Mercurial > repos > earlhaminst > lotus2
changeset 15:6e9fd3e0dcbb draft
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 589bb3ddd8e3ba973179db1fc21075ffc2422cda"
| author | earlhaminst |
|---|---|
| date | Fri, 11 Feb 2022 19:48:19 +0000 |
| parents | 30340f534fbe |
| children | 12599a8dd22f |
| files | lotus2.xml |
| diffstat | 1 files changed, 52 insertions(+), 27 deletions(-) [+] |
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--- a/lotus2.xml Mon Jun 14 16:54:46 2021 +0000 +++ b/lotus2.xml Fri Feb 11 19:48:19 2022 +0000 @@ -1,7 +1,7 @@ -<tool id="lotus2" name="LotuS2" version="@VERSION@" profile="20.01"> +<tool id="lotus2" name="LotuS2" version="@VERSION@" profile="20.09"> <description>fast OTU processing pipeline</description> <macros> - <token name="@VERSION@">2.09.2</token> + <token name="@VERSION@">2.19</token> <xml name="refDB_macro" token_ref_fasta_formats="fasta,fasta.gz"> <conditional name="refDB_cond"> <param argument="-refDB" type="select" label="Taxonomy reference database"> @@ -110,6 +110,7 @@ #if $offtarget_cond.offtargetDB != 'no': -offtargetDB '$offtarget_cond.ref_file' #end if +-useMini4map $useMini4map -clustering $clu_args.clu_cond.clustering #if $clu_args.clu_cond.clustering in ('1', '3'): @@ -172,7 +173,9 @@ #end if -lulu $tax_args.lulu -buildPhylo $tax_args.buildPhylo - +#if $tax_args.taxExcludeGrep: + -taxExcludeGrep '$tax_args.taxExcludeGrep' +#end if ; EXIT_VALUE=\$? ; zip -8 -r -v output.zip output/ @@ -248,18 +251,16 @@ <param name="ref_file" type="data" format="fasta,fasta.gz" label="FASTA reference genome" /> </when> </conditional> + <param argument="-useMini4map" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use minimap2 instead of VSEARCH to map back reads to OTUs" /> <section name="clu_args" title="Clustering Options"> <conditional name="clu_cond"> <param argument="-clustering" type="select" label="Clustering algorithm"> - <option value="1">UPARSE</option> <option value="2">swarm</option> <option value="3">cd-hit</option> <option value="6">unoise3</option> <option value="7" selected="true">dada2</option> + <option value="8">vsearch</option> </param> - <when value="1"> - <expand macro="id_macro" /> - </when> <when value="2"> <param argument="-swarm_distance" type="integer" min="1" value="1" optional="true" label="Clustering threshold for OTUs when using swarm clustering (optional)" /> </when> @@ -270,6 +271,8 @@ </when> <when value="7"> </when> + <when value="8"> + </when> </conditional> <param argument="-derepMin" type="text" value="" label="Minimum size of dereplicated raw reads (optional)" 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. If not specified, LotuS2 will select an appropriate default for the chosen clustering algorithm." /> <param argument="-deactivateChimeraCheck" type="select" label="Chimera check"> @@ -292,18 +295,18 @@ <when value="0"> <param argument="-rdp_thr" type="float" min="0" max="1" value="0.8" optional="true" label="Confidence threshold for RDP (optional)"/> </when> - <when value="1"> + <!-- <when value="1"> <expand macro="refDB_macro" ref_fasta_formats="fasta" /> - </when> + </when> --> <when value="2"> <expand macro="refDB_macro" /> </when> - <when value="3"> + <!-- <when value="3"> <param argument="-utax_thr" type="float" min="0" max="1" value="0.8" optional="true" label="Confidence threshold for UTAX (optional)"/> </when> <when value="4"> <expand macro="refDB_macro" /> - </when> + </when> --> </conditional> <conditional name="amplicon_cond"> <param argument="-amplicon_type" type="select" label="Amplicon type"> @@ -341,6 +344,14 @@ <option value="1" selected="true">Use fasttree2</option> <option value="2">Use iqtree2</option> </param> + <param argument="-taxExcludeGrep" type="text" value="" label="Taxonomic groups to exclude, as a regular expression" help="OTUs matching this regular expression will be assigned as unknown, and by default removed"> + <sanitizer> + <valid initial="default"> + <add value="|" /> + <add value="$" /> + </valid> + </sanitizer> + </param> </section> </inputs> @@ -355,29 +366,43 @@ <tests> <test> - <param name="paired_or_single" value="single"/> - <param name="input" value="Anh_sample1.fastq.gz,Anh_sample2.fastq.gz" ftype="fastqsanger.gz"/> + <conditional name="inputs"> + <param name="paired_or_single" value="single"/> + <param name="input" value="Anh_sample1.fastq.gz,Anh_sample2.fastq.gz" ftype="fastqsanger.gz"/> + </conditional> <param name="platform" value="454" /> - <param name="clustering" value="3" /> + <section name="clu_args"> + <conditional name="clu_cond"> + <param name="clustering" value="3" /> + </conditional> + <param name="derepMin" value="1" /> + </section> <output name="otu" file="OTU.txt" compare="sim_size" /> <output name="otu_fna" file="OTU.fna" compare="sim_size" /> <output name="mapping" file="mapping.txt" /> </test> <test> - <param name="paired_or_single" value="paired_collection"/> - <param name="pair_input"> - <collection type="list:paired"> - <element name="Anh_sample"> - <collection type="paired"> - <element name="forward" value="Anh_sample1.fastq.gz" ftype="fastqsanger.gz" /> - <element name="reverse" value="Anh_sample2.fastq.gz" ftype="fastqsanger.gz" /> - </collection> - </element> - </collection> - </param> - <param name="mapping" value="mapping_paired.txt" /> + <conditional name="inputs"> + <param name="paired_or_single" value="paired_collection"/> + <param name="pair_input"> + <collection type="list:paired"> + <element name="Anh_sample"> + <collection type="paired"> + <element name="forward" value="Anh_sample1.fastq.gz" ftype="fastqsanger.gz" /> + <element name="reverse" value="Anh_sample2.fastq.gz" ftype="fastqsanger.gz" /> + </collection> + </element> + </collection> + </param> + </conditional> + <param name="map" value="mapping_paired.txt" /> <param name="platform" value="454" /> - <param name="clustering" value="3" /> + <section name="clu_args"> + <conditional name="clu_cond"> + <param name="clustering" value="3" /> + </conditional> + <param name="derepMin" value="1" /> + </section> <output name="otu" file="OTU_paired.txt" compare="sim_size" /> <output name="otu_fna" file="OTU_paired.fna" compare="sim_size" /> </test>