| Previous changeset 0:478e767a0e7a (2021-05-13) Next changeset 2:cf56a6553385 (2021-05-19) |
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Commit message:
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 187ff34ae1ea6f850882ef0fbbc80dbb3ffc2a24" |
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modified:
lotus2.xml |
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| diff -r 478e767a0e7a -r 85da3173a488 lotus2.xml --- a/lotus2.xml Thu May 13 17:38:45 2021 +0000 +++ b/lotus2.xml Wed May 19 02:38:24 2021 +0000 |
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| b'@@ -1,7 +1,17 @@\n <tool id="lotus2" name="LotuS2" version="@VERSION@" profile="20.01">\n <description>fast OTU processing pipeline</description>\n <macros>\n- <token name="@VERSION@">2.04</token>\n+ <token name="@VERSION@">2.05.1</token>\n+ <xml name="refDB_macro">\n+ <param argument="-refDB" type="select" label="Reference Database">\n+ <option value="SLV" selected="true">Silva LSU (23/28S) or SSU (16/18S) (SLV)</option>\n+ <option value="GG">Greengenes (GG)</option>\n+ <option value="UNITE">ITS focused on fungi (UNITE)</option>\n+ <option value="PR2">SSU focused on Protists (PR2)</option>\n+ <option value="beetax">Bee gut specific database and tax names (beetax)</option>\n+ <option value="HITdb">Human gut microbiota (HITdb)</option>\n+ </param>\n+ </xml>\n </macros>\n <requirements>\n <requirement type="package" version="@VERSION@">lotus2</requirement>\n@@ -55,31 +65,34 @@\n \n -clustering $clu_args.clustering\n -id $clu_args.id\n--derepMin $clu_args.derepMin\n+#if $clu_args.derepMin:\n+ -derepMin \'$clu_args.derepMin\'\n+#end if\n+-deactivateChimeraCheck $clu_args.deactivateChimeraCheck\n -chim_skew $clu_args.chim_skew\n--deactivateChimeraCheck $clu_args.deactivateChimeraCheck\n -readOverlap $clu_args.readOverlap\n \n--refDB $tax_args.refDB\n+-taxAligner $tax_args.aligner_cond.taxAligner\n+#if $tax_args.aligner_cond.taxAligner == \'0\':\n+ -rdp_thr $tax_args.aligner_cond.rdp_thr\n+#elif $tax_args.aligner_cond.taxAligner == \'3\':\n+ -utax_thr $tax_args.aligner_cond.utax_thr\n+#else:\n+ -refDB $tax_args.aligner_cond.refDB\n+#end if\n -amplicon_type $tax_args.amplicon_type\n -tax_group $tax_args.tax_group\n--rdp_thr $tax_args.rdp_thr\n--utax_thr $tax_args.utax_thr\n -keepUnclassified $tax_args.keepUnclassified\n--taxAligner $tax_args.taxAligner\n -useBestBlastHitOnly $tax_args.useBestBlastHitOnly\n -LCA_cover $tax_args.LCA_cover\n -LCA_frac $tax_args.LCA_frac\n -greengenesSpecies $tax_args.greengenesSpecies\n--pseudoRefOTUcalling $tax_args.pseudoRefOTUcalling\n \n-&&\n+; EXIT_VALUE=\\$? ;\n \n-cd output/ &&\n-tar -cvzf higherLvl.tar.gz higherLvl/ &&\n-tar -cvzf ExtraFiles.tar.gz ExtraFiles/ &&\n-tar -cvzf LotuSLogS.tar.gz LotuSLogS/ &&\n-tar -cvzf primary.tar.gz primary/\n+tar -cvzf output.tar.gz output/\n+&&\n+exit \\$EXIT_VALUE\n ]]></command>\n \n <inputs>\n@@ -106,37 +119,53 @@\n <option value="454">454</option>\n <option value="PacBio">PacBio</option>\n </param>\n- <param argument="-barcode" type="data" format="fastqsanger" optional="true" label="Barcodes (MIDs)" help="FASTQ file with barcodes (in the processed mi/hiSeq format)" />\n+ <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" />\n <param argument="-forwardPrimer" type="text" value="" label="Forward primer used to amplify DNA region" help="E.g. 16S primer fwd" />\n <param argument="-reversePrimer" type="text" value="" label="Reverse primer used to amplify DNA region" help="E.g. 16S primer rev" />\n <section name="clu_args" title="Clustering Options">\n <param argument="-clustering" type="select" label="Clustering algorithm">\n <option value="1">UPARSE</option>\n <option value="2">swarm</option>\n- <option value="3" selected="true">cd-hit</option>\n+ <option value="3">cd-hit</option>\n <option value="6">unoise3</option>\n- <option value="7">dada2</option>\n+ <option value="7" selected="true">dada2</option>\n </param>\n <param argument="-id" type="float" min="0" max="1" value="0.97" label="Clustering threshold for OTUs" />\n- <param argument="-derepMin" type="integer" min="0" value="1" label='..b'gument="-utax_thr" type="float" min="0" max="1" value="0.8" label="Confidence threshold for UTAX"/>\n <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" />\n- <param argument="-taxAligner" type="select" label="Taxonomy aligner">\n- <option value="0" selected="true">Deactivated (just use RDP)</option>\n- <option value="1">Blast</option>\n- <option value="2">Use LAMBDA to search against a 16S reference database for taxonomic profiling of OTUs</option>\n- <option value="3">Use UTAX with custom databases</option>\n- <option value="4">Use VSEARCH to align OTUs to custom databases</option>\n- <option value="5">Use USEARCH to align OTUs to custom databases</option>\n- </param>\n <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)" />\n <param argument="-LCA_cover" type="float" min="0" max="1" value="0.9" label="Minimum horizontal coverage of an OTU sequence against ref DB"/>\n <param argument="-LCA_frac" type="float" min="0" max="1" value="0.9" label="Minimum fraction of reads with identical taxonomy"/>\n <param argument="-greengenesSpecies" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Create greengenes output labels instead of OTU" />\n- <param argument="-pseudoRefOTUcalling" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Create Reference based (open) OTUs" />\n </section>\n </inputs>\n \n@@ -174,10 +192,7 @@\n <data name="OTUphylo_nwk" format="newick" label="${tool.name} on ${on_string}: Newick-formatted phylogenetic tree between sequences" from_work_dir="output/OTUphylo.nwk" />\n <data name="hiera_blast" format="tabular" label="${tool.name} on ${on_string}: OTU taxonomy assignments based on Blastn" from_work_dir="output/hiera_BLAST.txt" />\n <data name="hiera_rdp" format="tabular" label="${tool.name} on ${on_string}: OTU taxonomy assignments based on RDP classifier" from_work_dir="output/hiera_RDP.txt" />\n- <data name="primary" format="tar" label="${tool.name} on ${on_string}: Copies of sdm options and mapping file" from_work_dir="output/primary.tar.gz" />\n- <data name="higherlvl" format="tar" label="${tool.name} on ${on_string}: Abundance matrices" from_work_dir="output/higherLvl.tar.gz" />\n- <data name="lotuslogs" format="tar" label="${tool.name} on ${on_string}: Log files" from_work_dir="output/LotuSLogS.tar.gz" />\n- <data name="extrafiles" format="tar" label="${tool.name} on ${on_string}: Extra files" from_work_dir="output/ExtraFiles.tar.gz" />\n+ <data name="primary" format="tar" label="${tool.name} on ${on_string}: All output files" from_work_dir="output.tar.gz" />\n </outputs>\n \n <tests>\n@@ -185,6 +200,7 @@\n <param name="paired_or_single" value="single"/>\n <param name="input" value="Anh_sample1.fastq.gz,Anh_sample2.fastq.gz" ftype="fastqsanger.gz"/>\n <param name="platform" value="454" />\n+ <param name="clustering" value="3" />\n <output name="otu" file="OTU.txt" compare="sim_size" />\n <output name="otu_fna" file="OTU.fna" compare="sim_size" />\n <output name="hiera_rdp" file="hiera_RDP.txt" compare="sim_size" />\n@@ -197,6 +213,6 @@\n Documentation can be found at `<http://lotus2.earlham.ac.uk/>`_.\n ]]></help>\n <citations>\n- <citation type="doi">10.1186/2049-2618-2-30</citation>\n+ <citation type="doi">10.1186/s40168-021-01012-1</citation>\n </citations>\n </tool>\n' |