Mercurial > repos > greg > phylogenomics_analysis
changeset 99:de42cdf6e10b draft
Uploaded
| author | greg |
|---|---|
| date | Mon, 27 Mar 2017 09:57:54 -0400 |
| parents | 56dbe45f4bfb |
| children | 283f6666daf7 |
| files | macros.xml phylogenomics_analysis.xml |
| diffstat | 2 files changed, 102 insertions(+), 64 deletions(-) [+] |
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--- a/macros.xml Thu Mar 23 15:01:27 2017 -0400 +++ b/macros.xml Mon Mar 27 09:57:54 2017 -0400 @@ -13,7 +13,7 @@ <regex match="Exception:"/> </stdio> </xml> - <token name="@REMOVE_GAPPY_SEQUENCES_COND@"> + <token name="@REMOVE_GAPPY_SEQUENCES_COND_PREP@"> #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': @@ -53,18 +53,57 @@ #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 = $multiple_sequence_alignments_option_cond.iterative_realignments + #else if str($multiple_sequence_alignments_option) == 'iterative_realignment': + #set iterative_realignment = $multiple_sequence_alignments_option_cond.iterative_realignment #end if #end if #end if #end if </token> - <token name="@SET_PHYLOGENETIC_TREES@"> + <token name="@REMOVE_GAPPY_SEQUENCES_COND_CMD@"> + #if str($remove_gappy_sequences) == 'no': + #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 $pasta_iter_limit + #end if + #end if + #else: + ## str($remove_gappy_sequences) == 'yes': + --trim_type $trim_type + #if str($trim_type) == 'gap_trimming': + --gap_trimming $gap_trimming + #end if + #if str($remove_sequences_with_gaps) == 'no': + #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 $pasta_iter_limit + #end if + #end if + #else: + ## str($remove_sequences_with_gaps) == 'yes': + --remove_sequences $remove_sequences_with_gaps_of + #if str($multiple_sequence_alignments) == 'yes': + --alignments_method $multiple_sequence_alignments_option + #if str($multiple_sequence_alignments_option) == 'pasta_alignments': + #if str($multiple_sequence_alignments_option) == 'pasta_alignments': + --pasta_script_path '$__tool_directory__/run_pasta.py' + --pasta_iter_limit $pasta_iter_limit + #else: + --iterative_realignment $iterative_realignment + #end if + #end if + #end if + #end if + </token> + <token name="@SET_PHYLOGENETIC_TREES_PREP@"> #set phylogenetic_trees_cond = $options_type_cond.phylogenetic_trees_cond #set phylogenetic_trees = $phylogenetic_trees_cond.phylogenetic_trees </token> - <token name="@TREE_INFERENCE_COND@"> + <token name="@TREE_INFERENCE_COND_PREP@"> #set tree_inference_cond = $phylogenetic_trees_cond.tree_inference_cond #set tree_inference = $tree_inference_cond.tree_inference #if str($tree_inference) == 'raxml': @@ -75,8 +114,21 @@ #end if #set bootstrap_replicates = $tree_inference_cond.bootstrap_replicates #end if + #set min_orthogroup_size = $phylogenetic_trees_cond.min_orthogroup_size #set max_orthogroup_size = $phylogenetic_trees_cond.max_orthogroup_size - #set min_orthogroup_size = $phylogenetic_trees_cond.min_orthogroup_size + </token> + <token name="@TREE_INFERENCE_COND_CMD@"> + --tree_inference $tree_inference + #if str($tree_inference) == 'raxml': + #if str($rooting_order_file) == 'yes': + --rooting_order '$rooting_order' + ## No else block needed here because the default rooting_order + ## configuration will be used if the --rooting_order flag is missing. + #end if + --bootstrap_replicates $bootstrap_replicates + #end if + --min_orthogroup_size $min_orthogroup_size + --max_orthogroup_size $max_orthogroup_size </token> <xml name="param_scaffold"> <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold"> @@ -142,10 +194,10 @@ <expand macro="options_multiple_sequence_alignments_option" /> </param> </xml> - <xml name="param_multiple_sequence_alignments_option_with_iterative_realignments"> + <xml name="param_multiple_sequence_alignments_option_with_iterative_realignment"> <param name="multiple_sequence_alignments_option" type="select" force_select="true" label="Select method for multiple sequence alignments"> <expand macro="options_multiple_sequence_alignments_option" /> - <option value="iterative_realignments">Iterative orthogroups realignment, trimming and fitering</option> + <option value="iterative_realignment">Iterative orthogroups realignment, trimming and fitering</option> </param> </xml> <xml name="whens_multiple_sequence_alignments_option_cond"> @@ -167,16 +219,16 @@ </when> </conditional> </xml> - <xml name="cond_multiple_sequence_alignments_with_iterative_realignments"> + <xml name="cond_multiple_sequence_alignments_with_iterative_realignment"> <conditional name="multiple_sequence_alignments_cond"> <expand macro="param_multiple_sequence_alignments" /> <when value="no" /> <when value="yes"> <conditional name="multiple_sequence_alignments_option_cond"> - <expand macro="param_multiple_sequence_alignments_option_with_iterative_realignments" /> + <expand macro="param_multiple_sequence_alignments_option_with_iterative_realignment" /> <expand macro="whens_multiple_sequence_alignments_option_cond" /> - <when value="iterative_realignments"> - <param name="iterative_realignments" type="integer" value="0" min="0" label="Maximum number of iterations" help="Zero value has no affect"/> + <when value="iterative_realignment"> + <param name="iterative_realignment" type="integer" value="0" min="0" label="Maximum number of iterations" help="Zero value has no affect"/> </when> </conditional> </when> @@ -282,7 +334,7 @@ </when> <when value="yes"> <param name="remove_sequences_with_gaps_of" type="float" value="0.5" min="0" max="1" label="Remove sequences with gaps of" help="0.5 removes sequences with 50% gaps" /> - <expand macro="cond_multiple_sequence_alignments_with_iterative_realignments" /> + <expand macro="cond_multiple_sequence_alignments_with_iterative_realignment" /> </when> </conditional> </when>
--- 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