| Previous changeset 5:7f33525b85d0 (2021-06-03) Next changeset 7:692832801d70 (2021-06-06) |
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Commit message:
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 8234e6652ddaa52bbd6ac041cd69470f1600832f" |
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modified:
lotus2.xml |
| b |
| diff -r 7f33525b85d0 -r fc78d02657a9 lotus2.xml --- a/lotus2.xml Thu Jun 03 16:23:18 2021 +0000 +++ b/lotus2.xml Sat Jun 05 09:49:25 2021 +0000 |
| [ |
| b'@@ -1,16 +1,17 @@\n-<tool id="lotus2" name="LotuS2" version="@VERSION@+galaxy3" profile="20.01">\n+<tool id="lotus2" name="LotuS2" version="@VERSION@" profile="20.01">\n <description>fast OTU processing pipeline</description>\n <macros>\n- <token name="@VERSION@">2.06</token>\n- <xml name="refDB_macro">\n+ <token name="@VERSION@">2.07</token>\n+ <xml name="refDB_macro" token_ref_fasta_formats="fasta,fasta.gz">\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+ <param argument="-ref_db" type="select" label="Using reference database" help="Select database from the list">\n+ <option value="" selected="true">(Default)</option>\n+ <option value="SLV">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@@ -20,14 +21,14 @@\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 name="ref_fasta" type="data" format="@REF_FASTA_FORMATS@" 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+ <param argument="-id" type="float" min="0.9" max="1" value="" optional="true" 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@@ -41,13 +42,20 @@\n #import os.path\n #import re\n #def symlink_basename($f):\n- #set fn = re.sub(\'[^\\w\\-_.]\', \'_\', $f.element_identifier)\n- #if fn.endswith(\'.gz\'):\n- #set fn = fn[:-3]\n+ #set $fn = re.sub(\'[^\\w\\-_.]\', \'_\', $f.element_identifier)\n+ #if $fn.endswith(\'.gz\'):\n+ #set $fn = $fn[:-3]\n #end if\n- #for ext in (\'.fq\', \'.fastq\', \'.fastqsanger\'):\n- #if fn.endswith($ext):\n- #set fn = fn[:-len($ext)]\n+ #if $f.ext.startswith(\'fastqsanger\'):\n+ #set $exts_to_drop = (\'.fq\', \'.fastq\', \'.fastqsanger\')\n+ #elif $f.ext.startswith(\'fasta\'):\n+ #set $exts_to_drop = (\'.fa\', \'.fasta\', \'.fna\')\n+ #else\n+ #set $exts_to_drop = []\n+ #end if\n+ #for $ext in $exts_to_drop:\n+ #if $fn.endswith($ext):\n+ '..b'plicated 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." />\n <param argument="-deactivateChimeraCheck" type="select" label="Chimera check">\n- <option value="0" selected="true">OTU chimera checks</option>\n+ <option value="" selected="true">(Default)</option>\n+ <option value="0">OTU chimera checks</option>\n <option value="1">No chimera check at all</option>\n <option value="2">Disable deNovo chimera check</option>\n <option value="3">Disable ref based chimera check</option>\n </param>\n- <param argument="-chim_skew" type="integer" min="0" value="2" label="Skew in chimeric fragment abundance" />\n+ <param argument="-chim_skew" type="integer" min="0" value="" optional="true" label="Skew in chimeric fragment abundance" />\n </section>\n <section name="tax_args" title="Taxonomy Options">\n <conditional name="aligner_cond">\n@@ -243,7 +280,7 @@\n <param argument="-rdp_thr" type="float" min="0" max="1" value="0.8" label="Confidence threshold for RDP"/>\n </when>\n <when value="1">\n- <expand macro="refDB_macro" />\n+ <expand macro="refDB_macro" ref_fasta_formats="fasta" />\n </when>\n <when value="2">\n <expand macro="refDB_macro" />\n@@ -257,8 +294,9 @@\n </conditional>\n <conditional name="amplicon_cond">\n <param argument="-amplicon_type" type="select" label="Amplicon type">\n+ <option value="" selected="true">(Default)</option>\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="SSU">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@@ -274,12 +312,13 @@\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="" selected="true">(Default)</option>\n+ <option value="bacteria">bacterial 16S rDNA annnotation</option>\n <option value="fungi">fungal 18S/23S/ITS annotation</option>\n </param>\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="-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="-LCA_cover" type="float" min="0" max="1" value="" optional="true" label="Minimum horizontal coverage of an OTU sequence against ref DB"/>\n+ <param argument="-LCA_frac" type="float" min="0" max="1" value="" optional="true" label="Minimum fraction of reads with identical taxonomy"/>\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' |