Mercurial > repos > greg > phylogenomics_analysis
changeset 65:534604580eb5 draft
Uploaded
| author | greg |
|---|---|
| date | Tue, 28 Feb 2017 09:40:01 -0500 |
| parents | a0c347192b08 |
| children | 6d93b214ec55 |
| files | phylogenomics_analysis.xml |
| diffstat | 1 files changed, 23 insertions(+), 60 deletions(-) [+] |
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--- a/phylogenomics_analysis.xml Tue Feb 28 09:39:54 2017 -0500 +++ b/phylogenomics_analysis.xml Tue Feb 28 09:40:01 2017 -0500 @@ -1,8 +1,7 @@ -<tool id="plant_tribes_phylogenomics_analysis" name="Create multiple sequence alignments" version="0.3"> +<tool id="plant_tribes_phylogenomics_analysis" name="Create multiple sequence alignments" version="0.6.0"> <description>and inferred maximum likelihood phylogenies</description> <requirements> - <requirement type="package" version="0.3">plant_tribes_phylogenomics_analysis - </requirement> + <requirement type="package" version="0.6">plant_tribes_phylogenomics_analysis</requirement> </requirements> <stdio> <!-- Anything other than zero is an error --> @@ -18,27 +17,13 @@ #import sys #set input_format = $input_format_cond.input_format - #set pipeline_output_dir = 'phylogenomicsAnalysis_dir' - #set src_aln_dir = $os.path.join($pipeline_output_dir, 'orthogroups_aln') - #set src_fasta_dir = $os.path.join($pipeline_output_dir, 'orthogroups_fasta') - #set src_tree_dir = $os.path.join($pipeline_output_dir, 'orthogroups_tree') - - #if str($input_format) == 'ptortho': - #set dest_fasta_dir = $output_fasta_ptortho.extra_files_path - #set multiple_codon_alignments = 'no' - #set use_corresponding_coding_sequences = 'no' - #else: - #set dest_fasta_dir = $output_fasta_ptorthocs.extra_files_path + #if str($input_format) == 'ptorthocs': #set multiple_codon_alignments_cond = $input_format_cond.multiple_codon_alignments_cond #set multiple_codon_alignments = $multiple_codon_alignments_cond.multiple_codon_alignments #if str($multiple_codon_alignments) == 'yes': - #set use_corresponding_coding_sequences_cond = $multiple_codon_alignments_cond.use_corresponding_coding_sequences_cond - #set use_corresponding_coding_sequences = $use_corresponding_coding_sequences_cond.use_corresponding_coding_sequences - #else: - #set use_corresponding_coding_sequences = 'no' + --sequence_type $multiple_codon_alignments_cond.sequence_type #end if #end if - mkdir -p $dest_fasta_dir && #if str($options_type.options_type_selector) == 'advanced': #set multiple_sequence_alignments_cond = $options_type.multiple_sequence_alignments_cond @@ -47,8 +32,6 @@ #set multiple_sequence_alignments_option_cond = $options_type.multiple_sequence_alignments_cond.multiple_sequence_alignments_option_cond #set multiple_sequence_alignments_option = $multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option #set generate_output_aln = True - #set dest_aln_dir = $output_aln.extra_files_path - mkdir -p $dest_aln_dir && #else: #set generate_output_aln = False #end if @@ -58,19 +41,17 @@ #if str($options_type.options_type_selector) == 'advanced' and str($options_type.phylogenetic_trees_cond.phylogenetic_trees) == 'yes': #set generate_output_tree = True - #set dest_tree_dir = $output_tree.extra_files_path - mkdir -p $dest_tree_dir && #else: #set generate_output_tree = False #end if - PhylogenomicsAnalysis + 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' - --orthogroup_fna + --orthogroup_fna 'true' #end if --config_dir '$scaffold.fields.path' --scaffold '$scaffold.fields.path' @@ -78,13 +59,9 @@ #if str($options_type.options_type_selector) == 'advanced': #if str($multiple_sequence_alignments) == 'yes': - #if str($multiple_sequence_alignments_option) == 'create_alignments': - --create_alignments - #else if str($multiple_sequence_alignments_option) == 'add_alignments': - --add_alignments - #else if str($multiple_sequence_alignments_option) == 'pasta_alignments': + --alignments_method $multiple_sequence_alignments_option + if str($multiple_sequence_alignments_option) == 'pasta_alignments': --pasta_script_path '$__tool_directory__/run_pasta.py' - --pasta_alignments --pasta_iter_limit $multiple_sequence_alignments_option_cond.pasta_iter_limit #end if #end if @@ -98,8 +75,8 @@ #set rooting_order_file = $rooting_order_file_cond.rooting_order_file #if str($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. + # 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 $tree_inference_cond.bootstrap_replicates #end if @@ -113,36 +90,30 @@ #if str($remove_gappy_sequences_cond) == 'yes': #set trim_type_cond = $remove_gappy_sequences_cond.trim_type_cond --remove_sequences $remove_gappy_sequences_cond.remove_sequences - #if str($trim_type_cond.trim_type) == 'automated_trimming': - --automated_trimming - #else: + --trim_type $trim_type_cond.trim_type + #if str($trim_type_cond.trim_type) == 'gap_trimming': --gap_trimming $trim_type_cond.gap_trimming #end if #end if #end if #end if - >/dev/null - && echo "Sequence alignments and corresponding phylogenies" #if str($input_format) == 'ptortho': - && echo -e "#Size\tName" > $output_fasta_ptortho - && ls -l $src_fasta_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_fasta_ptortho + --output_ptortho '$output_ptortho' + --output_ptortho_dir '$output_ptortho.files_path' #else: - && echo -e "#Size\tName" > $output_fasta_ptorthocs - && ls -l $src_fasta_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_fasta_ptorthocs + --output_ptorthocs '$output_ptorthocs' + --output_ptorthocs_dir '$output_ptorthocs.files_path' #end if - && mv $src_fasta_dir/* $dest_fasta_dir || true #if $generate_output_aln: - && echo -e "#Size\tName" > $output_aln - && ls -l $src_aln_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_aln - && mv $src_aln_dir/* $dest_aln_dir || true + --output_aln '$output_aln' + --output_aln_dir '$output_aln.files_path' #end if #if $generate_output_tree: - && echo -e "#Size\tName" > $output_tree - && ls -l $src_tree_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_tree - && mv $src_tree_dir/* $dest_tree_dir || true + --output_tree '$output_tree' + --output_tree_dir '$output_tree.files_path' #end if ]]> </command> @@ -168,14 +139,6 @@ <option value="protein" selected="true">Amino acid based</option> <option value="dna">Nucleotide based</option> </param> - <conditional name="use_corresponding_coding_sequences_cond"> - <param name="use_corresponding_coding_sequences" type="select" label="Use corresponding coding sequences?"> - <option value="no" selected="true">No</option> - <option value="yes">Yes</option> - </param> - <when value="no" /> - <when value="yes" /> - </conditional> </when> </conditional> </when> @@ -213,7 +176,7 @@ <when value="create_alignments" /> <when value="add_alignments" /> <when value="pasta_alignments"> - <param name="pasta_iter_limit" type="integer" value="3" min="0" label="Maximum number of iteration that the PASTA algorithm will run" /> + <param name="pasta_iter_limit" type="integer" value="3" min="0" label="Maximum number of iteration that the PASTA algorithm will execute" /> </when> </conditional> </when> @@ -282,10 +245,10 @@ </conditional> </inputs> <outputs> - <data name="output_fasta_ptortho" format="ptortho"> + <data name="output_ptortho" format="ptortho"> <filter>input_format_cond['input_format'] == 'ptortho'</filter> </data> - <data name="output_fasta_ptorthocs" format="ptorthocs"> + <data name="output_ptorthocs" format="ptorthocs"> <filter>input_format_cond['input_format'] == 'ptorthocs'</filter> </data> <data name="output_aln" format="ptalign" label="Multiple alignments using method ${options_type['multiple_sequence_alignments_cond']['multiple_sequence_alignments_option_cond']['multiple_sequence_alignments_option']} on ${on_string}">