Mercurial > repos > greg > phylogenomics_analysis
diff phylogenomics_analysis.xml @ 98:56dbe45f4bfb draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 23 Mar 2017 15:01:27 -0400 |
| parents | 6154253af263 |
| children | de42cdf6e10b |
line wrap: on
line diff
--- 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>