Mercurial > repos > earlhaminst > lotus2
changeset 1:85da3173a488 draft
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24"
| author | earlhaminst |
|---|---|
| date | Wed, 19 May 2021 02:38:24 +0000 |
| parents | 478e767a0e7a |
| children | cf56a6553385 |
| files | lotus2.xml |
| diffstat | 1 files changed, 59 insertions(+), 43 deletions(-) [+] |
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--- a/lotus2.xml Thu May 13 17:38:45 2021 +0000 +++ b/lotus2.xml Wed May 19 02:38:24 2021 +0000 @@ -1,7 +1,17 @@ <tool id="lotus2" name="LotuS2" version="@VERSION@" profile="20.01"> <description>fast OTU processing pipeline</description> <macros> - <token name="@VERSION@">2.04</token> + <token name="@VERSION@">2.05.1</token> + <xml name="refDB_macro"> + <param argument="-refDB" type="select" label="Reference Database"> + <option value="SLV" selected="true">Silva LSU (23/28S) or SSU (16/18S) (SLV)</option> + <option value="GG">Greengenes (GG)</option> + <option value="UNITE">ITS focused on fungi (UNITE)</option> + <option value="PR2">SSU focused on Protists (PR2)</option> + <option value="beetax">Bee gut specific database and tax names (beetax)</option> + <option value="HITdb">Human gut microbiota (HITdb)</option> + </param> + </xml> </macros> <requirements> <requirement type="package" version="@VERSION@">lotus2</requirement> @@ -55,31 +65,34 @@ -clustering $clu_args.clustering -id $clu_args.id --derepMin $clu_args.derepMin +#if $clu_args.derepMin: + -derepMin '$clu_args.derepMin' +#end if +-deactivateChimeraCheck $clu_args.deactivateChimeraCheck -chim_skew $clu_args.chim_skew --deactivateChimeraCheck $clu_args.deactivateChimeraCheck -readOverlap $clu_args.readOverlap --refDB $tax_args.refDB +-taxAligner $tax_args.aligner_cond.taxAligner +#if $tax_args.aligner_cond.taxAligner == '0': + -rdp_thr $tax_args.aligner_cond.rdp_thr +#elif $tax_args.aligner_cond.taxAligner == '3': + -utax_thr $tax_args.aligner_cond.utax_thr +#else: + -refDB $tax_args.aligner_cond.refDB +#end if -amplicon_type $tax_args.amplicon_type -tax_group $tax_args.tax_group --rdp_thr $tax_args.rdp_thr --utax_thr $tax_args.utax_thr -keepUnclassified $tax_args.keepUnclassified --taxAligner $tax_args.taxAligner -useBestBlastHitOnly $tax_args.useBestBlastHitOnly -LCA_cover $tax_args.LCA_cover -LCA_frac $tax_args.LCA_frac -greengenesSpecies $tax_args.greengenesSpecies --pseudoRefOTUcalling $tax_args.pseudoRefOTUcalling -&& +; EXIT_VALUE=\$? ; -cd output/ && -tar -cvzf higherLvl.tar.gz higherLvl/ && -tar -cvzf ExtraFiles.tar.gz ExtraFiles/ && -tar -cvzf LotuSLogS.tar.gz LotuSLogS/ && -tar -cvzf primary.tar.gz primary/ +tar -cvzf output.tar.gz output/ +&& +exit \$EXIT_VALUE ]]></command> <inputs> @@ -106,37 +119,53 @@ <option value="454">454</option> <option value="PacBio">PacBio</option> </param> - <param argument="-barcode" type="data" format="fastqsanger" optional="true" label="Barcodes (MIDs)" help="FASTQ file with barcodes (in the processed mi/hiSeq format)" /> + <param argument="-barcode" type="data" format="fastqsanger" optional="true" label="Barcode (MID) sequences (optional)" help="FASTQ file with barcodes (in the processed mi/hiSeq format), if provided by the sequencer" /> <param argument="-forwardPrimer" type="text" value="" label="Forward primer used to amplify DNA region" help="E.g. 16S primer fwd" /> <param argument="-reversePrimer" type="text" value="" label="Reverse primer used to amplify DNA region" help="E.g. 16S primer rev" /> <section name="clu_args" title="Clustering Options"> <param argument="-clustering" type="select" label="Clustering algorithm"> <option value="1">UPARSE</option> <option value="2">swarm</option> - <option value="3" selected="true">cd-hit</option> + <option value="3">cd-hit</option> <option value="6">unoise3</option> - <option value="7">dada2</option> + <option value="7" selected="true">dada2</option> </param> <param argument="-id" type="float" min="0" max="1" value="0.97" label="Clustering threshold for OTUs" /> - <param argument="-derepMin" type="integer" min="0" value="1" label="Minimum size of dereplicated clustered" /> - <param argument="-chim_skew" type="integer" min="0" value="2" label="Skew in chimeric fragment abundance" /> + <param argument="-derepMin" type="text" value="" label="Minimum size of dereplicated raw reads" help="E.g. 4:1,4:2,3:3 . See http://lotus2.earlham.ac.uk/images/Derep_options.pdf for how to specify this parameter" /> <param argument="-deactivateChimeraCheck" type="select" label="Chimera check"> <option value="0" selected="true">OTU chimera checks</option> <option value="1">No chimera check at all</option> <option value="2">Deactivate deNovo chimera check</option> <option value="3">Deactivate ref based chimera check</option> </param> + <param argument="-chim_skew" type="integer" min="0" value="2" label="Skew in chimeric fragment abundance" /> <param argument="-readOverlap" type="integer" min="0" value="300" label="Maximum number of basepairs that two reads are overlapping" /> </section> <section name="tax_args" title="Taxonomy Options"> - <param argument="-refDB" type="select" label="Reference Database"> - <option value="SLV" selected="true">Silva LSU (23/28S) or SSU (16/18S)</option> - <option value="GG">Greengenes</option> - <option value="UNITE">ITS focused on fungi</option> - <option value="PR2">SSU focused on Protists</option> - <option value="beetax">Bee gut specific database and tax names</option> - <option value="HITdb">Human gut microbiota</option> - </param> + <conditional name="aligner_cond"> + <param argument="-taxAligner" type="select" label="Taxonomy aligner"> + <option value="0" selected="true">Deactivated (just use RDP)</option> + <option value="1">Blast</option> + <option value="2">Use LAMBDA to search against a 16S reference database for taxonomic profiling of OTUs</option> + <option value="3">Use UTAX with custom databases</option> + <option value="4">Use VSEARCH to align OTUs to custom databases</option> + </param> + <when value="0"> + <param argument="-rdp_thr" type="float" min="0" max="1" value="0.8" label="Confidence threshold for RDP"/> + </when> + <when value="1"> + <expand macro="refDB_macro" /> + </when> + <when value="2"> + <expand macro="refDB_macro" /> + </when> + <when value="3"> + <param argument="-utax_thr" type="float" min="0" max="1" value="0.8" label="Confidence threshold for UTAX"/> + </when> + <when value="4"> + <expand macro="refDB_macro" /> + </when> + </conditional> <param argument="-amplicon_type" type="select" label="Amplicon type"> <option value="LSU">LSU Large subunit (23S/28S)</option> <option value="SSU" selected="true">SSU small subunit (16S/18S)</option> @@ -148,22 +177,11 @@ <option value="bacteria" selected="true">bacterial 16S rDNA annnotation</option> <option value="fungi">fungal 18S/23S/ITS annotation</option> </param> - <param argument="-rdp_thr" type="float" min="0" max="1" value="0.8" label="Confidence threshold for RDP"/> - <param argument="-utax_thr" type="float" min="0" max="1" value="0.8" label="Confidence threshold for UTAX"/> <param argument="-keepUnclassified" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Keep unclassified OTUs" help="Includes unclassified OTUs (i.e. no match in RDP/Blast database) in OTU and taxa abundance matrix calculations" /> - <param argument="-taxAligner" type="select" label="Taxonomy aligner"> - <option value="0" selected="true">Deactivated (just use RDP)</option> - <option value="1">Blast</option> - <option value="2">Use LAMBDA to search against a 16S reference database for taxonomic profiling of OTUs</option> - <option value="3">Use UTAX with custom databases</option> - <option value="4">Use VSEARCH to align OTUs to custom databases</option> - <option value="5">Use USEARCH to align OTUs to custom databases</option> - </param> <param argument="-useBestBlastHitOnly" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Use best blast hit only" help="If selected, do not use LCA (lowest common ancestor) to determine most likely taxonomic level (not recommended)" /> <param argument="-LCA_cover" type="float" min="0" max="1" value="0.9" label="Minimum horizontal coverage of an OTU sequence against ref DB"/> <param argument="-LCA_frac" type="float" min="0" max="1" value="0.9" label="Minimum fraction of reads with identical taxonomy"/> <param argument="-greengenesSpecies" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Create greengenes output labels instead of OTU" /> - <param argument="-pseudoRefOTUcalling" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Create Reference based (open) OTUs" /> </section> </inputs> @@ -174,10 +192,7 @@ <data name="OTUphylo_nwk" format="newick" label="${tool.name} on ${on_string}: Newick-formatted phylogenetic tree between sequences" from_work_dir="output/OTUphylo.nwk" /> <data name="hiera_blast" format="tabular" label="${tool.name} on ${on_string}: OTU taxonomy assignments based on Blastn" from_work_dir="output/hiera_BLAST.txt" /> <data name="hiera_rdp" format="tabular" label="${tool.name} on ${on_string}: OTU taxonomy assignments based on RDP classifier" from_work_dir="output/hiera_RDP.txt" /> - <data name="primary" format="tar" label="${tool.name} on ${on_string}: Copies of sdm options and mapping file" from_work_dir="output/primary.tar.gz" /> - <data name="higherlvl" format="tar" label="${tool.name} on ${on_string}: Abundance matrices" from_work_dir="output/higherLvl.tar.gz" /> - <data name="lotuslogs" format="tar" label="${tool.name} on ${on_string}: Log files" from_work_dir="output/LotuSLogS.tar.gz" /> - <data name="extrafiles" format="tar" label="${tool.name} on ${on_string}: Extra files" from_work_dir="output/ExtraFiles.tar.gz" /> + <data name="primary" format="tar" label="${tool.name} on ${on_string}: All output files" from_work_dir="output.tar.gz" /> </outputs> <tests> @@ -185,6 +200,7 @@ <param name="paired_or_single" value="single"/> <param name="input" value="Anh_sample1.fastq.gz,Anh_sample2.fastq.gz" ftype="fastqsanger.gz"/> <param name="platform" value="454" /> + <param name="clustering" value="3" /> <output name="otu" file="OTU.txt" compare="sim_size" /> <output name="otu_fna" file="OTU.fna" compare="sim_size" /> <output name="hiera_rdp" file="hiera_RDP.txt" compare="sim_size" /> @@ -197,6 +213,6 @@ Documentation can be found at `<http://lotus2.earlham.ac.uk/>`_. ]]></help> <citations> - <citation type="doi">10.1186/2049-2618-2-30</citation> + <citation type="doi">10.1186/s40168-021-01012-1</citation> </citations> </tool>