p "consensus.fasta"
+            #for $fa in sorted($cons, key=lambda f: f.element_identifier)
+                -n $fa.element_identifier -f $fa
+            #end for
+        > ./file                                                            &&
+        cat ./file                                                          &&
+        cfsan_snp_pipeline snp_matrix -o $snpma ./file                      &&
+        cfsan_snp_pipeline distance -p $pairws -m $distma $snpma            &&
+        cfsan_snp_pipeline snp_reference -l $snplist -o $referenceSNP $reference 
+    ]]></command>
+    <inputs>
+       <param type="data_collection" label="List of FASTA's" name="cons" format="fasta" collection_type="list" />
+       <conditional name="reference">
+    		<param name="ref" type="select" label="Use a curated GalaxyTrakr reference, or a reference from your history" help="Choose whether to use one of our references or your own from your history">
+    			<option value="curated">Use a GalaxyTrakr reference</option>
+    			<option value="history">Use a reference from your history</option>
+    		</param>
+    		<when value="curated">
+    			<param name="reference" type="select" label="Select reference fasta">
+    				<options from_data_table="all_fasta">
+    				    <filter type="sort_by" column="2"/>
+        				<validator type="no_options" message="No assemblies are available for the selected input dataset"/>
+    				</options>
+    			</param>
+    		</when>
+    		<when value="history">
+    			<param name="reference" type="data" format="fasta" label="Select reference fasta" />
+    		</when>
+    	</conditional>
+        <param type="data" format="txt" name="snplist" label="SNP list from your history" />
+    </inputs>
+    <outputs>
+        <data name="snpma" label="SNP matrix, fasta" format="fasta" />
+        <data name="pairws" label="SNP pairwise matrix" format="tsv" />
+        <data name="distma" label="SNP distance matrix" format="tsv" />
+        <data name="referenceSNP" format="fasta" />
+        <data name="metrics" format="tsv" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="cons">
+                <collection type="list">
+                    <element name="sample1" value="samples/sample1/consensus.fasta" />
+                    <element name="sample2" value="samples/sample2/consensus.fasta" />
+                    <element name="sample3" value="samples/sample3/consensus.fasta" />
+                    <element name="sample4" value="samples/sample4/consensus.fasta" />
+                </collection>
+            </param>
+            <param name="ref" value="history" />
+            <param name="reference" value="reference/lambda_virus.fasta" />
+            <param name="snplist" value="snplist.txt" />
+            <output name="snpma" value="snpma.fasta" />
+            <output name="pairws" value="snp_distance_pairwise.tsv" />
+            <output name="distma" value="snp_distance_matrix.tsv" />
+            <output name="referenceSNP" value="referenceSNP.fasta" />
+        </test>
+    </tests>
+    <help><![CDATA[
+        <a href="http://snp-pipeline.readthedocs.io/en/latest/index.html">http://snp-pipeline.readthedocs.io/en/latest/index.html</a>
+    ]]></help>
+    <citations>
+        <citation type="doi">10.7717/peerj-cs.20</citation>
+    </citations>
+</tool>
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