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author | cstrittmatter |
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date | Mon, 27 Apr 2020 12:36:27 -0400 |
parents | 9811f8cd313d |
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<tool id="seqsero2v110" name="SeqSero2 v1.1.0" version="2"> <description>Salmonella serotype prediction</description> <requirements> <requirement type="package" version="3.6">python</requirement> <requirement type="package" version="1.74">biopython</requirement> <requirement type="package" version="2.7.1">blast</requirement> <requirement type="package" version="1.9">samtools</requirement> <requirement type="package" version="2.9.1">sra-tools</requirement> <requirement type="package" version="0.7.17">bwa</requirement> <requirement type="package" version="3.13.1">spades</requirement> <requirement type="package" version="2.27.1">bedtools</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ echo "SeqSero2 v1.1.2" ; mkdir ./output; #if $reads.reads_select == 'history' #set $name = $reads.forward.name.split('.')[0].replace(' ','_') #set $forward = $reads.forward #set $reverse = $reads.reverse #set $infile = $name + "_1.fastq " + $name + "_2.fastq" #set $tval = 2 #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz') gunzip -c $reverse > reverse.fastq; #set $reverse = './reverse.fastq' gunzip -c $forward > forward.fastq; #set $forward = './forward.fastq' #end if ln -s $forward ${name}_1.fastq; ln -s $reverse ${name}_2.fastq; #else if $reads.reads_select == 'collection' #set $name = $reads.coll.name.replace(' ', '_') #set $forward = $reads.coll.forward #set $reverse = $reads.coll.reverse #set $infile = $name + "_1.fastq " + $name + "_2.fastq" #set $tval = 2 #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz') gunzip -c $reverse > reverse.fastq; #set $reverse = './reverse.fastq' gunzip -c $forward > forward.fastq; #set $forward = './forward.fastq' #end if ln -s $forward ${name}_1.fastq; ln -s $reverse ${name}_2.fastq; #else #set $name = $reads.assembly.name.replace(' ', '_') #set $ga = $reads.assembly #set $infile = $name + ".fasta" ln -s $ga ${name}.fasta; #set $tval = 4 #set $mode='k' #end if echo $name ; echo "-=-=-=-=-" ; touch output/SeqSero_log.txt ; python $__tool_directory__/bin/SeqSero2_package.py -p \${GALAXY_SLOTS:-4} -t $tval -m $mode -d ./output #if $mode == 'a': -b $maptype #end if -i $infile && echo "-=-=-=-=-" && cat output/SeqSero_log.txt && echo "-=-=-=-=-" && ls -lah ./output ]]></command> <inputs> <conditional name="reads"> <param name="reads_select" type="select" label="Genome assembly,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> <option value="genome">Genome Assembly</option> </param> <when value="collection"> <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" collection_type="paired" /> </when> <when value="history"> <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" /> <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" /> </when> <when value="genome"> <param label="Genome assembly" name="assembly" type="data" format="fasta"/> </when> </conditional> <!-- <param name="fastq1" type="data" format="fastq" label="FASTQ paired end read 1" /> <param name="fastq2" type="data" format="fastq" label="FASTQ paired end read 2" /> --> <!-- <param name="numofthr" type="select" label="Number of threads"> <option value="1">1</option> <option value="2">2</option> <option value="3">3</option> <option value="4">4</option> --> <!-- </param> --> <param label="Analysis mode" type="select" name="mode"> <option value="a">allele mode</option> <option value="k">k-mer mode</option> </param> <param name="maptype" type="select" label="Algorithms for BWA mapping"> <option value="mem">mem</option> <option value="sam">sam</option> </param> </inputs> <outputs> <data format="tabular" label="SeqSero Results" name="results" from_work_dir="output/SeqSero_result.txt"/> </outputs> <tests> <!-- <test> <param name="reads_select" value="history" /> <param name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" /> <param name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" /> <output name="results" file="Seqsero_result.tsv" /> </test> <test> <param name="reads_select" value="collection" /> <param name="coll"> <collection type="paired"> <element name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" /> <element name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" /> </collection> </param> <output name="results" file="Seqsero_result.tsv" /> </test> --> <test> <param name="mode" value="k" /> <param name="reads_select" value="history" /> <param name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger" /> <param name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger" /> <output name="results" file="Seqsero_result_25k.tsv" /> </test> <test> <param name="mode" value="k" /> <param name="reads_select" value="collection" /> <param name="coll"> <collection type="paired"> <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" /> <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" /> </collection> </param> <output name="results" file="Seqsero_result_25k_coll.tsv" /> </test> <test> <param name="mode" value="a" /> <param name="reads_select" value="history" /> <param name="forward" value="forward_250k.fastq.gz" ftype="fastqsanger" /> <param name="reverse" value="reverse_250k.fastq.gz" ftype="fastqsanger" /> <assert_stdout> <has_text text="predicted antigenic profile does not exist" /> </assert_stdout> </test> <!-- <test> <param name="mode" value="a" /> <param name="reads_select" value="collection" /> <param name="coll"> <collection type="paired"> <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" /> <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" /> </collection> </param> <output name="results" file="Seqsero_result_allele.tsv" /> </test> --> </tests> <help><![CDATA[ **Usage: SeqSero2.py** **Algorithms for BWA mapping** 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now SeqSero2 is only optimized for "mem" mode ]]></help> <citations> <citation type="bibtex"> @misc{zhang_yin_jones_zhang_deathrage_dinsmore_fitzgeral_fields_deng_2015, title={Salmonella serotype determination utilizing high-throughput genome sequencing data.}, journal={J Clin Microbiol}, publisher={ASM}, author={Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X.}, year={2015}, month={Max}, url={http://http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15}}, }</citation> <citation type="bibtex"> @misc{cfsan_biostatistics_group_2017, title={CFSAN Biostatistics Group fork of SeqSero2}, url={https://github.com/CFSAN-Biostatistics/SeqSero2.git}}, </citation> </citations> </tool>