| Next changeset 1:e2725e0b0113 (2017-05-04) |
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Commit message:
planemo upload |
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added:
neptune.xml |
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| diff -r 000000000000 -r 9121e9f3f285 neptune.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/neptune.xml Thu May 04 15:23:54 2017 -0400 |
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| @@ -0,0 +1,98 @@ +<tool id="neptune" name="Neptune: Signature Discovery" version="1.2.5.1"> + <description>Neptune identifies genomic signatures using an exact k-mer matching strategy while accommodating k-mer mismatches.</description> + + <requirements> + <requirement type="package" version="1.2.5">neptune</requirement> + </requirements> + + <stdio> + <exit_code range="1:" /> + </stdio> + + <command> + neptune + + --inclusion + #for $i in $inclusion + "$i" + #end for + + --exclusion + #for $i in $exclusion + "$i" + #end for + + #if $options.select == "advanced" + + #if $options.kmer: + --kmer "$options.kmer" + #end if + + #if $options.rate: + --rate "$options.rate" + #end if + + #if $options.exhits: + --exhits "$options.exhits" + #end if + + #if $options.size: + --size "$options.size" + #end if + + #end if + + --output results + + --parallelization \${GALAXY_SLOTS:-8} + + --organization 3 + + </command> + + <inputs> + <param name="inclusion" type="data_collection" collection_type="list" label="Inclusion" help="The inclusion targets in FASTA format." format="fasta"/> + <param name="exclusion" type="data_collection" collection_type="list" label="Exclusion" help="The exclusion targets in FASTA format." format="fasta"/> + + <conditional name="options"> + <param name="select" type="select" label="Options Type"> + <option value="basic">Basic</option> + <option value="advanced">Advanced</option> + </param> + <when value="basic"> + </when> + <when value="advanced"> + <param name="kmer" type="integer" label="k" help="The size of the k-mers. This value is automatically calculated if left blank." optional="true"/> + <param name="size" type="integer" label="Size" help="The minimum size of reported signatures. The default size is 4k." optional="true"/> + <param name="rate" type="float" label="Rate" help="The probability of a mutation or error at an arbitrary position. The default value is 0.01." optional="true" value="0.01"/> + <param name="exhits" type="integer" label="Minimum Exclusion" help="The minimum number of inclusion targets that must contain a k-mer observed in the reference to begin or continue building candidate signatures. This will be calculated if not specified." optional="true" value="1"/> + </when> + </conditional> + </inputs> + + <outputs> + <data name="consolidated" from_work_dir="results/consolidated/consolidated.fasta" format="fasta" label="Neptune Signatures: $inclusion.name and $exclusion.name"></data> + <data name="receipt" from_work_dir="results/receipt.txt" format="txt" label="Neptune Parameters: $inclusion.name and $exclusion.name"></data> + </outputs> + + <tests> + <test> + <output name="receipt"/> + </test> + </tests> + + <help> +Neptune locates genomic signatures using an exact k-mer matching strategy while +accommodating k-mer mismatches. The software identifies sequences that are +sufficiently represented within inclusion targets and sufficiently absent from +exclusion targets. The signature discovery process is accomplished using +probabilistic models instead of heuristic strategies. + +The inclusion and exclusion targets must be FASTA files. + </help> + + <citations> + <citation type="doi">10.1101/032227</citation> + </citations> + +</tool> |