Mercurial > repos > earlhaminst > lotus2
changeset 4:59b8864c9fa0 draft
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae"
| author | earlhaminst |
|---|---|
| date | Thu, 03 Jun 2021 15:44:44 +0000 |
| parents | 77cb867e9608 |
| children | 7f33525b85d0 |
| files | lotus2.xml |
| diffstat | 1 files changed, 72 insertions(+), 26 deletions(-) [+] |
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--- a/lotus2.xml Wed May 26 11:54:37 2021 +0000 +++ b/lotus2.xml Thu Jun 03 15:44:44 2021 +0000 @@ -1,21 +1,37 @@ -<tool id="lotus2" name="LotuS2" version="@VERSION@+galaxy1" profile="20.01"> +<tool id="lotus2" name="LotuS2" version="@VERSION@+galaxy2" profile="20.01"> <description>fast OTU processing pipeline</description> <macros> <token name="@VERSION@">2.06</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> + <conditional name="refDB_cond"> + <param argument="-refDB" type="select" label="Taxonomy reference database"> + <option value="cached">Use a built-in taxonomy database</option> + <option value="history">Use a taxonomy from history</option> + </param> + <when value="cached"> + <param argument="ref_db" type="select" label="Using reference database" help="Select database from the list"> + <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> + <param argument="-greengenesSpecies" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Create greengenes output labels instead of OTU" /> + </when> + <when value="history"> + <param name="ref_fasta" type="data" format="fasta" label="Taxonomy reference sequences" help="In FASTA format" /> + <param argument="-tax4refDB" type="data" format="tabular" label="Taxonomy reference lineages" help="Tab-separated file with 2 columns mapping each FASTA header of the reference sequences to a GTDB-style taxonomy string" /> + </when> + </conditional> <param argument="-useBestBlastHitOnly" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Use the best Blast hit only" help="Do not use LCA (lowest common ancestor) to determine the most likely taxonomic level (not recommended)" /> </xml> <xml name="id_macro"> <param argument="-id" type="float" min="0" max="1" value="0.97" label="Clustering threshold for OTUs" /> </xml> + <xml name="ITSx_macro"> + <param argument="-ITSx" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use ITSx to only retain OTUs fitting to ITS1/ITS2 hmm models" /> + </xml> </macros> <requirements> <requirement type="package" version="@VERSION@">lotus2</requirement> @@ -63,15 +79,18 @@ #end for #end if -lotus2 -create_map mapping.txt -i input/ && -cat mapping.txt && +#if not $map: + lotus2 -create_map mapping.txt -i input/ && + cat mapping.txt && + #set map = 'mapping.txt' +#end if lotus2 -i input/ -o output -tmpDir tmp_folder -threads "\${GALAXY_SLOTS:-1}" --map mapping.txt +-map '$map' -platform $platform #if $barcode: -barcode '$barcode' @@ -97,7 +116,6 @@ #end if -deactivateChimeraCheck $clu_args.deactivateChimeraCheck -chim_skew $clu_args.chim_skew --readOverlap $clu_args.readOverlap -taxAligner $tax_args.aligner_cond.taxAligner #if $tax_args.aligner_cond.taxAligner == '0': @@ -105,16 +123,24 @@ #elif $tax_args.aligner_cond.taxAligner == '3': -utax_thr $tax_args.aligner_cond.utax_thr #else: - -refDB $tax_args.aligner_cond.refDB + #if $tax_args.aligner_cond.refDB_cond.refDB == 'cached': + -refDB $tax_args.aligner_cond.refDB_cond.ref_db + -greengenesSpecies $tax_args.aligner_cond.refDB_cond.greengenesSpecies + #else: + -refDB $tax_args.aligner_cond.refDB_cond.ref_fasta + -tax4refDB $tax_args.aligner_cond.refDB_cond.tax4refDB + #end if -useBestBlastHitOnly $tax_args.aligner_cond.useBestBlastHitOnly #end if --amplicon_type $tax_args.amplicon_type +-amplicon_type $tax_args.amplicon_cond.amplicon_type +#if $tax_args.amplicon_cond.amplicon_type in ('ITS', 'ITS1', 'ITS2'): + -ITSx $tax_args.amplicon_cond.ITSx_macro +#end if -tax_group $tax_args.tax_group -keepUnclassified $tax_args.keepUnclassified -useBestBlastHitOnly $tax_args.useBestBlastHitOnly -LCA_cover $tax_args.LCA_cover -LCA_frac $tax_args.LCA_frac --greengenesSpecies $tax_args.greengenesSpecies -lulu $tax_args.lulu -buildPhylo $tax_args.buildPhylo @@ -144,6 +170,7 @@ <param name="pair_input" type="data_collection" collection_type="list:paired" format="fastqsanger,fastqsanger.gz" label="List of paired reads" /> </when> </conditional> + <param argument="-map" type="data" format="tabular" optional="true" label="Mapping file (optional)" help="Needed to demultiplex the FASTQ files using sdm. If the FASTQ are already demultiplexed, this can be omitted." /> <param argument="-platform" type="select" label="Sequencing platform"> <option value="miSeq" selected="true">miSeq</option> <option value="hiSeq">hiSeq</option> @@ -203,7 +230,6 @@ <option value="3">Disable 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"> <conditional name="aligner_cond"> @@ -230,13 +256,24 @@ <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> - <option value="ITS">ITS internal transcribed spacer</option> - <option value="ITS1">ITS1</option> - <option value="ITS2">ITS2</option> - </param> + <conditional name="amplicon_cond"> + <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> + <option value="ITS">ITS internal transcribed spacer</option> + <option value="ITS1">ITS1</option> + <option value="ITS2">ITS2</option> + </param> + <when value="ITS"> + <expand macro="ITSx_macro" /> + </when> + <when value="ITS1"> + <expand macro="ITSx_macro" /> + </when> + <when value="ITS2"> + <expand macro="ITSx_macro" /> + </when> + </conditional> <param argument="-tax_group" type="select" label="Tax group"> <option value="bacteria" selected="true">bacterial 16S rDNA annnotation</option> <option value="fungi">fungal 18S/23S/ITS annotation</option> @@ -245,8 +282,7 @@ <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="-lulu" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Use LULU to merge OTUs based on their occurence" /> + <param argument="-lulu" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Use LULU to merge OTUs based on their occurrence" /> <param argument="-buildPhylo" type="select" label="Build OTU phylogeny"> <option value="0">Disable</option> <option value="1" selected="true">Use fasttree2</option> @@ -261,6 +297,7 @@ <data name="otu_fna" format="fasta" label="${tool.name} on ${on_string}: FASTA-formatted extended OTU seed sequences" from_work_dir="output/OTU.fna" /> <data name="OTUphylo_nwk" format="newick" label="${tool.name} on ${on_string}: Newick-formatted phylogenetic tree between sequences" from_work_dir="output/OTUphylo.nwk" /> <data name="mapping" format="tabular" label="${tool.name} on ${on_string}: mapping file" from_work_dir="output/primary/in.map" /> + <data name="runlog" format="txt" label="${tool.name} on ${on_string}: main log file" from_work_dir="output/LotuSLogS/LotuS_run.log" /> <data name="outputs" format="tar" label="${tool.name} on ${on_string}: All output files" from_work_dir="output.tar.gz" /> </outputs> @@ -274,6 +311,15 @@ <output name="otu_fna" file="OTU.fna" compare="sim_size" /> <output name="mapping" file="mapping.txt" /> </test> + <test> + <param name="paired_or_single" value="single"/> + <param name="input" value="Anh_sample1.fastq.gz,Anh_sample2.fastq.gz" ftype="fastqsanger.gz"/> + <param name="mapping" value="mapping.txt" /> + <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" /> + </test> </tests> <help><![CDATA[