| Previous changeset 4:727c0e52e64e (2019-03-05) Next changeset 6:a39471bf7d13 (2019-03-08) |
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Commit message:
Fixed variable declaration |
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modified:
galaxy/tools/config_builder/config_builder.xml |
| b |
| diff -r 727c0e52e64e -r 343bce47219b galaxy/tools/config_builder/config_builder.xml --- a/galaxy/tools/config_builder/config_builder.xml Tue Mar 05 03:48:13 2019 -0500 +++ b/galaxy/tools/config_builder/config_builder.xml Tue Mar 05 03:59:00 2019 -0500 |
| b |
| @@ -9,79 +9,79 @@ $__tool_directory__/config_builder - #if snippy.snippy_checkbox + #if $snippy.snippy_checkbox --snippy --reference $snippy.reference - #if snippy.snippy_adv.snippy_adv_checkbox - --mapqual $snippy.mapqual - --basequal $snippy.basequal - --mincov $snippy.mincov - --minfrac $snippy.minfrac + #if $snippy.snippy_adv.snippy_adv_checkbox + --mapqual $snippy.snippy_adv.mapqual + --basequal $snippy.snippy_adv.basequal + --mincov $snippy.snippy_adv.mincov + --minfrac $snippy.snippy_adv.minfrac #end if $snippy.snp_fine --snp_thresh $snippy.snp_threshold #end if - #if mentalist.mentalist_checkbox + #if $mentalist.mentalist_checkbox --mentalist - #if mentalist.db_loc.db_selector == "local_file" + #if $mentalist.db_loc.db_selector == "local_file" --local_file - --local_db $mentalist.mlst_database + --local_db $mentalist.db_loc.mlst_database #end if - #if mentalist.db_loc.db_selector == "build_db" + #if $mentalist.db_loc.db_selector == "build_db" --build_db - --kmer $mentalist.k - --fasta_files $mentalist.fasta_files - --profile $mentalist.profile + --kmer $mentalist.db_loc.k + --fasta_files $mentalist.db_loc.fasta_files + --profile $mentalist.db_loc.profile #end if - #if mentalist.db_loc.db_selector == "download_pubmlst" + #if $mentalist.db_loc.db_selector == "download_pubmlst" --download_pubmlst - --kmer $mentalist.k - --scheme $mentalist.scheme + --kmer $mentalist.db_loc.k + --scheme $mentalist.db_loc.scheme #end if - #if mentalist.db_loc.db_selector == "download_cgmlst" + #if $mentalist.db_loc.db_selector == "download_cgmlst" --download_cgmlst - --kmer $mentalist.k - --scheme $mentalist.scheme + --kmer $mentalist.db_loc.k + --scheme $mentalist.db_loc.scheme #end if - #if mentalist.db_loc.db_selector == "download_enterobase" - --download_enterobase $mentalist.k - --entero_scheme $mentalist.scheme - --entero_type $mentalist.type + #if $mentalist.db_loc.db_selector == "download_enterobase" + --download_enterobase $mentalist.db_loc.k + --entero_scheme $mentalist.db_loc.scheme + --entero_type $mentalist.db_loc.type #end if - #if mentalist.mentalist_adv.mentalist_adv_checkbox - --mutation_threshold $mentalist.mutation_thresh - --kt $mentalist.kt + #if $mentalist.mentalist_adv.mentalist_adv_checkbox + --mutation_threshold $mentalist.mentalist_adv.mutation_thresh + --kt $mentalist.mentalist_adv.kt #end if $mentalist.mlst_fine --mlst_thresh $mentalist.mlst_threshold #end if - #if prince.prince_checkbox + #if $prince.prince_checkbox --prince $prince.cnv_fine --cnv_thresh $prince.cnv_threshold #end if - #if kwip.kwip_checkbox + #if $kwip.kwip_checkbox --kwip - #if kwip.kwip_adv.kwip_adv_checkbox - --N $kwip.N - --x $kwip.x - --ksize $kwip.ksize - --unique_kmers $kwip.unique_kmers + #if $kwip.kwip_adv.kwip_adv_checkbox + --N $kwip.kwip_adv.N + --x $kwip.kwip_adv.x + --ksize $kwip.kwip_adv.ksize + --unique_kmers $kwip.kwip_adv.unique_kmers #end if $kwip.kwip_fine --kwip_thresh $kwip.kwip_threshold #end if - #if spotyping.spotyping_checkbox + #if $spotyping.spotyping_checkbox --spotyping $spotyping.spoligo_fine --spoligo_thresh $spotyping.spoligo_threshold #end if - #if adv_clustering.adv_clustering_checkbox + #if $adv_clustering.adv_clustering_checkbox $adv_clustering.all_constraints --method $adv_clustering.method $adv_clustering.presolve |