--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/2_call_sites.xml	Wed Jan 24 14:18:21 2018 -0500
@@ -0,0 +1,74 @@
+<tool id="call_sites" name="2. Call Sites" version="1.0.1" profile="16.10">
+    <description>of high-confidence SNPs, or lookup cached sitecall</description>
+    <requirements>
+        <requirement type="package" version="2.3.4">bowtie2</requirement>
+        <requirement type="package" version="1.6">samtools</requirement>
+        <requirement type="package">picard</requirement>
+        <requirement type="package">varscan</requirement>
+        <requirement type="package" version="1.5.11">boto3</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+    $__tool_directory__/snp-cache.py snp_sitecalls 
+        "\$(md5sum $input $sample | cut -c -32 | md5sum | cut -c -32)"
+        -c "
+            cp $input ./reference.fasta                    &&
+            samtools faidx ./reference.fasta               &&  
+            samtools view -bS -F 4 $sample |
+            samtools sort -o ./sorted.bam -                &&
+            picard MarkDuplicates INPUT=./sorted.bam
+                                  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
+            && tar -zcf /dev/stdout ./metrics ./pileup ./calls
+        "
+        -o ./archive.tar.gz
+        -l $cache_log
+        && cat $cache_log
+        && tar -zxvf ./archive.tar.gz
+        && cp ./metrics $metrics
+        && cp ./pileup $pileup
+        && cp ./calls $calls
+    ]]></command>
+    <inputs>
+        <param name="input" label="FASTA Reference from your history" type="data" format="fasta" />
+        <!-- <conditional name="reads">
+            <param name="reads_select" type="select" label="Paired-end collection, or two datasets from your history">
+                <option value="collection">Paired collection from your history</option>
+                <option value="history">Two FASTQ datasets from your history</option>
+            </param>
+            <when value="collection">
+                <param name="coll" type="data_collection" format="fastq,fastqsanger" collection_type="paired">
+            </when>
+            <when value="history">
+                <param type="data" name="forward" format="fastq,fastqsanger" />
+                <param type="data" name="reverse" format="fastq,fastqsanger" />
+            </when>
+        </conditional> -->
+        <param name="sample" label="Read alignment to reference" type="data" format="sam" />
+    </inputs>
+    <outputs>
+        <data name="calls" label="${sample.name.split(' ')[0]} unfiltered SNPs" format="vcf" />
+        <data name="pileup" label="${sample.name.split(' ')[0]} pileup" format="pileup" hidden="true" />
+        <data name="metrics" label="Metrics from Picard" format="txt" hidden="true" />
+        <data label="S3 Cache log" name="cache_log" format="txt" hidden="true" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="reference/lambda_virus.fasta" />
+            <param name="sample" value="samples/sample2/reads.sam" />
+            <output name="calls" value="samples/sample2/var.flt.vcf" />
+            <output name="pileup" value="samples/sample2/reads.all.pileup" />
+        </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