| Previous changeset 9:82ff4f47436a (2021-06-08) Next changeset 11:8f732780e0f3 (2021-06-08) |
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Commit message:
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 682b3a4e52117b2a5ca5737b458c8e8e33218330" |
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modified:
lotus2.xml |
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| diff -r 82ff4f47436a -r 6d55d9464719 lotus2.xml --- a/lotus2.xml Tue Jun 08 12:02:17 2021 +0000 +++ b/lotus2.xml Tue Jun 08 17:21:29 2021 +0000 |
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| @@ -1,4 +1,4 @@ -<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@">2.07</token> @@ -28,7 +28,7 @@ <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="0.9" max="1" value="" optional="true" label="Clustering threshold for OTUs" /> + <param argument="-id" type="float" min="0.9" max="1" value="" optional="true" label="Clustering threshold for OTUs (optional)" /> </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" /> @@ -125,10 +125,14 @@ #end if -clustering $clu_args.clu_cond.clustering -#if $clu_args.clu_cond.clustering in ('1', '3') and str($clu_args.clu_cond.id): - -id $clu_args.clu_cond.id +#if $clu_args.clu_cond.clustering in ('1', '3'): + #if str($clu_args.clu_cond.id): + -id $clu_args.clu_cond.id + #end if #elif $clu_args.clu_cond.clustering == '2': - -swarm_distance $clu_args.clu_cond.swarm_distance + #if str($clu_args.clu_cond.swarm_distance): + -swarm_distance $clu_args.clu_cond.swarm_distance + #end if #end if #if $clu_args.derepMin: -derepMin '$clu_args.derepMin' @@ -143,9 +147,13 @@ -taxAligner $tax_args.aligner_cond.taxAligner #if $tax_args.aligner_cond.taxAligner == '0': - -rdp_thr $tax_args.aligner_cond.rdp_thr + #if str($tax_args.aligner_cond.rdp_thr): + -rdp_thr $tax_args.aligner_cond.rdp_thr + #end if #elif $tax_args.aligner_cond.taxAligner == '3': - -utax_thr $tax_args.aligner_cond.utax_thr + #if str($tax_args.aligner_cond.utax_thr): + -utax_thr $tax_args.aligner_cond.utax_thr + #end if #else: #if $tax_args.aligner_cond.refDB_cond.refDB == 'cached': #if $tax_args.aligner_cond.refDB_cond.ref_db != '': @@ -214,8 +222,8 @@ <option value="PacBio">PacBio</option> </param> <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" /> - <param argument="-forwardPrimer" type="text" value="" label="Forward primer used to amplify DNA region" help="E.g. 16S primer fwd" /> - <param argument="-reversePrimer" type="text" value="" label="Reverse primer used to amplify DNA region" help="E.g. 16S primer rev" /> + <param argument="-forwardPrimer" type="text" value="" label="Forward primer used to amplify DNA region (optional)" help="E.g. 16S primer fwd" /> + <param argument="-reversePrimer" type="text" value="" label="Reverse primer used to amplify DNA region (optional)" help="E.g. 16S primer rev" /> <conditional name="offtarget_cond"> <param argument="-offtargetDB" type="select" label="Remove likely contaminant OTUs/ASVs based on alignment to host genome" help="Useful for low-bacterial biomass samples to remove possible host genome contaminations"> <option value="no" selected="true">Disabled</option> @@ -248,7 +256,7 @@ <expand macro="id_macro" /> </when> <when value="2"> - <param argument="-swarm_distance" type="integer" min="1" value="1" label="Clustering threshold for OTUs when using swarm clustering" /> + <param argument="-swarm_distance" type="integer" min="1" value="1" optional="true" label="Clustering threshold for OTUs when using swarm clustering (optional)" /> </when> <when value="3"> <expand macro="id_macro" /> @@ -272,13 +280,12 @@ <conditional name="aligner_cond"> <param argument="-taxAligner" type="select" label="Taxonomy aligner for taxonomic profiling of OTUs"> <option value="0" selected="true">RDPclassifier (max likelihood)</option> - <option value="1">Blast LCA against custom reference database</option> + <!-- <option value="1">Blast LCA against custom reference database</option> --> <option value="2">LAMBDA LCA against custom reference database</option> - <option value="3">UTAX likelihood corrected</option> - <option value="4">VSEARCH LCA against custom reference database</option> + <!-- <option value="4">VSEARCH LCA against custom reference database</option> --> </param> <when value="0"> - <param argument="-rdp_thr" type="float" min="0" max="1" value="0.8" label="Confidence threshold for RDP"/> + <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"> <expand macro="refDB_macro" ref_fasta_formats="fasta" /> @@ -287,7 +294,7 @@ <expand macro="refDB_macro" /> </when> <when value="3"> - <param argument="-utax_thr" type="float" min="0" max="1" value="0.8" label="Confidence threshold for UTAX"/> + <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" /> @@ -321,8 +328,8 @@ <option value="fungi">fungal 18S/23S/ITS annotation</option> </param> <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" /> - <param argument="-LCA_cover" type="float" min="0" max="1" value="" optional="true" label="Minimum horizontal coverage of an OTU sequence against ref DB"/> - <param argument="-LCA_frac" type="float" min="0" max="1" value="" optional="true" label="Minimum fraction of reads with identical taxonomy"/> + <param argument="-LCA_cover" type="float" min="0" max="1" value="" optional="true" label="Minimum horizontal coverage of an OTU sequence against ref DB (optional)"/> + <param argument="-LCA_frac" type="float" min="0" max="1" value="" optional="true" label="Minimum fraction of reads with identical taxonomy (optional)"/> <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> |