Mercurial > repos > greg > phylogenomics_analysis
comparison phylogenomics_analysis.xml @ 82:7d07e0ebe8c9 draft
Uploaded
| author | greg |
|---|---|
| date | Wed, 22 Mar 2017 14:47:52 -0400 |
| parents | e528feaa44bd |
| children | f0f02b73d5fe |
comparison
equal
deleted
inserted
replaced
| 81:3296048d5ea0 | 82:7d07e0ebe8c9 |
|---|---|
| 22 #end if | 22 #end if |
| 23 #set phylogenetic_trees_cond = $options_type_cond.phylogenetic_trees_cond | 23 #set phylogenetic_trees_cond = $options_type_cond.phylogenetic_trees_cond |
| 24 #set phylogenetic_trees = $phylogenetic_trees_cond.phylogenetic_trees | 24 #set phylogenetic_trees = $phylogenetic_trees_cond.phylogenetic_trees |
| 25 #set remove_gappy_sequences_cond = $options_type_cond.remove_gappy_sequences_cond | 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 | 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: | |
| 30 #set sequence_type = $phylogenetic_trees_cond.sequence_type | |
| 31 #set orthogroup_fna = $input_format_cond.orthogroup_fna | |
| 32 #end if | |
| 27 #end if | 33 #end if |
| 28 | 34 |
| 29 python $__tool_directory__/phylogenomics_analysis.py | 35 python $__tool_directory__/phylogenomics_analysis.py |
| 30 --num_threads \${GALAXY_SLOTS:-4} | 36 --num_threads \${GALAXY_SLOTS:-4} |
| 31 #if str($input_format) == 'ptortho': | 37 #if str($input_format) == 'ptortho': |
| 32 --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path' | 38 --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path' |
| 33 #else: | 39 #else: |
| 34 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path' | 40 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path' |
| 35 --orthogroup_fna 'true' | 41 #if str($orthogroup_fna) == 'yes': |
| 42 --orthogroup_fna 'true' | |
| 43 #end if | |
| 36 #set multiple_codon_alignments = $input_format_cond.multiple_codon_alignments | 44 #set multiple_codon_alignments = $input_format_cond.multiple_codon_alignments |
| 37 #if str($multiple_codon_alignments) == 'yes': | 45 #if str($multiple_codon_alignments) == 'yes': |
| 38 --codon_alignments 'true' | 46 --codon_alignments 'true' |
| 39 #end if | 47 #end if |
| 40 #end if | 48 #end if |
| 65 #end if | 73 #end if |
| 66 --bootstrap_replicates $tree_inference_cond.bootstrap_replicates | 74 --bootstrap_replicates $tree_inference_cond.bootstrap_replicates |
| 67 #end if | 75 #end if |
| 68 --max_orthogroup_size $options_type_cond.phylogenetic_trees_cond.max_orthogroup_size | 76 --max_orthogroup_size $options_type_cond.phylogenetic_trees_cond.max_orthogroup_size |
| 69 --min_orthogroup_size $options_type_cond.phylogenetic_trees_cond.min_orthogroup_size | 77 --min_orthogroup_size $options_type_cond.phylogenetic_trees_cond.min_orthogroup_size |
| 70 #if str($input_format) == 'ptortho': | 78 --sequence_type $sequence_type |
| 71 --sequence_type 'protein' | |
| 72 #else: | |
| 73 --sequence_type $phylogenetic_trees_cond.sequence_type | |
| 74 #end if | |
| 75 #end if | 79 #end if |
| 76 | 80 |
| 77 #if str($remove_gappy_sequences) == 'yes': | 81 #if str($remove_gappy_sequences) == 'yes': |
| 78 #set trim_type_cond = $remove_gappy_sequences_cond.trim_type_cond | 82 #set trim_type_cond = $remove_gappy_sequences_cond.trim_type_cond |
| 79 #set trim_type = $trim_type_cond.trim_type | 83 #set trim_type = $trim_type_cond.trim_type |
| 128 </when> | 132 </when> |
| 129 </conditional> | 133 </conditional> |
| 130 </when> | 134 </when> |
| 131 <when value="ptorthocs"> | 135 <when value="ptorthocs"> |
| 132 <param name="input_ptorthocs" format="ptorthocs" type="data" label="Precomputed orthologous gene family clusters with corresponding coding sequences" /> | 136 <param name="input_ptorthocs" format="ptorthocs" type="data" label="Precomputed orthologous gene family clusters with corresponding coding sequences" /> |
| 137 <expand macro="param_orthogroup_fna" /> | |
| 133 <expand macro="param_scaffold" /> | 138 <expand macro="param_scaffold" /> |
| 134 <expand macro="param_method" /> | 139 <expand macro="param_method" /> |
| 135 <conditional name="options_type_cond"> | 140 <conditional name="options_type_cond"> |
| 136 <expand macro="param_options_type" /> | 141 <expand macro="param_options_type" /> |
| 137 <when value="basic" /> | 142 <when value="basic" /> |