estrain@1: <tool id="seqsero2_v1_0_2" name="SeqSero 2 v1.0.2" version="1.0.2">
estrain@1:     <description>Salmonella serotype prediction</description>
estrain@1:     <requirements>
estrain@1:       <requirement type="package" version="3.6">python</requirement>
estrain@1:       <requirement type="package" version="1.74">biopython</requirement>
estrain@1:       <requirement type="package" version="2.7.1">blast</requirement>
estrain@1:       <requirement type="package" version="1.9">samtools</requirement>
estrain@1:       <requirement type="package" version="2.9.1">sra-tools</requirement>
estrain@1:       <requirement type="package" version="0.7.17">bwa</requirement>
estrain@1:       <requirement type="package" version="3.13.1">spades</requirement>
estrain@1:       <requirement type="package" version="2.27.1">bedtools</requirement>
estrain@1:     </requirements>
estrain@1:     <command detect_errors="exit_code"><![CDATA[
estrain@1:       echo "SeqSero 2 v. 1.0.2" ;
estrain@1:       mkdir ./output;
estrain@1: 
estrain@1:       #if $reads.reads_select == 'history'
estrain@1:         #set $name = $reads.forward.name.split('.')[0].replace(' ','_')
estrain@1:         #set $forward = $reads.forward
estrain@1:         #set $reverse = $reads.reverse
estrain@1:         #set $infile = $name + "_1.fastq " +  $name + "_2.fastq" 
estrain@1:         #set $tval = 2
estrain@1:         #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
estrain@1:           gunzip -c $reverse > reverse.fastq;
estrain@1:           #set $reverse = './reverse.fastq'
estrain@1:           gunzip -c $forward > forward.fastq;
estrain@1:           #set $forward = './forward.fastq'
estrain@1:         #end if
estrain@1:         ln -s $forward ${name}_1.fastq;
estrain@1:         ln -s $reverse ${name}_2.fastq;
estrain@1:       #else if $reads.reads_select == 'collection'
estrain@1:         #set $name = $reads.coll.name.replace(' ', '_')
estrain@1:         #set $forward = $reads.coll.forward
estrain@1:         #set $reverse = $reads.coll.reverse
estrain@1:         #set $infile = $name + "_1.fastq " +  $name + "_2.fastq" 
estrain@1:         #set $tval = 2
estrain@1:         #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
estrain@1:           gunzip -c $reverse > reverse.fastq;
estrain@1:           #set $reverse = './reverse.fastq'
estrain@1:           gunzip -c $forward > forward.fastq;
estrain@1:           #set $forward = './forward.fastq'
estrain@1:         #end if
estrain@1:         ln -s $forward ${name}_1.fastq;
estrain@1:         ln -s $reverse ${name}_2.fastq;
estrain@1:       #else 
estrain@1:         #set $name = $reads.assembly.name.replace(' ', '_')
estrain@1:         #set $ga = $reads.assembly
estrain@1:         #set $infile = $name + ".fasta" 
estrain@1:         ln -s $ga ${name}.fasta;
estrain@1:         #set $tval = 4
estrain@1:         #set $mode='k'
estrain@1:       #end if
estrain@1:       echo $name ;
estrain@1:       echo "-=-=-=-=-" ;
estrain@1:       touch output/SeqSero_log.txt ;
estrain@1:       python $__tool_directory__/SeqSero2_package.py
estrain@1:         -p \${GALAXY_SLOTS:-4}
estrain@1:         -t $tval 
estrain@1:         -m $mode
estrain@1:         -d ./output
estrain@1:       #if $mode == 'a':
estrain@1:         -b $maptype 
estrain@1:       #end if
estrain@1:         -i $infile &&
estrain@1:         echo "-=-=-=-=-" &&
estrain@1:         cat output/SeqSero_log.txt &&
estrain@1:         echo "-=-=-=-=-" &&
estrain@1:         ls -lah ./output
estrain@1:     ]]></command>
estrain@1:     <inputs>
estrain@1:         
estrain@1:         <conditional name="reads">
estrain@1:             <param name="reads_select" type="select" label="Genome assembly,paired-end collection, or two datasets from your history">
estrain@1:                 <option value="collection">Paired collection from your history</option>
estrain@1:                 <option value="history">Two FASTQ datasets from your history</option>
estrain@1:                 <option value="genome">Genome Assembly</option>
estrain@1:             </param>
estrain@1:             <when value="collection">
estrain@1:                 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" collection_type="paired" />
estrain@1:             </when>
estrain@1:             <when value="history">
estrain@1:                 <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
estrain@1:                 <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
estrain@1:             </when>
estrain@1:             <when value="genome">
estrain@1:                 <param label="Genome assembly" name="assembly" type="data" format="fasta"/>
estrain@1:             </when>
estrain@1:         </conditional>
estrain@1:      
estrain@1:           <!-- <param name="fastq1" type="data" format="fastq" label="FASTQ paired end read 1" />
estrain@1:           <param name="fastq2" type="data" format="fastq" label="FASTQ paired end read 2" /> -->
estrain@1:           <!-- <param name="numofthr" type="select" label="Number of threads">
estrain@1:           <option value="1">1</option>
estrain@1:           <option value="2">2</option>
estrain@1:           <option value="3">3</option>
estrain@1:           <option value="4">4</option> -->
estrain@1:         <!-- </param> -->
estrain@1:         
estrain@1:         <param label="Analysis mode" type="select" name="mode">
estrain@1:          <option value="a">allele mode</option>
estrain@1:          <option value="k">k-mer mode</option>
estrain@1:         </param>
estrain@1: 
estrain@1:         <param name="maptype" type="select" label="Algorithms for BWA mapping">
estrain@1:           <option value="mem">mem</option>
estrain@1:           <option value="sam">sam</option>
estrain@1:         </param>
estrain@1: 
estrain@1:     
estrain@1: 
estrain@1:     </inputs>
estrain@1:     <outputs>
estrain@1:       <data format="tabular" label="SeqSero Results" name="results" from_work_dir="output/SeqSero_result.txt"/>
estrain@1:     </outputs>
estrain@1:     <tests>
estrain@1:        <!-- <test>
estrain@1:          <param name="reads_select" value="history" />
estrain@1:          <param name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
estrain@1:          <param name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />
estrain@1:          <output name="results" file="Seqsero_result.tsv" />
estrain@1:        </test>
estrain@1:        <test>
estrain@1:         <param name="reads_select" value="collection" />
estrain@1:         <param name="coll">
estrain@1:             <collection type="paired">
estrain@1:                 <element name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
estrain@1:                 <element name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />
estrain@1:             </collection>
estrain@1:         </param>
estrain@1:         <output name="results" file="Seqsero_result.tsv" />
estrain@1:        </test> -->
estrain@1:         <test>
estrain@1:          <param name="mode" value="k" />
estrain@1:          <param name="reads_select" value="history" />
estrain@1:          <param name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger" />
estrain@1:          <param name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger" />
estrain@1:          <output name="results" file="Seqsero_result_25k.tsv" />
estrain@1:        </test>
estrain@1:        <test>
estrain@1:         <param name="mode" value="k" />
estrain@1:         <param name="reads_select" value="collection" />
estrain@1:         <param name="coll">
estrain@1:             <collection type="paired">
estrain@1:                 <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
estrain@1:                 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
estrain@1:             </collection>
estrain@1:         </param>
estrain@1:         <output name="results" file="Seqsero_result_25k_coll.tsv" />
estrain@1:        </test>
estrain@1:         <test>
estrain@1:          <param name="mode" value="a" />
estrain@1:          <param name="reads_select" value="history" />
estrain@1:          <param name="forward" value="forward_250k.fastq.gz" ftype="fastqsanger" />
estrain@1:          <param name="reverse" value="reverse_250k.fastq.gz" ftype="fastqsanger" />
estrain@1:          <assert_stdout>
estrain@1:           <has_text text="predicted antigenic profile does not exist" />
estrain@1:          </assert_stdout>
estrain@1:        </test>
estrain@1:        <!-- <test>
estrain@1:         <param name="mode" value="a" />
estrain@1:         <param name="reads_select" value="collection" />
estrain@1:         <param name="coll">
estrain@1:             <collection type="paired">
estrain@1:                 <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
estrain@1:                 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
estrain@1:             </collection>
estrain@1:         </param>
estrain@1:         <output name="results" file="Seqsero_result_allele.tsv" />
estrain@1:        </test> -->
estrain@1:     </tests>
estrain@1:     <help><![CDATA[
estrain@1:     
estrain@1: **Usage: SeqSero2.py** 
estrain@1: 
estrain@1: **Algorithms for BWA mapping**
estrain@1: 
estrain@1: 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now SeqSero2 is only optimized for "mem" mode
estrain@1:    
estrain@1:     ]]></help>
estrain@1:     <citations>
estrain@1:        <citation type="bibtex">
estrain@1:         @misc{zhang_yin_jones_zhang_deathrage_dinsmore_fitzgeral_fields_deng_2015,
estrain@1:         title={Salmonella serotype determination utilizing high-throughput genome sequencing data.},
estrain@1:         journal={J Clin Microbiol}, publisher={ASM},
estrain@1:         author={Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X.},
estrain@1:         year={2015}, month={Max},
estrain@1:         url={http://http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15}},
estrain@1:        }</citation>
estrain@1:        <citation type="bibtex">
estrain@1:         @misc{cfsan_biostatistics_group_2017,
estrain@1:         title={CFSAN Biostatistics Group fork of SeqSero2},
estrain@1:         url={https://github.com/CFSAN-Biostatistics/SeqSero2.git}},
estrain@1:        </citation>
estrain@1:     </citations>
estrain@1: 
estrain@1: </tool>