| Previous changeset 16:12599a8dd22f (2022-03-22) Next changeset 18:6c22795e1be0 (2022-11-18) |
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Commit message:
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/lotus2 commit 501bb8e75e2245e0ce1ff93308d12be84198d6fd |
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modified:
lotus2.xml |
| b |
| diff -r 12599a8dd22f -r 28f284a679ce lotus2.xml --- a/lotus2.xml Tue Mar 22 13:45:18 2022 +0000 +++ b/lotus2.xml Fri Oct 28 12:22:34 2022 +0000 |
| [ |
| b'@@ -1,7 +1,7 @@\n <tool id="lotus2" name="LotuS2" version="@VERSION@" profile="20.09">\n <description>fast OTU processing pipeline</description>\n <macros>\n- <token name="@VERSION@">2.19</token>\n+ <token name="@VERSION@">2.21</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@@ -27,9 +27,6 @@\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="0.9" max="1" value="" optional="true" label="Clustering threshold for OTUs (optional)" />\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@@ -75,10 +72,10 @@\n #end for\n #end if\n \n-#if $tax_args.aligner_cond.taxAligner not in (\'0\', \'3\') and $tax_args.aligner_cond.refDB_cond.refDB == \'history\':\n- #set $ext = $tax_args.aligner_cond.refDB_cond.ref_fasta.ext\n- #set $ref_fasta_symlink = $symlink_basename($tax_args.aligner_cond.refDB_cond.ref_fasta, strip_ext=True) + \'.\' + $ext\n- ln -s \'$tax_args.aligner_cond.refDB_cond.ref_fasta\' \'$ref_fasta_symlink\' &&\n+#if $aligner_cond.taxAligner not in (\'0\', \'3\') and $aligner_cond.refDB_cond.refDB == \'history\':\n+ #set $ext = $aligner_cond.refDB_cond.ref_fasta.ext\n+ #set $ref_fasta_symlink = $symlink_basename($aligner_cond.refDB_cond.ref_fasta, strip_ext=True) + \'.\' + $ext\n+ ln -s \'$aligner_cond.refDB_cond.ref_fasta\' \'$ref_fasta_symlink\' &&\n #end if\n \n #if not $map:\n@@ -92,14 +89,14 @@\n -tmpDir tmp_folder\n -threads "\\${GALAXY_SLOTS:-1}"\n -map \'$map\'\n-#if $sdmopt:\n- -sdmopt \'$sdmopt\'\n+#if $other_opts.sdmopt:\n+ -sdmopt \'$other_opts.sdmopt\'\n #end if\n-#if $platform != \'\':\n- -platform $platform\n+#if $other_opts.platform != \'\':\n+ -platform $other_opts.platform\n #end if\n-#if $barcode:\n- -barcode \'$barcode\'\n+#if $other_opts.barcode:\n+ -barcode \'$other_opts.barcode\'\n #end if\n #if $forwardPrimer:\n -forwardPrimer \'$forwardPrimer\'\n@@ -107,19 +104,19 @@\n #if $reversePrimer:\n -reversePrimer \'$reversePrimer\'\n #end if\n-#if $offtarget_cond.offtargetDB != \'no\':\n- -offtargetDB \'$offtarget_cond.ref_file\'\n+#if $other_opts.offtarget_cond.offtargetDB != \'no\':\n+ -offtargetDB \'$other_opts.offtarget_cond.ref_file\'\n #end if\n--useMini4map $useMini4map\n+-useMini4map $other_opts.useMini4map\n \n--clustering $clu_args.clu_cond.clustering\n-#if $clu_args.clu_cond.clustering in (\'1\', \'3\'):\n- #if str($clu_args.clu_cond.id):\n- -id $clu_args.clu_cond.id\n+-clustering $clu_cond.clustering\n+#if $clu_cond.clustering in (\'1\', \'3\'):\n+ #if str($clu_cond.id):\n+ -id $clu_cond.id\n #end if\n-#elif $clu_args.clu_cond.clustering == \'2\':\n- #if str($clu_args.clu_cond.swarm_distance):\n- -swarm_distance $clu_args.clu_cond.swarm_distance\n+#elif $clu_cond.clustering == \'2\':\n+ #if str($clu_cond.swarm_distance):\n+ -swarm_distance $clu_cond.swarm_distance\n #end if\n #end if\n #if $clu_args.derepMin:\n@@ -133,26 +130,26 @@\n -chim_skew $clu_args.chim_skew\n #end if\n \n--taxAligner $tax_args.aligner_cond.taxAligner\n-#if $tax_args.aligner_cond.taxAligner == \'0\':\n- #if str($tax_args.aligner_cond.rdp_thr):\n- -rdp_thr $tax_args.aligner_cond.rdp_thr\n+-taxAligner $aligner_cond.taxAligner\n+#if $aligner_cond.taxAligner == \'0\':\n+ #if str($aligner_cond.rdp_thr):\n+ -rdp_thr $aligner_cond.rdp_thr\n #end if\n-#elif $tax_args.aligner_cond.taxAligner == \'3\':\n- #if str($tax_args.aligner_cond.utax_thr):\n- -u'..b' help="Useful for low-bacterial biomass samples to remove possible host genome contaminations">\n+ <option value="no" selected="true">Disabled</option>\n+ <option value="cached">Use a built-in genome</option>\n+ <option value="history">Use a genome from history</option>\n+ </param>\n+ <when value="no" />\n+ <when value="cached">\n+ <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">\n+ <options from_data_table="all_fasta">\n+ <filter type="sort_by" column="2" />\n+ <validator type="no_options" message="No reference genomes are available" />\n+ </options>\n+ </param>\n+ </when>\n+ <when value="history">\n+ <param name="ref_file" type="data" format="fasta,fasta.gz" label="FASTA reference genome" />\n+ </when>\n+ </conditional>\n+ <param argument="-useMini4map" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use minimap2 instead of VSEARCH to map back reads to OTUs" />\n+ </section>\n </inputs>\n \n <outputs>\n@@ -370,13 +366,18 @@\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 </conditional>\n- <param name="platform" value="454" />\n+ <conditional name="clu_cond">\n+ <param name="clustering" value="3" />\n+ </conditional>\n <section name="clu_args">\n- <conditional name="clu_cond">\n- <param name="clustering" value="3" />\n- </conditional>\n <param name="derepMin" value="1" />\n </section>\n+ <section name="tax_args">\n+ <param name="lulu" value="false" />\n+ </section>\n+ <section name="other_opts">\n+ <param name="platform" value="454" />\n+ </section>\n <output name="otu" file="OTU.txt" compare="sim_size" />\n <output name="otu_fna" file="OTU.fna" compare="sim_size" />\n <output name="mapping" file="mapping.txt" />\n@@ -396,13 +397,18 @@\n </param>\n </conditional>\n <param name="map" value="mapping_paired.txt" />\n- <param name="platform" value="454" />\n+ <conditional name="clu_cond">\n+ <param name="clustering" value="3" />\n+ </conditional>\n <section name="clu_args">\n- <conditional name="clu_cond">\n- <param name="clustering" value="3" />\n- </conditional>\n <param name="derepMin" value="1" />\n </section>\n+ <section name="tax_args">\n+ <param name="lulu" value="false" />\n+ </section>\n+ <section name="other_opts">\n+ <param name="platform" value="454" />\n+ </section>\n <output name="otu" file="OTU_paired.txt" compare="sim_size" />\n <output name="otu_fna" file="OTU_paired.fna" compare="sim_size" />\n </test>\n@@ -411,9 +417,12 @@\n <help><![CDATA[\n If you have separate FASTA and quality files, these can be combined in a FASTQ file using the "Combine FASTA and QUAL into FASTQ" tool.\n \n-Documentation can be found at `<http://lotus2.earlham.ac.uk/>`_.\n+.. class:: infomark\n+\n+The full LotuS2 **documentation** can be found at `<http://lotus2.earlham.ac.uk/>`_.\n ]]></help>\n <citations>\n- <citation type="doi">10.1101/2021.12.24.474111</citation>\n+ <citation type="doi">10.1186/s40168-022-01365-1</citation>\n+ <citation type="doi">10.1186/s40168-021-01012-1</citation>\n </citations>\n </tool>\n' |