Mercurial > repos > estrain > serotypefinder
view serotypefinder.xml @ 0:1577ee103ed1 draft default tip
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author | estrain |
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date | Wed, 12 Jul 2023 17:09:33 +0000 |
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<tool id="serotypefinder" name="serotypefinder" version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05"> <requirements> <requirement type="package">serotypefinder</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ #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" #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; #end if serotypefinder -x -i $infile ]]></command> <inputs> <conditional name="reads"> <param name="reads_select" type="select" label="Genome assembly or paired-end collection"> <option value="collection">Paired collection 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="genome"> <param label="Genome assembly" name="assembly" type="data" format="fasta"/> </when> </conditional> </inputs> <outputs> <data name="results" format="tabular" from_work_dir="results_tab.tsv" /> </outputs> <help><![CDATA[ Serotype predictions for E.coli. ]]></help> <citations> <citation type="bibtex"> @misc{fleming, title={serotypefinder - Serotype Prediction for E. coli}, journal={epub}, publisher={epub}, author={Scheutz, Flemming}, year={2023}, month={Max}, url={https://bitbucket.org/genomicepidemiology/serotypefinder/src/master}}, </citation> </citations> </tool>