Mercurial > repos > greg > phylogenomics_analysis
changeset 98:56dbe45f4bfb draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 23 Mar 2017 15:01:27 -0400 |
| parents | 7389c8a99491 |
| children | de42cdf6e10b |
| files | macros.xml phylogenomics_analysis.xml |
| diffstat | 2 files changed, 109 insertions(+), 27 deletions(-) [+] |
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--- a/macros.xml Thu Mar 23 11:54:44 2017 -0400 +++ b/macros.xml Thu Mar 23 15:01:27 2017 -0400 @@ -13,6 +13,71 @@ <regex match="Exception:"/> </stdio> </xml> + <token name="@REMOVE_GAPPY_SEQUENCES_COND@"> + #set remove_gappy_sequences_cond = $options_type_cond.remove_gappy_sequences_cond + #set remove_gappy_sequences = $remove_gappy_sequences_cond.remove_gappy_sequences + #if str($remove_gappy_sequences) == 'no': + #set multiple_sequence_alignments_cond = $remove_gappy_sequences_cond.multiple_sequence_alignments_cond + #set multiple_sequence_alignments = $multiple_sequence_alignments_cond.multiple_sequence_alignments + #if str($multiple_sequence_alignments) == 'yes': + #set multiple_sequence_alignments_option_cond = $multiple_sequence_alignments_cond.multiple_sequence_alignments_option_cond + #set multiple_sequence_alignments_option = $multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option + #if str($multiple_sequence_alignments_option) == 'pasta_alignments': + #set pasta_iter_limit = $multiple_sequence_alignments_option_cond.pasta_iter_limit + #end if + #end if + #else: + #set trim_type_cond = $remove_gappy_sequences_cond.trim_type_cond + #set trim_type = $trim_type_cond.trim_type + #if str($trim_type) == 'gap_trimming': + #set gap_trimming = $trim_type_cond.gap_trimming + #end if + #set remove_sequences_with_gaps_cond = $remove_gappy_sequences_cond.remove_sequences_with_gaps_cond + #set remove_sequences_with_gaps = $remove_sequences_with_gaps_cond.remove_sequences_with_gaps + #if str($remove_sequences_with_gaps) == 'no': + #set multiple_sequence_alignments_cond = $remove_sequences_with_gaps_cond.multiple_sequence_alignments_cond + #set multiple_sequence_alignments = $multiple_sequence_alignments_cond.multiple_sequence_alignments + #if str($multiple_sequence_alignments) == 'yes': + #set multiple_sequence_alignments_option_cond = $multiple_sequence_alignments_cond.multiple_sequence_alignments_option_cond + #set multiple_sequence_alignments_option = $multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option + #if str($multiple_sequence_alignments_option) == 'pasta_alignments': + #set pasta_iter_limit = $multiple_sequence_alignments_option_cond.pasta_iter_limit + #end if + #end if + #else: + #set remove_sequences_with_gaps_of = $remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of + #set multiple_sequence_alignments_cond = $remove_sequences_with_gaps_cond.multiple_sequence_alignments_cond + #set multiple_sequence_alignments = $multiple_sequence_alignments_cond.multiple_sequence_alignments + #if str($multiple_sequence_alignments) == 'yes': + #set multiple_sequence_alignments_option_cond = $multiple_sequence_alignments_cond.multiple_sequence_alignments_option_cond + #set multiple_sequence_alignments_option = $multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option + #if str($multiple_sequence_alignments_option) == 'pasta_alignments': + #set pasta_iter_limit = $multiple_sequence_alignments_option_cond.pasta_iter_limit + #else if str($multiple_sequence_alignments_option) == 'iterative_realignments': + #set iterative_realignments = $multiple_sequence_alignments_option_cond.iterative_realignments + #end if + #end if + #end if + #end if + </token> + <token name="@SET_PHYLOGENETIC_TREES@"> + #set phylogenetic_trees_cond = $options_type_cond.phylogenetic_trees_cond + #set phylogenetic_trees = $phylogenetic_trees_cond.phylogenetic_trees + </token> + <token name="@TREE_INFERENCE_COND@"> + #set tree_inference_cond = $phylogenetic_trees_cond.tree_inference_cond + #set tree_inference = $tree_inference_cond.tree_inference + #if str($tree_inference) == 'raxml': + #set rooting_order_file_cond = $tree_inference_cond.rooting_order_file_cond + #set rooting_order_file = $rooting_order_file_cond.rooting_order_file + #if str($rooting_order_file) == 'yes': + #set rooting_order = $rooting_order_file_cond.rooting_order + #end if + #set bootstrap_replicates = $tree_inference_cond.bootstrap_replicates + #end if + #set max_orthogroup_size = $phylogenetic_trees_cond.max_orthogroup_size + #set min_orthogroup_size = $phylogenetic_trees_cond.min_orthogroup_size + </token> <xml name="param_scaffold"> <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold"> <options from_data_table="plant_tribes_scaffolds" /> @@ -202,10 +267,10 @@ <option value="gap_trimming" selected="true">Nucleotide based </option> <option value="automated_trimming">Trim alignments using trimAl's ML heuristic trimming approach</option> </param> - <when value="automated_trimming" /> <when value="gap_trimming"> <param name="gap_trimming" type="float" value="0.1" min="0" max="1.0" label="Remove sites in alignments with gaps of" help="0.1 removes sites with 90% gaps" /> </when> + <when value="automated_trimming" /> </conditional> <conditional name="remove_sequences_with_gaps_cond"> <param name="remove_sequences_with_gaps" type="select" label="Remove sequences with specified gaps?">
--- a/phylogenomics_analysis.xml Thu Mar 23 11:54:44 2017 -0400 +++ b/phylogenomics_analysis.xml Thu Mar 23 15:01:27 2017 -0400 @@ -10,25 +10,50 @@ #set input_format = $input_format_cond.input_format #set scaffold = $input_format_cond.scaffold #set method = $input_format_cond.method - #set options_type_cond = $input_format_cond.options_type_cond + + #if str($input_format) == 'ptortho': + #set options_type_cond = $input_format_cond.options_type_cond + #else: + #set orthogroup_fna_cond = $input_format_cond.orthogroup_fna_cond + #set orthogroup_fna= $orthogroup_fna_cond.orthogroup_fna + #set options_type_cond = $orthogroup_fna_cond.options_type_cond + #endif #set options_type= $options_type_cond.options_type #if str($options_type) == 'advanced': - #set multiple_sequence_alignments_cond = $options_type_cond.multiple_sequence_alignments_cond - #set multiple_sequence_alignments = $multiple_sequence_alignments_cond.multiple_sequence_alignments - #if str($multiple_sequence_alignments) == 'yes': - #set multiple_sequence_alignments_option_cond = $options_type_cond.multiple_sequence_alignments_cond.multiple_sequence_alignments_option_cond - #set multiple_sequence_alignments_option = $multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option - #end if - #set phylogenetic_trees_cond = $options_type_cond.phylogenetic_trees_cond - #set phylogenetic_trees = $phylogenetic_trees_cond.phylogenetic_trees - #set remove_gappy_sequences_cond = $options_type_cond.remove_gappy_sequences_cond - #set remove_gappy_sequences = $remove_gappy_sequences_cond.remove_gappy_sequences - #if str(input_format) == 'ptortho': - #set sequence_type = 'protein' + #if str($input_format) == 'ptortho': + @REMOVE_GAPPY_SEQUENCES_COND@ + @SET_PHYLOGENETIC_TREES@ + #if str($phylogenetic_trees) == 'yes': + @TREE_INFERENCE_COND@ + #set sequence_type = 'protein' + #end if #else: - #set sequence_type = $phylogenetic_trees_cond.sequence_type - #set orthogroup_fna = $input_format_cond.orthogroup_fna + ## str($input_format) == 'ptorthocs' + #set orthogroup_fna_cond = $input_format_cond.orthogroup_fna_cond + #set orthogroup_fna = $orthogroup_fna_cond.orthogroup_fna + #set options_type_cond = orthogroup_fna_cond.options_type_cond + #set options_type = $options_type_cond.options_type + #if str($orthogroup_fna) == 'yes': + #if str(options_type) == 'advanced': + @REMOVE_GAPPY_SEQUENCES_COND@ + #set multiple_codon_alignments = $options_type_cond.multiple_codon_alignments + @SET_PHYLOGENETIC_TREES@ + #if str($phylogenetic_trees) == 'yes': + @TREE_INFERENCE_COND@ + #set sequence_type = $phylogenetic_trees_cond.sequence_type + #end if + #end if + #else: + #if str(options_type) == 'advanced': + @REMOVE_GAPPY_SEQUENCES_COND@ + @SET_PHYLOGENETIC_TREES@ + #if str($phylogenetic_trees) == 'yes': + @TREE_INFERENCE_COND@ + #set sequence_type = $phylogenetic_trees_cond.sequence_type + #end if + #end if + #end if #end if #end if @@ -60,12 +85,8 @@ #end if #if str($phylogenetic_trees) == 'yes': - #set tree_inference_cond = $options_type_cond.phylogenetic_trees_cond.tree_inference_cond - #set tree_inference_method = $tree_inference_cond.tree_inference - --tree_inference $tree_inference_method - #if str($tree_inference_method) == 'raxml': - #set rooting_order_file_cond = $tree_inference_cond.rooting_order_file_cond - #set rooting_order_file = $rooting_order_file_cond.rooting_order_file + --tree_inference $tree_inference + #if str($tree_inference) == 'raxml': #if str($rooting_order_file) == 'yes': --rooting_order '$rooting_order_file_cond.rooting_order' # No else block needed here because the default rooting_order @@ -79,10 +100,6 @@ #end if #if str($remove_gappy_sequences) == 'yes': - #set trim_type_cond = $remove_gappy_sequences_cond.trim_type_cond - #set trim_type = $trim_type_cond.trim_type - #set remove_sequences_with_gaps_cond = $remove_gappy_sequences_cond.remove_sequences_with_gaps_cond - #set remove_sequences_with_gaps = $remove_sequences_with_gaps_cond.remove_sequences_with_gaps #if str($remove_sequences_with_gaps) == 'yes': --remove_sequences $remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of #end if @@ -126,8 +143,8 @@ <expand macro="param_options_type" /> <when value="basic" /> <when value="advanced"> + <expand macro="cond_remove_gappy_sequences" /> <expand macro="cond_phylogenetic_trees_ptortho" /> - <expand macro="cond_remove_gappy_sequences" /> </when> </conditional> </when>