| Next changeset 1:c8158764b7a7 (2018-10-21) |
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Commit message:
Uploaded |
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added:
confindr.xml |
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| diff -r 000000000000 -r 454e2f1ccff4 confindr.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/confindr.xml Sun Oct 21 08:19:08 2018 -0400 |
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| @@ -0,0 +1,93 @@ +<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> |