| Previous changeset 3:77cb867e9608 (2021-05-26) Next changeset 5:7f33525b85d0 (2021-06-03) |
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Commit message:
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit ac59e1bfb1ef3b5104e84d4d65fb9bef50fed8ae" |
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modified:
lotus2.xml |
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| diff -r 77cb867e9608 -r 59b8864c9fa0 lotus2.xml --- a/lotus2.xml Wed May 26 11:54:37 2021 +0000 +++ b/lotus2.xml Thu Jun 03 15:44:44 2021 +0000 |
| [ |
| b'@@ -1,21 +1,37 @@\n-<tool id="lotus2" name="LotuS2" version="@VERSION@+galaxy1" profile="20.01">\n+<tool id="lotus2" name="LotuS2" version="@VERSION@+galaxy2" profile="20.01">\n <description>fast OTU processing pipeline</description>\n <macros>\n <token name="@VERSION@">2.06</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+ <conditional name="refDB_cond">\n+ <param argument="-refDB" type="select" label="Taxonomy reference database">\n+ <option value="cached">Use a built-in taxonomy database</option>\n+ <option value="history">Use a taxonomy from history</option>\n+ </param>\n+ <when value="cached">\n+ <param argument="ref_db" type="select" label="Using reference database" help="Select database from the list">\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+ <param argument="-greengenesSpecies" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Create greengenes output labels instead of OTU" />\n+ </when>\n+ <when value="history">\n+ <param name="ref_fasta" type="data" format="fasta" label="Taxonomy reference sequences" help="In FASTA format" />\n+ <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" />\n+ </when>\n+ </conditional>\n <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)" />\n </xml>\n <xml name="id_macro">\n <param argument="-id" type="float" min="0" max="1" value="0.97" label="Clustering threshold for OTUs" />\n </xml>\n+ <xml name="ITSx_macro">\n+ <param argument="-ITSx" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use ITSx to only retain OTUs fitting to ITS1/ITS2 hmm models" />\n+ </xml>\n </macros>\n <requirements>\n <requirement type="package" version="@VERSION@">lotus2</requirement>\n@@ -63,15 +79,18 @@\n #end for\n #end if\n \n-lotus2 -create_map mapping.txt -i input/ &&\n-cat mapping.txt &&\n+#if not $map:\n+ lotus2 -create_map mapping.txt -i input/ &&\n+ cat mapping.txt &&\n+ #set map = \'mapping.txt\'\n+#end if\n \n lotus2\n -i input/\n -o output\n -tmpDir tmp_folder\n -threads "\\${GALAXY_SLOTS:-1}"\n--map mapping.txt\n+-map \'$map\'\n -platform $platform\n #if $barcode:\n -barcode \'$barcode\'\n@@ -97,7 +116,6 @@\n #end if\n -deactivateChimeraCheck $clu_args.deactivateChimeraCheck\n -chim_skew $clu_args.chim_skew\n--readOverlap $clu_args.rea'..b'\n- <option value="ITS2">ITS2</option>\n- </param>\n+ <conditional name="amplicon_cond">\n+ <param argument="-amplicon_type" type="select" label="Amplicon type">\n+ <option value="LSU">LSU Large subunit (23S/28S)</option>\n+ <option value="SSU" selected="true">SSU small subunit (16S/18S)</option>\n+ <option value="ITS">ITS internal transcribed spacer</option>\n+ <option value="ITS1">ITS1</option>\n+ <option value="ITS2">ITS2</option>\n+ </param>\n+ <when value="ITS">\n+ <expand macro="ITSx_macro" />\n+ </when>\n+ <when value="ITS1">\n+ <expand macro="ITSx_macro" />\n+ </when>\n+ <when value="ITS2">\n+ <expand macro="ITSx_macro" />\n+ </when>\n+ </conditional>\n <param argument="-tax_group" type="select" label="Tax group">\n <option value="bacteria" selected="true">bacterial 16S rDNA annnotation</option>\n <option value="fungi">fungal 18S/23S/ITS annotation</option>\n@@ -245,8 +282,7 @@\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="-lulu" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Use LULU to merge OTUs based on their occurence" />\n+ <param argument="-lulu" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Use LULU to merge OTUs based on their occurrence" />\n <param argument="-buildPhylo" type="select" label="Build OTU phylogeny">\n <option value="0">Disable</option>\n <option value="1" selected="true">Use fasttree2</option>\n@@ -261,6 +297,7 @@\n <data name="otu_fna" format="fasta" label="${tool.name} on ${on_string}: FASTA-formatted extended OTU seed sequences" from_work_dir="output/OTU.fna" />\n <data name="OTUphylo_nwk" format="newick" label="${tool.name} on ${on_string}: Newick-formatted phylogenetic tree between sequences" from_work_dir="output/OTUphylo.nwk" />\n <data name="mapping" format="tabular" label="${tool.name} on ${on_string}: mapping file" from_work_dir="output/primary/in.map" />\n+ <data name="runlog" format="txt" label="${tool.name} on ${on_string}: main log file" from_work_dir="output/LotuSLogS/LotuS_run.log" />\n <data name="outputs" format="tar" label="${tool.name} on ${on_string}: All output files" from_work_dir="output.tar.gz" />\n </outputs>\n \n@@ -274,6 +311,15 @@\n <output name="otu_fna" file="OTU.fna" compare="sim_size" />\n <output name="mapping" file="mapping.txt" />\n </test>\n+ <test>\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="mapping" value="mapping.txt" />\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+ </test>\n </tests>\n \n <help><![CDATA[\n' |