Mercurial > repos > matnguyen > pathogist
comparison galaxy/tools/config_builder/config_builder.xml @ 5:343bce47219b draft
Fixed variable declaration
| author | matnguyen |
|---|---|
| date | Tue, 05 Mar 2019 03:59:00 -0500 |
| parents | 727c0e52e64e |
| children | a39471bf7d13 |
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| 4:727c0e52e64e | 5:343bce47219b |
|---|---|
| 7 <command><![CDATA[ | 7 <command><![CDATA[ |
| 8 PATHOGIST all blank_config.yaml --new_config | 8 PATHOGIST all blank_config.yaml --new_config |
| 9 | 9 |
| 10 $__tool_directory__/config_builder | 10 $__tool_directory__/config_builder |
| 11 | 11 |
| 12 #if snippy.snippy_checkbox | 12 #if $snippy.snippy_checkbox |
| 13 --snippy | 13 --snippy |
| 14 --reference $snippy.reference | 14 --reference $snippy.reference |
| 15 #if snippy.snippy_adv.snippy_adv_checkbox | 15 #if $snippy.snippy_adv.snippy_adv_checkbox |
| 16 --mapqual $snippy.mapqual | 16 --mapqual $snippy.snippy_adv.mapqual |
| 17 --basequal $snippy.basequal | 17 --basequal $snippy.snippy_adv.basequal |
| 18 --mincov $snippy.mincov | 18 --mincov $snippy.snippy_adv.mincov |
| 19 --minfrac $snippy.minfrac | 19 --minfrac $snippy.snippy_adv.minfrac |
| 20 #end if | 20 #end if |
| 21 $snippy.snp_fine | 21 $snippy.snp_fine |
| 22 --snp_thresh $snippy.snp_threshold | 22 --snp_thresh $snippy.snp_threshold |
| 23 #end if | 23 #end if |
| 24 | 24 |
| 25 #if mentalist.mentalist_checkbox | 25 #if $mentalist.mentalist_checkbox |
| 26 --mentalist | 26 --mentalist |
| 27 #if mentalist.db_loc.db_selector == "local_file" | 27 #if $mentalist.db_loc.db_selector == "local_file" |
| 28 --local_file | 28 --local_file |
| 29 --local_db $mentalist.mlst_database | 29 --local_db $mentalist.db_loc.mlst_database |
| 30 #end if | 30 #end if |
| 31 #if mentalist.db_loc.db_selector == "build_db" | 31 #if $mentalist.db_loc.db_selector == "build_db" |
| 32 --build_db | 32 --build_db |
| 33 --kmer $mentalist.k | 33 --kmer $mentalist.db_loc.k |
| 34 --fasta_files $mentalist.fasta_files | 34 --fasta_files $mentalist.db_loc.fasta_files |
| 35 --profile $mentalist.profile | 35 --profile $mentalist.db_loc.profile |
| 36 #end if | 36 #end if |
| 37 #if mentalist.db_loc.db_selector == "download_pubmlst" | 37 #if $mentalist.db_loc.db_selector == "download_pubmlst" |
| 38 --download_pubmlst | 38 --download_pubmlst |
| 39 --kmer $mentalist.k | 39 --kmer $mentalist.db_loc.k |
| 40 --scheme $mentalist.scheme | 40 --scheme $mentalist.db_loc.scheme |
| 41 #end if | 41 #end if |
| 42 #if mentalist.db_loc.db_selector == "download_cgmlst" | 42 #if $mentalist.db_loc.db_selector == "download_cgmlst" |
| 43 --download_cgmlst | 43 --download_cgmlst |
| 44 --kmer $mentalist.k | 44 --kmer $mentalist.db_loc.k |
| 45 --scheme $mentalist.scheme | 45 --scheme $mentalist.db_loc.scheme |
| 46 #end if | 46 #end if |
| 47 #if mentalist.db_loc.db_selector == "download_enterobase" | 47 #if $mentalist.db_loc.db_selector == "download_enterobase" |
| 48 --download_enterobase $mentalist.k | 48 --download_enterobase $mentalist.db_loc.k |
| 49 --entero_scheme $mentalist.scheme | 49 --entero_scheme $mentalist.db_loc.scheme |
| 50 --entero_type $mentalist.type | 50 --entero_type $mentalist.db_loc.type |
| 51 #end if | 51 #end if |
| 52 #if mentalist.mentalist_adv.mentalist_adv_checkbox | 52 #if $mentalist.mentalist_adv.mentalist_adv_checkbox |
| 53 --mutation_threshold $mentalist.mutation_thresh | 53 --mutation_threshold $mentalist.mentalist_adv.mutation_thresh |
| 54 --kt $mentalist.kt | 54 --kt $mentalist.mentalist_adv.kt |
| 55 #end if | 55 #end if |
| 56 $mentalist.mlst_fine | 56 $mentalist.mlst_fine |
| 57 --mlst_thresh $mentalist.mlst_threshold | 57 --mlst_thresh $mentalist.mlst_threshold |
| 58 #end if | 58 #end if |
| 59 | 59 |
| 60 #if prince.prince_checkbox | 60 #if $prince.prince_checkbox |
| 61 --prince | 61 --prince |
| 62 $prince.cnv_fine | 62 $prince.cnv_fine |
| 63 --cnv_thresh $prince.cnv_threshold | 63 --cnv_thresh $prince.cnv_threshold |
| 64 #end if | 64 #end if |
| 65 | 65 |
| 66 #if kwip.kwip_checkbox | 66 #if $kwip.kwip_checkbox |
| 67 --kwip | 67 --kwip |
| 68 #if kwip.kwip_adv.kwip_adv_checkbox | 68 #if $kwip.kwip_adv.kwip_adv_checkbox |
| 69 --N $kwip.N | 69 --N $kwip.kwip_adv.N |
| 70 --x $kwip.x | 70 --x $kwip.kwip_adv.x |
| 71 --ksize $kwip.ksize | 71 --ksize $kwip.kwip_adv.ksize |
| 72 --unique_kmers $kwip.unique_kmers | 72 --unique_kmers $kwip.kwip_adv.unique_kmers |
| 73 #end if | 73 #end if |
| 74 $kwip.kwip_fine | 74 $kwip.kwip_fine |
| 75 --kwip_thresh $kwip.kwip_threshold | 75 --kwip_thresh $kwip.kwip_threshold |
| 76 #end if | 76 #end if |
| 77 | 77 |
| 78 #if spotyping.spotyping_checkbox | 78 #if $spotyping.spotyping_checkbox |
| 79 --spotyping | 79 --spotyping |
| 80 $spotyping.spoligo_fine | 80 $spotyping.spoligo_fine |
| 81 --spoligo_thresh $spotyping.spoligo_threshold | 81 --spoligo_thresh $spotyping.spoligo_threshold |
| 82 #end if | 82 #end if |
| 83 | 83 |
| 84 #if adv_clustering.adv_clustering_checkbox | 84 #if $adv_clustering.adv_clustering_checkbox |
| 85 $adv_clustering.all_constraints | 85 $adv_clustering.all_constraints |
| 86 --method $adv_clustering.method | 86 --method $adv_clustering.method |
| 87 $adv_clustering.presolve | 87 $adv_clustering.presolve |
| 88 $adv_clustering.visualize | 88 $adv_clustering.visualize |
| 89 #end if | 89 #end if |