Galaxy |

Changeset 1:96e6283e4745 (2022-08-24)

Previous changeset 0:637ec5d5368c (2017-06-23)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gubbins commit d55207b02be0d64287be1629fb28056d31a98823

modified:
gubbins.xml

diff -r 637ec5d5368c -r 96e6283e4745 gubbins.xml
--- a/gubbins.xml Fri Jun 23 08:29:43 2017 -0400
+++ b/gubbins.xml Wed Aug 24 07:37:39 2022 +0000

b'@@ -1,7 +1,14 @@\n-<tool id="gubbins" name="Gubbins" version="0.1.0">\n+<tool id="gubbins" name="Gubbins" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">\n <description>Recombination detection in Bacteria</description>\n+ <macros>\n+ <token name="@TOOL_VERSION@">3.2.1</token>\n+ <token name="@VERSION_SUFFIX@">0</token>\n+ </macros>\n+ <xrefs>\n+ <xref type="bio.tools">gubbins</xref>\n+ </xrefs>\n <requirements>\n- <requirement type="package" version="2.2.1">gubbins</requirement>\n+ <requirement type="package" version="@TOOL_VERSION@">gubbins</requirement>\n </requirements>\n \n <version_command>run_gubbins.py --version</version_command>\n@@ -14,49 +21,44 @@\n \n --threads \\${GALAXY_SLOTS:-1}\n \n- #if $adv.iters\n- -i \'$adv.iters\'\n- #end if\n- \n- #if $adv.conv_meth\n- -z \'$adv.conv_meth\'\n- #end if\n- \n+ -i \'$adv.iterations\'\n+ -z \'$adv.converge_method\'\n+ $adv.extensive_search\n+\n #if $adv.outgroup\n -o \'$adv.outgroup\'\n #end if\n \n- #if $really_adv.tree_builder\n- -t \'$really_adv.tree_builder\'\n- #end if\n- \n- #if $really_adv.min_snps\n- -m \'$really_adv.min_snps\'\n- #end if\n- \n- #if $really_adv.filter_percentage\n- -f \'$really_adv.filter_percentage\'\n- #end if\n- \n- #if $really_adv.min_window_size\n- -a \'$really_adv.min_window_size\'\n- #end if\n- \n- #if $really_adv.max_window_size\n- -b \'$really_adv.max_window_size\'\n- #end if\n- \n- $really_adv.remove_duplicates\n- \n+ -t \'$really_adv.tree_builder\'\n+ -m \'$really_adv.min_snps\'\n+ -f \'$really_adv.filter_percentage\'\n+ -a \'$really_adv.min_window_size\'\n+ -b \'$really_adv.max_window_size\'\n+ -p \'$really_adv.p_value\'\n+ --trimming-ratio \'$really_adv.trimming_ratio\'\n+ $really_adv.remove_identical_sequences\n+\n foo.aln\n- \n+\n+ ## Requited because the p-value is included as prefix\n+\n+ && mv *branch_base_reconstruction.embl branch_base_reconstruction.embl\n+ && mv *filtered_polymorphic_sites.fasta filtered_polymorphic_sites.fasta\n+ && mv *filtered_polymorphic_sites.phylip filtered_polymorphic_sites.phylip\n+ && mv *node_labelled.final_tree.tre node_labelled.final_tree\n+ && mv *final_tree.tre final_tree.tre\n+ && mv *per_branch_statistics.csv per_branch_statistics.csv\n+ && mv *recombination_predictions.embl recombination_predictions.embl\n+ && mv *recombination_predictions.gff recombination_predictions.gff\n+ && mv *summary_of_snp_distribution.vcf summary_of_snp_distribution.vcf\n+\n ]]></command>\n <inputs>\n \n <param type="data" name="alignment_file" format="fasta" label="Whole genome alignment file" help="Whole genome alignment file in fasta format"/>\n \n \n- <param type="select" name="outfiles" multiple="true" display="checkboxes" label="Select the required output files" help="Default selections are the Final Tree in Newick format, the Recombination Predictions in gff3 format and the Summary of SNP Distribution">\n+ <param name="outfiles" type="select" multiple="true" display="checkboxes" label="Select the required output files" help="Default selections are the Final Tree in Newick format, the Recombination Predictions in gff3 format and the Summary of SNP Distribution">\n <option value="ftree" selected="true">Final Tree in newick format</option>\n <option value="gff" selected="true">Recombination Predictions in gff3 format</option>\n <option value="vcf" selected="true">Summary of SNP Distribution in vcf format</option>\n@@ -69,61 +71,77 @@\n \n \n+ <test expect_num_outputs="8" >\n+ <param name="alignment_file" value="multiple_recombinations.aln" ftype="fasta" />\n+ <param name="outfiles" value="ftree,gff,vcf,recomb_embl,fpoly,ppoly,stats,baseb"/>\n+ <section name="adv">\n+ <param name="expensive_research" value="true"/>\n+ </section>\n+ <section name="really_adv">\n+ <param name="tree_builder" value="fasttree"/>\n+ <param name="remove_identical_sequences" value="true"/>\n+ </section>\n+ <output name="recomb_pred_gff">\n+ <assert_contents>\n+ <has_text text="##gff-version 3" />\n+ <has_text text="sequence_4" />\n+ </assert_contents>\n+ </output>\n+ <output name="sum_snp_vcf">\n+ <assert_contents>\n+ <has_text text="##fileformat=VCFv4.2" />\n+ </assert_contents>\n+ </output>\n+ <output name="base_branch_embl">\n+ <assert_contents>\n+ <has_n_lines n="1638"/>\n+ <has_text text="sequence_8" />\n+ </assert_contents>\n+ </output>\n+ <output name="final_tree">\n+ <assert_contents>\n+ <has_n_lines n="1"/>\n+ <has_text text="sequence_10" />\n+ </assert_contents>\n+ </output>\n+ <output name="recomb_pred_embl">\n+ <assert_contents>\n+ <has_n_lines n="24"/>\n+ <has_text text="sequence_2" />\n+ </assert_contents>\n+ </output>\n+ <output name="filt_polymorph_fna">\n+ <assert_contents>\n+ <has_n_lines n="18"/>\n+ <has_text text="GAAAA" />\n+ </assert_contents>\n+ </output>\n+ <output name="filt_polymorph_phy">\n+ <assert_contents>\n+ <has_n_lines n="10"/>\n+ <has_text text="GAAAA" />\n+ </assert_contents>\n+ </output>\n+ <output name="per_b_stat_csv">\n+ <assert_contents>\n+ <has_n_lines n="18"/>\n+ <has_text text="Number of SNPs Inside Recombinations" />\n+ </assert_contents>\n+ </output>\n+ <output name="sum_snp_vcf">\n+ <assert_contents>\n+ <has_text text="ID=1,length=242" />\n+ </assert_contents>\n+ </output>\n+ </test>\n </tests>\n \n \n'