jpayne@4: <tool id="seqsero_v2" name="SeqSero 2" version="65b863a">
jpayne@0:     <description>Salmonella serotype prediction</description>
jpayne@0:     <requirements>
jpayne@1:       <requirement type="package" version="3.6">python</requirement>
jpayne@1:       <requirement type="package" version="1.70">biopython</requirement>
jpayne@1:       <requirement type="package" version="2.7.1">blast</requirement>
jpayne@0:       <requirement type="package" version="1.9">samtools</requirement>
jpayne@1:       <requirement type="package" version="2.9.1">sra-tools</requirement>
jpayne@0:       <requirement type="package" version="0.7.17">bwa</requirement>
jpayne@1:       <requirement type="package" version="3.12.0">spades</requirement>
jpayne@0:       <requirement type="package" version="2.27.1">bedtools</requirement>
jpayne@0:     </requirements>
jpayne@0:     <command detect_errors="exit_code"><![CDATA[
jpayne@3:       #if $reads.reads_select == 'history'
jpayne@3:       #set $name = $reads.forward.name.split('.')[0].replace(' ','_')
jpayne@3:       #set $forward = $reads.forward
jpayne@3:       #set $reverse = $reads.reverse
jpayne@0:       #else
jpayne@3:       #set $name = $reads.coll.name.replace(' ', '_')
jpayne@3:       #set $forward = $reads.coll.forward
jpayne@3:       #set $reverse = $reads.coll.reverse
jpayne@0:       #end if
jpayne@2:         echo $name ;
jpayne@2:         echo "-=-=-=-=-" ;
jpayne@3:       #if $forward.is_of_type('fastq.gz', 'fastqsanger.gz')
jpayne@2:         gunzip -c $forward > forward.fastq;
jpayne@3:       #set $forward = './forward.fastq'
jpayne@0:       #end if
jpayne@3:       #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
jpayne@2:         gunzip -c $reverse > reverse.fastq;
jpayne@3:       #set $reverse = './reverse.fastq'
jpayne@0:       #end if
jpayne@3:         ln -s $forward ${name}_1.fastq;
jpayne@3:         ln -s $reverse ${name}_2.fastq;
jpayne@3:         mkdir ./output;
jpayne@2:         python $__tool_directory__/SeqSero2/SeqSero2_package.py
jpayne@2:         -p \${GALAXY_SLOTS:-4}
jpayne@2:         -t 2
jpayne@2:         -m $mode
jpayne@2:         -d ./output
jpayne@2:       #if $mode == 'a':
jpayne@2:         -b $maptype 
jpayne@2:       #end if
jpayne@2:         -i ${name}_1.fastq ${name}_2.fastq &&
jpayne@2:         echo "-=-=-=-=-" &&
jpayne@2:         cat output/SeqSero_log.txt &&
jpayne@2:         echo "-=-=-=-=-" &&
jpayne@2:         ls -lah ./output
jpayne@0:     ]]></command>
jpayne@0:     <inputs>
jpayne@0:         
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@0:                 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" 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" />
jpayne@0:                 <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
jpayne@0:             </when>
jpayne@0:         </conditional>
jpayne@0:      
jpayne@0:           <!-- <param name="fastq1" type="data" format="fastq" label="FASTQ paired end read 1" />
jpayne@0:           <param name="fastq2" type="data" format="fastq" label="FASTQ paired end read 2" /> -->
jpayne@0:           <!-- <param name="numofthr" type="select" label="Number of threads">
jpayne@0:           <option value="1">1</option>
jpayne@0:           <option value="2">2</option>
jpayne@0:           <option value="3">3</option>
jpayne@0:           <option value="4">4</option> -->
jpayne@0:         <!-- </param> -->
jpayne@2:         
jpayne@2:         <param label="Analysis mode" type="select" name="mode">
jpayne@2:             <option value="k">k-mer mode</option>
jpayne@2:             <option value="a">allele mode</option>
jpayne@2:         </param>
jpayne@2: 
jpayne@2:         <param name="maptype" type="select" label="Algorithms for BWA mapping">
jpayne@0:           <option value="mem">mem</option>
jpayne@0:           <option value="sam">sam</option>
jpayne@0:         </param>
jpayne@2: 
jpayne@0:     
jpayne@0: 
jpayne@0:     </inputs>
jpayne@0:     <outputs>
jpayne@1:       <data format="tabular" label="SeqSero Results" name="results" from_work_dir="output/Seqsero_result.tsv"/>
jpayne@0:     </outputs>
jpayne@0:     <tests>
jpayne@1:        <!-- <test>
jpayne@1:          <param name="reads_select" value="history" />
jpayne@1:          <param name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
jpayne@1:          <param name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />
jpayne@1:          <output name="results" file="Seqsero_result.tsv" />
jpayne@1:        </test>
jpayne@0:        <test>
jpayne@1:         <param name="reads_select" value="collection" />
jpayne@1:         <param name="coll">
jpayne@1:             <collection type="paired">
jpayne@1:                 <element name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
jpayne@1:                 <element name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />
jpayne@1:             </collection>
jpayne@1:         </param>
jpayne@1:         <output name="results" file="Seqsero_result.tsv" />
jpayne@1:        </test> -->
jpayne@1:         <test>
jpayne@1:          <param name="mode" value="k" />
jpayne@0:          <param name="reads_select" value="history" />
jpayne@3:          <param name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger" />
jpayne@3:          <param name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger" />
jpayne@1:          <output name="results" file="Seqsero_result_25k.tsv" />
jpayne@0:        </test>
jpayne@0:        <test>
jpayne@1:         <param name="mode" value="k" />
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_25k.fastq.gz" ftype="fastqsanger.gz" />
jpayne@0:                 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
jpayne@0:             </collection>
jpayne@0:         </param>
jpayne@1:         <output name="results" file="Seqsero_result_25k_coll.tsv" />
jpayne@0:        </test>
jpayne@1:        <!-- <test>
jpayne@1:         <param name="mode" value="a" />
jpayne@1:         <param name="reads_select" value="collection" />
jpayne@1:         <param name="coll">
jpayne@1:             <collection type="paired">
jpayne@1:                 <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
jpayne@1:                 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
jpayne@1:             </collection>
jpayne@1:         </param>
jpayne@1:         <output name="results" file="Seqsero_result_allele.tsv" />
jpayne@1:        </test> -->
jpayne@0:     </tests>
jpayne@0:     <help><![CDATA[
jpayne@0:     
jpayne@0: **Usage: SeqSero2.py** 
jpayne@0: 
jpayne@0: **Algorithms for BWA mapping**
jpayne@0: 
jpayne@0: 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now SeqSero2 is only optimized for "mem" mode
jpayne@0:    
jpayne@0:     ]]></help>
jpayne@0:     <citations>
jpayne@0:        <citation type="bibtex">
jpayne@0:         @misc{zhang_yin_jones_zhang_deathrage_dinsmore_fitzgeral_fields_deng_2015,
jpayne@0:         title={Salmonella serotype determination utilizing high-throughput genome sequencing data.},
jpayne@0:         journal={J Clin Microbiol}, publisher={ASM},
jpayne@0:         author={Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X.},
jpayne@0:         year={2015}, month={Max},
jpayne@0:         url={http://http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15}},
jpayne@0:        }</citation>
jpayne@0:     </citations>
jpayne@0: 
jpayne@0: </tool>