Mercurial > repos > greg > phylogenomics_analysis
comparison phylogenomics_analysis.xml @ 98:56dbe45f4bfb draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 23 Mar 2017 15:01:27 -0400 |
| parents | 6154253af263 |
| children | de42cdf6e10b |
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| 97:7389c8a99491 | 98:56dbe45f4bfb |
|---|---|
| 8 <command> | 8 <command> |
| 9 <![CDATA[ | 9 <![CDATA[ |
| 10 #set input_format = $input_format_cond.input_format | 10 #set input_format = $input_format_cond.input_format |
| 11 #set scaffold = $input_format_cond.scaffold | 11 #set scaffold = $input_format_cond.scaffold |
| 12 #set method = $input_format_cond.method | 12 #set method = $input_format_cond.method |
| 13 #set options_type_cond = $input_format_cond.options_type_cond | 13 |
| 14 #if str($input_format) == 'ptortho': | |
| 15 #set options_type_cond = $input_format_cond.options_type_cond | |
| 16 #else: | |
| 17 #set orthogroup_fna_cond = $input_format_cond.orthogroup_fna_cond | |
| 18 #set orthogroup_fna= $orthogroup_fna_cond.orthogroup_fna | |
| 19 #set options_type_cond = $orthogroup_fna_cond.options_type_cond | |
| 20 #endif | |
| 14 #set options_type= $options_type_cond.options_type | 21 #set options_type= $options_type_cond.options_type |
| 15 | 22 |
| 16 #if str($options_type) == 'advanced': | 23 #if str($options_type) == 'advanced': |
| 17 #set multiple_sequence_alignments_cond = $options_type_cond.multiple_sequence_alignments_cond | 24 #if str($input_format) == 'ptortho': |
| 18 #set multiple_sequence_alignments = $multiple_sequence_alignments_cond.multiple_sequence_alignments | 25 @REMOVE_GAPPY_SEQUENCES_COND@ |
| 19 #if str($multiple_sequence_alignments) == 'yes': | 26 @SET_PHYLOGENETIC_TREES@ |
| 20 #set multiple_sequence_alignments_option_cond = $options_type_cond.multiple_sequence_alignments_cond.multiple_sequence_alignments_option_cond | 27 #if str($phylogenetic_trees) == 'yes': |
| 21 #set multiple_sequence_alignments_option = $multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option | 28 @TREE_INFERENCE_COND@ |
| 22 #end if | 29 #set sequence_type = 'protein' |
| 23 #set phylogenetic_trees_cond = $options_type_cond.phylogenetic_trees_cond | 30 #end if |
| 24 #set phylogenetic_trees = $phylogenetic_trees_cond.phylogenetic_trees | |
| 25 #set remove_gappy_sequences_cond = $options_type_cond.remove_gappy_sequences_cond | |
| 26 #set remove_gappy_sequences = $remove_gappy_sequences_cond.remove_gappy_sequences | |
| 27 #if str(input_format) == 'ptortho': | |
| 28 #set sequence_type = 'protein' | |
| 29 #else: | 31 #else: |
| 30 #set sequence_type = $phylogenetic_trees_cond.sequence_type | 32 ## str($input_format) == 'ptorthocs' |
| 31 #set orthogroup_fna = $input_format_cond.orthogroup_fna | 33 #set orthogroup_fna_cond = $input_format_cond.orthogroup_fna_cond |
| 34 #set orthogroup_fna = $orthogroup_fna_cond.orthogroup_fna | |
| 35 #set options_type_cond = orthogroup_fna_cond.options_type_cond | |
| 36 #set options_type = $options_type_cond.options_type | |
| 37 #if str($orthogroup_fna) == 'yes': | |
| 38 #if str(options_type) == 'advanced': | |
| 39 @REMOVE_GAPPY_SEQUENCES_COND@ | |
| 40 #set multiple_codon_alignments = $options_type_cond.multiple_codon_alignments | |
| 41 @SET_PHYLOGENETIC_TREES@ | |
| 42 #if str($phylogenetic_trees) == 'yes': | |
| 43 @TREE_INFERENCE_COND@ | |
| 44 #set sequence_type = $phylogenetic_trees_cond.sequence_type | |
| 45 #end if | |
| 46 #end if | |
| 47 #else: | |
| 48 #if str(options_type) == 'advanced': | |
| 49 @REMOVE_GAPPY_SEQUENCES_COND@ | |
| 50 @SET_PHYLOGENETIC_TREES@ | |
| 51 #if str($phylogenetic_trees) == 'yes': | |
| 52 @TREE_INFERENCE_COND@ | |
| 53 #set sequence_type = $phylogenetic_trees_cond.sequence_type | |
| 54 #end if | |
| 55 #end if | |
| 56 #end if | |
| 32 #end if | 57 #end if |
| 33 #end if | 58 #end if |
| 34 | 59 |
| 35 python $__tool_directory__/phylogenomics_analysis.py | 60 python $__tool_directory__/phylogenomics_analysis.py |
| 36 --num_threads \${GALAXY_SLOTS:-4} | 61 --num_threads \${GALAXY_SLOTS:-4} |
| 58 --pasta_iter_limit $multiple_sequence_alignments_option_cond.pasta_iter_limit | 83 --pasta_iter_limit $multiple_sequence_alignments_option_cond.pasta_iter_limit |
| 59 #end if | 84 #end if |
| 60 #end if | 85 #end if |
| 61 | 86 |
| 62 #if str($phylogenetic_trees) == 'yes': | 87 #if str($phylogenetic_trees) == 'yes': |
| 63 #set tree_inference_cond = $options_type_cond.phylogenetic_trees_cond.tree_inference_cond | 88 --tree_inference $tree_inference |
| 64 #set tree_inference_method = $tree_inference_cond.tree_inference | 89 #if str($tree_inference) == 'raxml': |
| 65 --tree_inference $tree_inference_method | |
| 66 #if str($tree_inference_method) == 'raxml': | |
| 67 #set rooting_order_file_cond = $tree_inference_cond.rooting_order_file_cond | |
| 68 #set rooting_order_file = $rooting_order_file_cond.rooting_order_file | |
| 69 #if str($rooting_order_file) == 'yes': | 90 #if str($rooting_order_file) == 'yes': |
| 70 --rooting_order '$rooting_order_file_cond.rooting_order' | 91 --rooting_order '$rooting_order_file_cond.rooting_order' |
| 71 # No else block needed here because the default rooting_order | 92 # No else block needed here because the default rooting_order |
| 72 # configuration will be used if the --rooting_order flag is missing. | 93 # configuration will be used if the --rooting_order flag is missing. |
| 73 #end if | 94 #end if |
| 77 --min_orthogroup_size $options_type_cond.phylogenetic_trees_cond.min_orthogroup_size | 98 --min_orthogroup_size $options_type_cond.phylogenetic_trees_cond.min_orthogroup_size |
| 78 --sequence_type $sequence_type | 99 --sequence_type $sequence_type |
| 79 #end if | 100 #end if |
| 80 | 101 |
| 81 #if str($remove_gappy_sequences) == 'yes': | 102 #if str($remove_gappy_sequences) == 'yes': |
| 82 #set trim_type_cond = $remove_gappy_sequences_cond.trim_type_cond | |
| 83 #set trim_type = $trim_type_cond.trim_type | |
| 84 #set remove_sequences_with_gaps_cond = $remove_gappy_sequences_cond.remove_sequences_with_gaps_cond | |
| 85 #set remove_sequences_with_gaps = $remove_sequences_with_gaps_cond.remove_sequences_with_gaps | |
| 86 #if str($remove_sequences_with_gaps) == 'yes': | 103 #if str($remove_sequences_with_gaps) == 'yes': |
| 87 --remove_sequences $remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of | 104 --remove_sequences $remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of |
| 88 #end if | 105 #end if |
| 89 --trim_type $trim_type_cond.trim_type | 106 --trim_type $trim_type_cond.trim_type |
| 90 #if str($trim_type_cond.trim_type) == 'gap_trimming': | 107 #if str($trim_type_cond.trim_type) == 'gap_trimming': |
| 124 <expand macro="param_method" /> | 141 <expand macro="param_method" /> |
| 125 <conditional name="options_type_cond"> | 142 <conditional name="options_type_cond"> |
| 126 <expand macro="param_options_type" /> | 143 <expand macro="param_options_type" /> |
| 127 <when value="basic" /> | 144 <when value="basic" /> |
| 128 <when value="advanced"> | 145 <when value="advanced"> |
| 146 <expand macro="cond_remove_gappy_sequences" /> | |
| 129 <expand macro="cond_phylogenetic_trees_ptortho" /> | 147 <expand macro="cond_phylogenetic_trees_ptortho" /> |
| 130 <expand macro="cond_remove_gappy_sequences" /> | |
| 131 </when> | 148 </when> |
| 132 </conditional> | 149 </conditional> |
| 133 </when> | 150 </when> |
| 134 <when value="ptorthocs"> | 151 <when value="ptorthocs"> |
| 135 <param name="input_ptorthocs" format="ptorthocs" type="data" label="Precomputed orthologous gene family clusters with corresponding coding sequences" /> | 152 <param name="input_ptorthocs" format="ptorthocs" type="data" label="Precomputed orthologous gene family clusters with corresponding coding sequences" /> |