Mercurial > repos > estrain > confindr
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author | estrain |
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date | Sun, 21 Oct 2018 08:19:28 -0400 |
parents | 454e2f1ccff4 |
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<tool id="confindr" name="confindr" label="Detect sequence contamination using rMLST" version="0.1.3"> <requirements> <requirement type="package" version="0.4.3">confindr</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ mkdir in out; #if $jobtype.select == "fastq_single" perl $__tool_directory__/makein.pl in $jobtype.fastq1 $jobtype.fastq1.name; #else if $jobtype.select == "fastq_fr" perl $__tool_directory__/makein.pl in $jobtype.fastq1 $jobtype.fastq1.name; perl $__tool_directory__/makein.pl in $jobtype.fastq2 $jobtype.fastq2.name; #else if $jobtype.select == "fastq_pair" perl $__tool_directory__/makein.pl in $jobtype.coll.forward $jobtype.coll.forward.name; perl $__tool_directory__/makein.pl in $jobtype.coll.reverse $jobtype.coll.reverse.name; #end if confindr.py -i in -o out #if $options.select=="advanced" #if $options.threads -t $options.threads #end if #if $options.quality -q $options.quality #end if #if $options.basecut -b $options.basecut #end if #if $options.basefrac -bf $options.basefrac #end if #if $options.datatype -dt $options.datatype #end if #else if $options.select=="basic" -t \${GALAXY_SLOTS:-1} #end if ]]></command> <inputs> <conditional name="jobtype"> <param name="select" type="select" label="Select Input"> <option value="fastq_single">Single FASTQ</option> <option value="fastq_fr">Forward and Reverse FASTQ</option> <option value="fastq_pair">Paired FASTQ Collection</option> </param> <when value="fastq_single"> <param name="fastq1" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="FASTQ" /> </when> <when value="fastq_fr"> <param name="fastq1" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="Forward FASTQ" /> <param name="fastq2" type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" label="Reverse FASTQ" /> </when> <when value="fastq_pair"> <param name="coll" label="Paired FASTQ" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz,fastq.bz2,fastqsanger.bz2" collection_type="paired" /> </when> </conditional> <conditional name="options"> <param name="select" type="select" label="Basic or Advanced Settings"> <option value="basic">Basic</option> <option value="advanced">Advanced</option> </param> <when value="advanced"> <param name="threads" optional="true" type="integer" label="Number of threads (Default=all)" value=""/> <param name="quality" optional="true" type="integer" label="Base quality needed to support a multiple allele call (Default=20)" value=""/> <param name="basecut" optional="true" type="integer" label="Number of bases necessary to support a multiple allele call (Default=2)" value=""/> <param name="basefrac" optional="true" type="float" label="Fraction of bases necessary to support a multiple call." value=""> <validator type="in_range" message="Must be float(0,1)." min="0" max="1"/> </param> <param name="datatype" type="select" label="Data Type"> <option value="Illumina">Illumina</option> <option value="Nanopore">Nanopore</option> <option value="auto">auto</option> </param> </when> <when value="basic"> </when> </conditional> </inputs> <outputs> <data name="output" type="data" label="${tool.name} on ${on_string}" format="tabular" from_work_dir="out/confindr_report.csv" /> </outputs> <help><![CDATA[ ]]></help> <citations> <citation type="bibtex"> @misc{githubconfindr, author = {Low,Andrew}, year = {2018}, title = {confindr}, publisher = {GitHub}, journal = {GitHub repository}, url = {https://github.com/lowandrew/ConFindr}, }</citation> </citations> </tool>