--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snp-pipeline.xml.old	Wed Jan 24 14:18:21 2018 -0500
@@ -0,0 +1,113 @@
+<tool id="snp-pipeline" name="CFSAN SNP Pipeline" version="1.0.1">
+	<description>Build SNP table in VCF format from fastq collections</description>
+    <requirements>
+        <requirement type="package">bowtie2</requirement>
+        <requirement type="package">smalt</requirement>
+        <requirement type="package">samtools</requirement>
+        <requirement type="package">picard</requirement>
+        <requirement type="package">varscan</requirement>
+        <requirement type="package">tabix</requirement>
+        <requirement type="package">bgzip</requirement>
+        <requirement type="package">fastq-dump</requirement>
+        <requirement type="package">biopython</requirement>
+        <requirement type="python-module">snp-pipeline</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        cfsan_snp_pipeline $command -i <(
+        	$__tool_directory__/snp-wind.py 
+        	#for $e in $fastqs
+        		-n $e.forward.display_name -f $e.forward.fastq -r $e.reverse.fastq 
+        	#end for
+        	.
+        )
+        && cat ./error.log 1>&2
+        && source ./snp-unwind.sh
+    ]]></command>
+    <configfiles>
+    	<configfile name="config_file">
+    		
+    	</configfile>
+    </configfiles>
+    <inputs>
+    	<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 GalaxyTraker reference</option>
+    			<option value="history">Use a reference from your history</option>
+    		</param>
+    		<when value="curated">
+    			<param name="reference_fasta" 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_fasta" type="data" format="fasta" label="Select reference fasta" />
+    		</when>
+    	</conditional>
+<!-- 
+    	<param name="fa_vcf" type="select" label="Select FASTA or VCF output for consensus results">
+    		<option value="fa">Consensus results in FASTA format</option>
+    		<option value="vc">Consensus results in VCF format<option>
+    	</param>
+ -->
+ 		<conditional name="input_arrangement">
+ 			<param name="inp" type="select" label="Input data layout">
+ 				<option value="manual">Define paired collections of files from your history</option>
+ 				<option value="collection">Use a paired-end dataset collection</option>
+ 			</param>
+ 		</conditional>
+    	<repeat name="fastqs" title="FASTQ collections">
+    		<param name="forward" type="data" format="fastq,fastqsanger" label="Forward reads" />
+    		<param name="reverse" type="data" format="fastq,fastqsanger" label="Reverse reads" />
+    	</repeat>
+    </inputs>
+
+    <outputs>
+    	<data format="txt" label="SNP List" name="snplist" from_work_dir="snplist.txt"/>
+<!--     	<conditional name="fasta_vcf"> -->
+    		
+    		<data format="fasta" label="Consensus base calls" name="confasta" from_work_dir="consensus.fasta"/>
+    		<data format="fasta" label="Filtered consensus base calls" name="confastafil" from_work_dir="consensus.fasta"/>
+    		<data format="vcf" label="Consensus base calls" name="convcf" from_work_dir="consensus.vcf"/>
+    		<data format="vcf" label="Filtered consensus base calls" name="convcffil" from_work_dir="consensus_preserved.vcf"/>
+<!--     	</conditional> -->
+		<data format="fasta" label="SNP matrix" name="snpma" from_work_dir="snpma.fasta"/>
+		<data format="fasta" label="Filtered SNP matrix" name="snpmalfil" from_work_dir="snpma_preserved.fasta"/>
+		<data format="vcf" label="SNP matrix" name="snpmav" from_work_dir="snpma.vcf"/>
+		<data format="vcf" label="Filtered SNP matrix" name="snpmavfil" from_work_dir="snpma_preserved.vcf"/>
+		
+		<data format="tsv" label="SNP distance, pairwise" name="snpdi" from_work_dir="snp_distance_pairwise.tsv"/>
+		<data format="tsv" label="Filtered SNP distance, pairwise" name="snpdifil" from_work_dir="snp_distance_pairwise_preserved.tsv"/>
+		<data format="tsv" label="SNP distance matrix" name="snpdima" from_work_dir="snp_distance_matrix.tsv"/>
+		<data format="tsv" label="Filtered SNP distance matrix" name="snpdimafil" from_work_dir="snp_distance_matrix_preserved.tsv"/>
+		<data format="fasta" label="Reference SNPs" name="refsnp" from_work_dir="referenceSNP.fasta"/>
+		<data format="fasta" label="Filtered reference SNPs" name="refsnpfil" from_work_dir="referenceSNP_preserved.fasta"/>
+		<data format="tsv" label="Metrics" name="metrics" from_work_dir="metrics.tsv"/>
+
+
+    </outputs>
+    <help><![CDATA[
+<p>
+The <b>CFSAN SNP Pipeline</b> is a Python-based system for the production of SNP matrices from sequence data used in the phylogenetic analysis of pathogenic organisms sequenced from samples of interest to food safety.
+<p>
+The SNP Pipeline was developed by the <b>United States Food and Drug Administration, Center for Food Safety and Applied Nutrition</b>.
+<p>
+Free software.
+Documentation: <a target="_blank" href="http://snp-pipeline.readthedocs.io/en/latest/readme.html">http://snp-pipeline.readthedocs.io/en/latest/readme.html</a>
+Source Code: <a target="_blank" href="https://github.com/CFSAN-Biostatistics/snp-pipeline">https://github.com/CFSAN-Biostatistics/snp-pipeline</a>
+PyPI Distribution: <a target="_blank" href="https://pypi.python.org/pypi/snp-pipeline">https://pypi.python.org/pypi/snp-pipeline</a>
+    ]]></help>
+    <citations>
+        <citation type="doi">10.7717/peerj-cs.20</citation>
+        <citation type="bibtex">
+@misc{cfsan-snp-pipeline,
+  author = {Steve Davis and James Pettengill and Yan Luo and Justin Payne and Albert Shpuntoff and Rugh Rand and Errol Strain},
+  year = {2015},
+  title = {CFSAN SNP Pipeline: an automated method for constructing SNP matrices from next-generation sequence data},
+  url = {https://doi.org/10.7717/peerj-cs.20},
+  journal = {PeerJ Computer Science},
+}</citation>
+    </citations>
+</tool>
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