jpayne@0: <tool id="map_reads" name="1. Map Reads" version="1.0.1" profile="16.10">
jpayne@0:     <description>to index, or lookup cached alignment</description>
jpayne@0:     <requirements>
jpayne@62:         <container type="docker">quay.io/staphb/cfsan-snp-pipeline</container>
jpayne@62:         <!-- <requirement type="package" version="1.0.8">bzip2</requirement>
jpayne@58:         <requirement type="package" version="2.4.5">bowtie2</requirement>
jpayne@62:         <requirement type="package" version="1.9.134">boto3</requirement> -->
jpayne@58:         <!-- <requirement type="package" version="3.6.8">python</requirement> -->
jpayne@0:     </requirements>
jpayne@0:     <command detect_errors="exit_code"><![CDATA[
jpayne@40:         export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
jpayne@0:         #if $reads.reads_select == 'collection'
jpayne@44:             #set forward=$reads.coll.forward
jpayne@44:             #set reverse=$reads.coll.reverse
jpayne@0:         #end if
jpayne@9:         python ${__tool_directory__}/snp-cache.py snp_mapped_reads 
jpayne@0:             "\$(md5sum  $reference
jpayne@44:                         $forward
jpayne@44:                         $reverse 
jpayne@0:                         | cut -c -32 | md5sum | cut -c -32)"
jpayne@0:             -c "
jpayne@0:                 cp $reference ./reference.fasta
jpayne@44:                 #if $forward.is_of_type("fastq.gz","fastqsanger.gz")
jpayne@44:                     && cp $forward ./forward.gz
jpayne@44:                     #set $forward="./forward.gz"
jpayne@44:                 #else if $forward.is_of_type("fastq.bz2", "fastqsanger.bz2")
jpayne@44:                     && cp $forward ./forward.bz2
jpayne@44:                     #set $forward="./forward.bz2"
jpayne@44:                 #end if
jpayne@44:                 #if $reverse.is_of_type("fastq.gz","fastqsanger.gz")
jpayne@44:                     && cp $reverse ./reverse.gz
jpayne@44:                     #set $reverse="./reverse.gz"
jpayne@44:                 #else if $reverse.is_of_type("fastq.bz2", "fastqsanger.bz2")
jpayne@44:                     && cp $reverse ./reverse.bz2
jpayne@44:                     #set $reverse="./reverse.bz2"
jpayne@44:                 #end if
jpayne@0:                 && bowtie2-build ./reference.fasta --quiet --threads \${GALAXY_SLOTS:-4} ./reference
jpayne@44:                 && bowtie2 -q -x ./reference -1 $forward -2 $reverse  -p \${GALAXY_SLOTS:-4} --reorder -X 1000
jpayne@0:                 "
jpayne@0:         #if $reads.reads_select == 'collection'
jpayne@0:             -o ${align_from_collection}
jpayne@0:         #else
jpayne@0:             -o ${align_from_history}
jpayne@0:         #end if
jpayne@0:             -l $cache_log
jpayne@0:         && cat $cache_log
jpayne@0:         #if $source.source_select == 'curated'
jpayne@0:         && cp $reference $ref_out
jpayne@0:         #end if
jpayne@0:     ]]></command>
jpayne@0:     <inputs>
jpayne@0:         <!-- <conditional name="source">
jpayne@0:             <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">
jpayne@0:                 <option value="bioproject">Provide a BioProject</option>
jpayne@0:                 <option value="curated">Use a GalaxyTrakr reference</option>
jpayne@0:                 <option value="history">Use a reference from your history</option>
jpayne@0:             </param>
jpayne@0:             <when value="bioproject">
jpayne@0:                 <param type="data" name="bioproject" format="text" />
jpayne@0:             </when>
jpayne@0:             <when value="curated">
jpayne@0:     			<param name="input" type="select" label="Select reference fasta">
jpayne@0:     				<options from_data_table="all_fasta">
jpayne@0:     				    <filter type="sort_by" column="2"/>
jpayne@0:         				<validator type="no_options" message="No assemblies are available for the selected input dataset"/>
jpayne@0:     				</options>
jpayne@0:     			</param>
jpayne@0:     		</when>
jpayne@0:             <when value="history">
jpayne@0:                 <param type="data" name="input" format="fasta" label="Select reference FASTA"/>
jpayne@0:             </when>
jpayne@0:         </conditional> -->
jpayne@0:         <conditional name="source">
jpayne@0:             <param name="source_select" type="select" label="Use a curated GalaxyTrakr reference or a reference from your history">
jpayne@0:                 <option value="curated">Use a GalaxyTrakr reference</option>
jpayne@0:                 <option value="history">Use a reference from your history</option>
jpayne@0:             </param>
jpayne@0:             <when value="curated">
jpayne@0:     			<param name="reference" type="select" label="Select reference fasta">
jpayne@0:     				<options from_data_table="all_fasta">
jpayne@0:     				    <filter type="sort_by" column="2"/>
jpayne@0:         				<validator type="no_options" message="No assemblies are available for the selected input dataset"/>
jpayne@0:     				</options>
jpayne@0:     			</param>
jpayne@0:     		</when>
jpayne@0:             <when value="history">
jpayne@0:                 <param type="data" name="reference" format="fasta" label="Select reference FASTA"/>
jpayne@0:             </when>
jpayne@0:         </conditional>
jpayne@0:         <conditional name="reads">
jpayne@0:             <param name="reads_select" type="select" label="Paired-end collection, or two datasets from your history">
jpayne@0:                 <option value="collection">Paired collection from your history</option>
jpayne@0:                 <option value="history">Two FASTQ datasets from your history</option>
jpayne@0:             </param>
jpayne@0:             <when value="collection">
jpayne@44:                 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" />
jpayne@0:             </when>
jpayne@0:             <when value="history">
jpayne@44:                 <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" />
jpayne@44:                 <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" />
jpayne@0:             </when>
jpayne@0:         </conditional>
jpayne@0:     </inputs>
jpayne@0:     <outputs>
jpayne@0:         <data label="${reads.coll.name} alignment" name="align_from_collection" format="sam">
jpayne@0:             <filter>reads['reads_select'] == 'collection'</filter>
jpayne@0:         </data>
jpayne@0:         <data label="${reads.forward.name.split('_')[0]} alignment" name="align_from_history" format="sam">
jpayne@0:             <filter>reads['reads_select'] == 'history'</filter>
jpayne@0:         </data>
jpayne@0:         <data label="S3 Cache log" name="cache_log" format="txt" hidden="true" />
jpayne@0:         <data label="Reference" name="ref_out" format="fasta" hidden="true">
jpayne@0:             <filter>source['source_select'] == curated</filter>
jpayne@0:         </data>
jpayne@0:     </outputs>
jpayne@0:     <tests>
jpayne@0:         <test>
jpayne@0:             <param name="source_select" value="history" />
jpayne@0:             <param name="reference" value="reference/lambda_virus.fasta" ftype="fasta" />
jpayne@0:             <param name="reads_select" value="history" />
jpayne@0:             <param name="forward" value="samples/sample1/sample1_1.fastq" ftype="fastqsanger" />
jpayne@0:             <param name="reverse" value="samples/sample1/sample1_2.fastq" ftype="fastqsanger" />
jpayne@0:             <output name="align_from_history" value="samples/sample1/reads.sam" lines_diff="3" />
jpayne@0:         </test>
jpayne@0:         <test>
jpayne@0:             <param name="source_select" value="history" />
jpayne@0:             <param name="reference" value="reference/lambda_virus.fasta" ftype="fasta" />
jpayne@0:             <param name="reads_select" value="collection" />
jpayne@0:             <param name="coll">
jpayne@0:                 <collection type="paired">
jpayne@0:                     <element name="forward" value="samples/sample1/sample1_1.fastq" ftype="fastqsanger" />
jpayne@0:                     <element name="reverse" value="samples/sample1/sample1_2.fastq" ftype="fastqsanger" />
jpayne@0:                 </collection>
jpayne@0:             </param>
jpayne@0:             <output name="align_from_collection" value="samples/sample1/reads.sam" lines_diff="3" />
jpayne@0:         </test>
jpayne@44:         <test>
jpayne@44:             <param name="source_select" value="history" />
jpayne@44:             <param name="reference" value="reference/lambda_virus.fasta" ftype="fasta" />
jpayne@44:             <param name="reads_select" value="history" />
jpayne@44:             <param name="forward" value="samples/sample1/sample1_1.fastq.gz" ftype="fastqsanger.gz" />
jpayne@44:             <param name="reverse" value="samples/sample1/sample1_2.fastq.gz" ftype="fastqsanger.gz" />
jpayne@44:             <output name="align_from_history" value="samples/sample1/reads.sam" lines_diff="3" />
jpayne@44:         </test>
jpayne@0:     </tests>
jpayne@0:     <help><![CDATA[
jpayne@0:        <a href="http://snp-pipeline.readthedocs.io/en/latest/index.html">http://snp-pipeline.readthedocs.io/en/latest/index.html</a>
jpayne@0:     ]]></help>
jpayne@0:     <citations>
jpayne@0:         <citation type="doi">10.7717/peerj-cs.20</citation>
jpayne@0:         <!-- <citation type="bibtex">
jpayne@0: @misc{cfsan-snp-pipeline,
jpayne@0:   author = {Steve Davis and James Pettengill and Yan Luo and Justin Payne and Albert Shpuntoff and Rugh Rand and Errol Strain},
jpayne@0:   year = {2015},
jpayne@0:   title = {CFSAN SNP Pipeline: an automated method for constructing SNP matrices from next-generation sequence data},
jpayne@0:   url = {https://doi.org/10.7717/peerj-cs.20},
jpayne@0:   journal = {PeerJ Computer Science},
jpayne@0: }</citation> -->
jpayne@0:     </citations>
jpayne@0: </tool>