--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0_index_ref.xml.old	Wed Jan 24 14:18:21 2018 -0500
@@ -0,0 +1,82 @@
+<tool id="index_ref" name="0. Get or Build Index" version="1.0.1" profile="16.10">
+    <description>by lookup from BioProject or from an assembly</description>
+    <requirements>
+        <requirement type="package" version="2.3.4">bowtie2</requirement>
+        <requirement type="package" version="1.6">samtools</requirement>
+        <requirement type="package" version="1.5.11">boto3</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        #if $source.source_select == 'bioproject'
+            ${__tool_directory__}/snp-cache.py snp_bioproject_references "${bioproject}" -o ${output}   &&
+            ${__tool_directory__}/snp-cache.py snp_bioproject_indexes "${bioproject}" -o ${faidx}
+        #else
+        mkdir ./reference                                       &&
+        cp ${input} ./reference/reference.fasta                 &&
+        export ID=\$(md5sum $input | cut -c -32)                &&
+        ${__tool_directory__}/snp-cache.py snp_local_references \$ID
+                -c "
+                    bowtie2-build ./reference/reference.fasta --quiet --threads \${GALAXY_SLOTS:-4} ./reference/reference &&
+                    tar -zcf /dev/stdout ./reference/ref*bt2
+                    "
+                -o ${output}
+                -l $cache_log
+        
+        ##&& ${__tool_directory__}/snp-cache.py snp_local_indexes \$ID
+        ##        -c "
+        ##            samtools faidx ./reference/reference.fasta && cat ./reference/reference.fasta.fai
+        ##        "
+        ##        -o ${faidx}
+        #end if
+        && cat $cache_log
+    ]]></command>
+    <inputs>
+    	<conditional name="source">
+            <param name="source_select" type="select" label="Use the reference associated with a provided BioProject, a curated GalaxyTrakr reference, or a reference from your history">
+                <option value="bioproject">Provide a BioProject</option>
+                <option value="curated">Use a GalaxyTrakr reference</option>
+                <option value="history">Use a reference from your history</option>
+            </param>
+            <when value="bioproject">
+                <param type="data" name="bioproject" format="text"/>
+            </when>
+            <when value="curated">
+    			<param name="input" 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 type="data" name="input" format="fasta" label="Select reference FASTA"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data label="Indexed reference (bt2)" name="output" format="tar" />
+        <!-- <data label="Indexed reference (faidx)" name="faidx" format="fai" /> -->
+        <data label="S3 Cache log" name="cache_log" format="txt" hidden="true" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="source_select" value="history" />
+            <param name="input" value="reference/lambda_virus.fasta" />
+            <output name="output" value="reference/reference.tar.gz" decompress="true" lines_diff="10" />
+            <!-- <output name="faidx" value="reference/reference.fasta.fai" /> -->
+        </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>
+<!--        <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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