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view qiime2/qiime_alignment_mafft.xml @ 0:370e0b6e9826 draft
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author | florianbegusch |
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date | Wed, 17 Jul 2019 03:05:17 -0400 |
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children | f190567fe3f6 |
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<?xml version="1.0" ?> <tool id="qiime_alignment_mafft" name="qiime alignment mafft" version="2019.4"> <description> - De novo multiple sequence alignment with MAFFT</description> <requirements> <requirement type="package" version="2019.4">qiime2</requirement> </requirements> <command><![CDATA[ qiime alignment mafft --i-sequences=$isequences --o-alignment=oalignment #set $pnthreads = '${GALAXY_SLOTS:-4}' #if str($pnthreads): --p-n-threads="$pnthreads" #end if #if $pparttree: --p-parttree #end if ; cp oalignment.qza $oalignment ]]></command> <inputs> <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The sequences to be aligned. [required]" name="isequences" optional="False" type="data"/> <param label="--p-parttree: --p-no-parttree This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default [default: False]" name="pparttree" selected="False" type="boolean"/> </inputs> <outputs> <data format="qza" label="${tool.name} on ${on_string}: alignment.qza" name="oalignment"/> </outputs> <help><![CDATA[ De novo multiple sequence alignment with MAFFT ############################################## Perform de novo multiple sequence alignment using MAFFT. Parameters ---------- sequences : FeatureData[Sequence] The sequences to be aligned. parttree : Bool, optional This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default Returns ------- alignment : FeatureData[AlignedSequence] The aligned sequences. ]]></help> <macros> <import>qiime_citation.xml</import> </macros> <expand macro="qiime_citation"/> </tool>