jpayne@0: <tool id="reads_subsampler" name="Subsample FASTQ Reads" version="1.0.0" python_template_version="3.5">
jpayne@0:     <description>to reduce excess genomic coverage</description>
jpayne@0:     <requirements>
jpayne@1:         <requirement type="package" version="3.7">python</requirement>
jpayne@0:     </requirements>
jpayne@0:     <command detect_errors="exit_code"><![CDATA[
jpayne@0:         #if $reads.reads_select == 'collection'
jpayne@0:             python3 ${__tool_directory__}/subsamplr.py '$reads.coll.forward' '$reads.coll.reverse' '$downsampled.forward' '$downsampled.reverse' $coverage $genome_size '$seed'
jpayne@5:         #elif $reads.reads_select == 'single'
jpayne@5:             python3 ${__tool_directory__}/subsamplr.py '$forward' '$forward_out' $coverage $genome_size '$seed'
jpayne@5:         #else 
jpayne@5:             python3 ${__tool_directory__}/subsamplr.py '$forward' '$reverse' $forward_out $reverse_out $coverage $genome_size '$seed'
jpayne@0:         #end if
jpayne@0:     ]]></command>
jpayne@0:     <inputs>
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 representing paired reads, forward and reverse</option>
jpayne@0:                 <option value="single">One FASTQ dataset representing single-end sequencing</option>
jpayne@0:             </param>
jpayne@0:             <when value="collection">
jpayne@0:                 <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@0:                 <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" />
jpayne@0:                 <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" />
jpayne@0:             </when>
jpayne@0:             <when value="single">
jpayne@0:                 <param label="Reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" />
jpayne@0:             </when>
jpayne@0:         </conditional>
jpayne@0:         <param name="coverage" type="integer" label="Maximum Coverage" value="200" />
jpayne@0:         <param name="genome_size" type="select" label="Assumed Genome Size">
jpayne@5:             <option value="5000000">Salmonella, E. Coli, Vibrio p. (5000000)</option>
jpayne@5:             <option value="4000000">Vibrio cholerae (4000000)</option>
jpayne@0:             <option value="2700000">Listeria (2700000)</option>
jpayne@5:             <option value="1600000">Campylobacter (1600000)</option>
jpayne@0:             <option value="29900">SARS-CoV-2 (29900)</option>
jpayne@0:         </param>
jpayne@0:         <param name="seed" type="text" value="ed2b99d842cddc1ac81d7c01a0bf0555" label="Random seed (you don't have to change this)"/>
jpayne@0:     </inputs>
jpayne@0:     <outputs>
jpayne@2:         <data name="forward_out" label="${reads.forward.name}.downsampled" format_source="forward">
jpayne@0:             <filter>reads['reads_select'] == "history" or reads['reads_select'] == "single"</filter>
jpayne@0:         </data>
jpayne@3:         <data name="reverse_out" label="${reads.reverse.name}.downsampled" format_source="reverse">
jpayne@0:             <filter>reads['reads_select'] == "history"</filter>
jpayne@0:         </data>
jpayne@0:         <collection name="downsampled" type="paired" label="${reads.coll.name}" structured_like="reads|coll" format_source="reads|coll">
jpayne@0:             <filter>reads['reads_select'] == "collection"</filter>
jpayne@0:             <data name="forward" label="${reads.coll.forward.name}.downsampled" format_source="reads.coll.forward" />
jpayne@0:             <data name="reverse" label="${reads.coll.reverse.name}.downsampled" format_source="reads.coll.reverse" />
jpayne@0:         </collection>
jpayne@0:     </outputs>
jpayne@0:     <tests>
jpayne@0:         <test>
jpayne@0:             <conditional name="reads">
jpayne@5:                 <param name="reads_select" value="single" />
jpayne@5:                 <param name="forward" value="forward.fastq" />
jpayne@5:             </conditional>
jpayne@5:             <param name="coverage" value="20" />
jpayne@5:             <param name="genome_size" value="29900" />
jpayne@5:             <output name="forward_out" value="forward_out.fastq" />
jpayne@5:         </test>
jpayne@5:         <test>
jpayne@5:             <conditional name="reads">
jpayne@0:                 <param name="reads_select" value="collection" />
jpayne@0:                 <param name="coll">
jpayne@0:                     <collection type="paired">
jpayne@0:                         <element name="forward" value="forward.fastq" ftype="fastqsanger" />
jpayne@0:                         <element name="reverse" value="reverse.fastq" ftype="fastqsanger" />
jpayne@0:                     </collection>
jpayne@0:                 </param>
jpayne@0:             </conditional>
jpayne@0:             <param name="coverage" value="20" />
jpayne@0:             <param name="genome_size" value="29900" />
jpayne@0:             <output_collection name="downsampled" type="paired">
jpayne@0:                 <element name="forward" file="forward_out.fastq" />
jpayne@0:                 <element name="reverse" file="reverse_out.fastq" />
jpayne@0:             </output_collection>
jpayne@0:         </test>
jpayne@0:         <test>
jpayne@0:             <conditional name="reads">
jpayne@0:                 <param name="reads_select" value="history" />
jpayne@0:                 <param name="forward" value="forward.fastq" />
jpayne@0:                 <param name="reverse" value="reverse.fastq" />
jpayne@0:             </conditional>
jpayne@0:             <param name="coverage" value="20" />
jpayne@0:             <param name="genome_size" value="29900" />
jpayne@0:             <output name="forward_out" value="forward_out.fastq" />
jpayne@0:             <output name="reverse_out" value="reverse_out.fastq" /> 
jpayne@0:         </test>
jpayne@0:         <test>
jpayne@0:             <conditional name="reads">
jpayne@0:                 <param name="reads_select" value="history" />
jpayne@0:                 <param name="forward" value="forward.fastq.gz" />
jpayne@0:                 <param name="reverse" value="reverse.fastq.gz" />
jpayne@0:             </conditional>
jpayne@0:             <param name="coverage" value="20" />
jpayne@0:             <param name="genome_size" value="29900" />
jpayne@0:             <output name="forward_out" value="forward_out.fastq.gz"  decompress="true" />
jpayne@0:             <output name="reverse_out" value="reverse_out.fastq.gz"  decompress="true" /> 
jpayne@0:         </test>
jpayne@0:         <test>
jpayne@0:             <conditional name="reads">
jpayne@0:                 <param name="reads_select" value="history" />
jpayne@0:                 <param name="forward" value="forward.fastq.bz2" />
jpayne@0:                 <param name="reverse" value="reverse.fastq.bz2" />
jpayne@0:             </conditional>
jpayne@0:             <param name="coverage" value="20" />
jpayne@0:             <param name="genome_size" value="29900" />
jpayne@0:             <output name="forward_out" value="forward_out.fastq.bz2" decompress="true" />
jpayne@0:             <output name="reverse_out" value="reverse_out.fastq.bz2" decompress="true" /> 
jpayne@0:         </test>
jpayne@0:     </tests>
jpayne@0:     <help><![CDATA[
jpayne@0:         Randomly subsample single or paired-end FASTQ reads to target a certain genomic coverage depth.
jpayne@0:     ]]></help>
jpayne@0:     <citations />
jpayne@0: </tool>