--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/1_map_reads.xml	Wed Jan 24 14:18:21 2018 -0500
@@ -0,0 +1,136 @@
+<tool id="map_reads" name="1. Map Reads" version="1.0.1" profile="16.10">
+    <description>to index, or lookup cached alignment</description>
+    <requirements>
+        <requirement type="package" version="2.3.4">bowtie2</requirement>
+        <requirement type="package" version="1.5.11">boto3</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        #if $reads.reads_select == 'collection'
+            export files="$reads.coll.forward $reads.coll.reverse"          &&
+            export params="-1 $reads.coll.forward -2 $reads.coll.reverse"   &&
+        #else
+            export files="$forward $reverse"                    &&
+            export params="-1 $forward -2 $reverse"             &&
+        #end if
+        ${__tool_directory__}/snp-cache.py snp_mapped_reads 
+            "\$(md5sum  $reference
+                        \$files 
+                        | cut -c -32 | md5sum | cut -c -32)"
+            -c "
+                cp $reference ./reference.fasta
+                && bowtie2-build ./reference.fasta --quiet --threads \${GALAXY_SLOTS:-4} ./reference
+                && bowtie2 -q -x ./reference \$params  -p \${GALAXY_SLOTS:-4} --reorder -X 1000
+                "
+        #if $reads.reads_select == 'collection'
+            -o ${align_from_collection}
+        #else
+            -o ${align_from_history}
+        #end if
+            -l $cache_log
+        && cat $cache_log
+        #if $source.source_select == 'curated'
+        && cp $reference $ref_out
+        #end if
+    ]]></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> -->
+        <conditional name="source">
+            <param name="source_select" type="select" label="Use a curated GalaxyTrakr reference or a reference from your history">
+                <option value="curated">Use a GalaxyTrakr reference</option>
+                <option value="history">Use a reference from your history</option>
+            </param>
+            <when value="curated">
+    			<param name="reference" 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="reference" format="fasta" label="Select reference FASTA"/>
+            </when>
+        </conditional>
+        <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 label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger" collection_type="paired" />
+            </when>
+            <when value="history">
+                <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger" />
+                <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger" />
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data label="${reads.coll.name} alignment" name="align_from_collection" format="sam">
+            <filter>reads['reads_select'] == 'collection'</filter>
+        </data>
+        <data label="${reads.forward.name.split('_')[0]} alignment" name="align_from_history" format="sam">
+            <filter>reads['reads_select'] == 'history'</filter>
+        </data>
+        <data label="S3 Cache log" name="cache_log" format="txt" hidden="true" />
+        <data label="Reference" name="ref_out" format="fasta" hidden="true">
+            <filter>source['source_select'] == curated</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="source_select" value="history" />
+            <param name="reference" value="reference/lambda_virus.fasta" ftype="fasta" />
+            <param name="reads_select" value="history" />
+            <param name="forward" value="samples/sample1/sample1_1.fastq" ftype="fastqsanger" />
+            <param name="reverse" value="samples/sample1/sample1_2.fastq" ftype="fastqsanger" />
+            <output name="align_from_history" value="samples/sample1/reads.sam" lines_diff="3" />
+        </test>
+        <test>
+            <param name="source_select" value="history" />
+            <param name="reference" value="reference/lambda_virus.fasta" ftype="fasta" />
+            <param name="reads_select" value="collection" />
+            <param name="coll">
+                <collection type="paired">
+                    <element name="forward" value="samples/sample1/sample1_1.fastq" ftype="fastqsanger" />
+                    <element name="reverse" value="samples/sample1/sample1_2.fastq" ftype="fastqsanger" />
+                </collection>
+            </param>
+            <output name="align_from_collection" value="samples/sample1/reads.sam" lines_diff="3" />
+        </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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