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seqsero.xml |
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| diff -r 2f81c626194a -r ff697abc6b11 seqsero.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/seqsero.xml Wed Sep 11 06:50:04 2019 -0400 |
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| @@ -0,0 +1,79 @@ +<tool id="seqsero_v1" name="seqsero_v1" version="1.0"> + <requirements> + <requirement type="package" version="2.7">python</requirement> + <requirement type="package" version="1.65">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> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + #if $jobtype.select == "asm" + ln -s $jobtype.draft sample.fasta; + #else if $jobtype.select == "se" + ln -s $jobtype.fastq1 sample_1.fastq; + #else if $jobtype.select == "pe" + ln -s $jobtype.fastq1 sample_1.fastq; + ln -s $jobtype.fastq2 sample_2.fastq; + #end if + + $__tool_directory__/SeqSero.py + #if $jobtype.select == "asm" + -m 4 + -i sample.fasta + #else if $jobtype.select == "se" + -m 3 + -i sample_1.fastq + #else if $jobtype.select == "pe" + -m 2 + -i sample_1.fastq sample_2.fastq + #end if + -b $maptype.select + ; cat SeqSero_result*/Seqsero_result.txt > results.txt; + + ]]></command> + <inputs> + <conditional name="jobtype"> + <param name="select" type="select" label="Assembly or FASTQ Reads?"> + <option value="asm">Genome Assembly</option> + <option value="se">Single-End Reads</option> + <option value="pe">Paired-End Reads</option> + </param> + <when value="asm"> + <param name="draft" type="data" format="fasta" label="FASTA" /> + </when> + <when value="se"> + <param name="fastq1" type="data" format="fastq" label="FASTQ" /> + </when> + <when value="pe"> + <param name="fastq1" type="data" format="fastq" label="FASTQ" /> + <param name="fastq2" type="data" format="fastq" label="FASTQ" /> + </when> + </conditional> + + <conditional name="maptype"> + <param name="select" type="select" label="Algorithms for BWA mapping?"> + <option value="sam">sam</option> + <option value="mem">mem</option> + </param> + </conditional> + + </inputs> + <outputs> + <data format="txt" label="SeqSero Results" name="results" from_work_dir="results.txt"/> + </outputs> + <help><![CDATA[ + + ]]></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> + </citations> + +</tool> |