--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/5_call_consensus.xml	Wed Jan 24 14:18:21 2018 -0500
@@ -0,0 +1,47 @@
+<tool id="call_consensus" name="5. Call consensus SNPs" version="1.0.1" profile="16.10">
+    <description>for a sample, or lookup cached consensus SNP calls</description>
+    <requirements>
+        <requirement type="package" version="1.0.1">snp-pipeline</requirement>
+        <requirement type="package" version="1.5.11">boto3</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        #set $identifier = $call_pileup.name.split(' ')[0]
+        $__tool_directory__/snp-cache.py snp_consenus_calls
+            "\$(md5sum $snps $calls $call_pileup | cut -c -32 | md5sum | cut -c -32)"
+            -c "
+                mkdir ./$identifier/
+                && cp $call_pileup ./$identifier/reads.all.pileup
+                && cfsan_snp_pipeline call_consensus -v 4 -l $snps --vcfFileName "consensus.vcf" ./$identifier/reads.all.pileup 1>&2 && tar zcv ./consensus.vcf ./consensus.fasta
+            "
+            -l $cache_log
+            | tar zvx ./
+            && cp ./consensus.fasta $calls_consensus_fa
+            && cp ./consensus.vcf $calls_consensus_vcf
+            && cat $cache_log
+    ]]></command>
+    <inputs>
+        <param type="data" name="snps" format="txt" />
+        <param type="data" name="calls" format="vcf" />
+        <param type="data" name="call_pileup" format="pileup" />
+    </inputs>
+    <outputs>
+        <data label="${calls.name.split(' ')[0]} consensus SNPs (VCF)" name="calls_consensus_vcf" format="vcf" />
+        <data label="${calls.name.split(' ')[0]} consensus SNPs (FASTA)" name="calls_consensus_fa" format="fasta" hidden="true"/>
+        <data label="S3 Cache log" name="cache_log" format="txt" hidden="true" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="snps" value="snplist.txt" />
+            <param name="calls" value="samples/sample1/var.flt.vcf" />
+            <param name="call_pileup" value="samples/sample1/reads.all.pileup" />
+            <output name="calls_consensus_vcf" value="samples/sample1/consensus.vcf" lines_diff="6" />
+            <output name="calls_consensus_fa" value="samples/sample1/consensus.fasta" lines_diff="2" />
+        </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>
\ No newline at end of file