Mercurial > repos > greg > phylogenomics_analysis
diff phylogenomics_analysis.xml @ 99:de42cdf6e10b draft
Uploaded
| author | greg |
|---|---|
| date | Mon, 27 Mar 2017 09:57:54 -0400 |
| parents | 56dbe45f4bfb |
| children | 283f6666daf7 |
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--- a/phylogenomics_analysis.xml Thu Mar 23 15:01:27 2017 -0400 +++ b/phylogenomics_analysis.xml Mon Mar 27 09:57:54 2017 -0400 @@ -22,11 +22,10 @@ #if str($options_type) == 'advanced': #if str($input_format) == 'ptortho': - @REMOVE_GAPPY_SEQUENCES_COND@ - @SET_PHYLOGENETIC_TREES@ + @REMOVE_GAPPY_SEQUENCES_COND_PREP@ + @SET_PHYLOGENETIC_TREES_PREP@ #if str($phylogenetic_trees) == 'yes': - @TREE_INFERENCE_COND@ - #set sequence_type = 'protein' + @TREE_INFERENCE_COND_PREP@ #end if #else: ## str($input_format) == 'ptorthocs' @@ -36,20 +35,19 @@ #set options_type = $options_type_cond.options_type #if str($orthogroup_fna) == 'yes': #if str(options_type) == 'advanced': - @REMOVE_GAPPY_SEQUENCES_COND@ + @REMOVE_GAPPY_SEQUENCES_COND_PREP@ #set multiple_codon_alignments = $options_type_cond.multiple_codon_alignments - @SET_PHYLOGENETIC_TREES@ + @SET_PHYLOGENETIC_TREES_PREP@ #if str($phylogenetic_trees) == 'yes': - @TREE_INFERENCE_COND@ - #set sequence_type = $phylogenetic_trees_cond.sequence_type + @TREE_INFERENCE_COND_PREP@ #end if #end if #else: #if str(options_type) == 'advanced': - @REMOVE_GAPPY_SEQUENCES_COND@ - @SET_PHYLOGENETIC_TREES@ + @REMOVE_GAPPY_SEQUENCES_COND_PREP@ + @SET_PHYLOGENETIC_TREES_PREP@ #if str($phylogenetic_trees) == 'yes': - @TREE_INFERENCE_COND@ + @TREE_INFERENCE_COND_PREP@ #set sequence_type = $phylogenetic_trees_cond.sequence_type #end if #end if @@ -58,54 +56,42 @@ #end if python $__tool_directory__/phylogenomics_analysis.py - --num_threads \${GALAXY_SLOTS:-4} - #if str($input_format) == 'ptortho': - --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path' - #else: - --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path' - #if str($orthogroup_fna) == 'yes': - --orthogroup_fna 'true' - #end if - #set multiple_codon_alignments = $input_format_cond.multiple_codon_alignments - #if str($multiple_codon_alignments) == 'yes': - --codon_alignments 'true' - #end if - #end if --config_dir '$scaffold.fields.path' --scaffold '$scaffold.fields.path' --method $method + --num_threads \${GALAXY_SLOTS:-4} - #if str($options_type) == 'advanced': - #if str($multiple_sequence_alignments) == 'yes': - --alignments_method $multiple_sequence_alignments_option - #if str($multiple_sequence_alignments_option) == 'pasta_alignments': - --pasta_script_path '$__tool_directory__/run_pasta.py' - --pasta_iter_limit $multiple_sequence_alignments_option_cond.pasta_iter_limit + #if str($input_format) == 'ptortho': + --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path' + #if str($options_type) == 'advanced': + @REMOVE_GAPPY_SEQUENCES_COND_CMD@ + #if str($phylogenetic_trees) == 'yes': + @TREE_INFERENCE_COND_CMD@ + --sequence_type 'protein' #end if #end if - - #if str($phylogenetic_trees) == 'yes': - --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 - # configuration will be used if the --rooting_order flag is missing. + #else: + ## str($input_format) == 'ptorthocs' + --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path' + #if str($orthogroup_fna) == 'yes': + --orthogroup_fna 'true' + #if str(options_type) == 'advanced': + @REMOVE_GAPPY_SEQUENCES_COND_CMD@ + #if str($multiple_codon_alignments) == 'yes': + --codon_alignments 'true' #end if - --bootstrap_replicates $tree_inference_cond.bootstrap_replicates + #if str($phylogenetic_trees) == 'yes': + @TREE_INFERENCE_COND_CMD@ + --sequence_type = $phylogenetic_trees_cond.sequence_type + #end if #end if - --max_orthogroup_size $options_type_cond.phylogenetic_trees_cond.max_orthogroup_size - --min_orthogroup_size $options_type_cond.phylogenetic_trees_cond.min_orthogroup_size - --sequence_type $sequence_type - #end if - - #if str($remove_gappy_sequences) == 'yes': - #if str($remove_sequences_with_gaps) == 'yes': - --remove_sequences $remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of - #end if - --trim_type $trim_type_cond.trim_type - #if str($trim_type_cond.trim_type) == 'gap_trimming': - --gap_trimming $trim_type_cond.gap_trimming + #else: + #if str(options_type) == 'advanced': + @REMOVE_GAPPY_SEQUENCES_COND_CMD@ + #if str($phylogenetic_trees) == 'yes': + @TREE_INFERENCE_COND_CMD@ + --sequence_type = $phylogenetic_trees_cond.sequence_type + #end if #end if #end if #end if