--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cfsan_snp_pipeline_call_sites.xml	Tue Nov 21 21:04:31 2023 +0000
@@ -0,0 +1,44 @@
+<tool id="call_sites" name="CFSAN SNP pipeline: call sites" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>of high-confidence SNPs</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+    cp '$reference' 'reference.fasta' &&
+    samtools faidx 'reference.fasta' &&  
+    picard MarkDuplicates INPUT='$input' OUTPUT=/dev/stdout METRICS_FILE='$metrics' | samtools mpileup -f ./reference.fasta - -o '$pileup' &&
+    varscan mpileup2snp '$pileup' --min_var-freq 0.90 --output-vcf 1 > '$calls' 
+    ]]></command>
+    <inputs>
+        <param name="input" label="Read alignment to reference" type="data" format="bam"/>
+        <param name="reference" label="FASTA Reference from your history" type="data" format="fasta"/>
+    </inputs>
+    <outputs>
+        <data name="calls" label="${input.name.split(' ')[0]} unfiltered SNPs" format="vcf"/>
+        <data name="pileup" label="${input.name.split(' ')[0]} pileup" format="pileup"/>
+        <data name="metrics" label="Metrics from Picard" format="txt"/>
+        <data label="S3 Cache log" name="cache_log" format="txt"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="reference" value="lambda_virus.fasta"/>
+            <param name="input" value="reads.bam"/>
+            <output name="calls" ftype="vcf">
+                <assert_contents>
+                    <has_size value="9976" delta="100"/>
+        </assert_contents>
+            </output>
+            <output name="pileup" ftype="pileup">
+                <assert_contents>
+                    <has_size value="4259620" delta="100"/>
+        </assert_contents>
+            </output>
+        </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>
+    <expand macro="citations"/>
+</tool>
+