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comparison phylogenomics_analysis.xml @ 7:505c38cafb9c draft

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author greg
date Thu, 05 Jan 2017 14:26:38 -0500
parents 21298684d201
children 9c43870f6c51
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6:21298684d201 7:505c38cafb9c
15 #import os 15 #import os
16 #set src_dir = $os.path.join('phylogenomicsAnalysis_dir', 'orthogroups_fasta') 16 #set src_dir = $os.path.join('phylogenomicsAnalysis_dir', 'orthogroups_fasta')
17 #set dest_dir = $output.extra_files_path 17 #set dest_dir = $output.extra_files_path
18 mkdir -p $dest_dir && 18 mkdir -p $dest_dir &&
19 PhylogenomicsAnalysis 19 PhylogenomicsAnalysis
20 --orthogroup_faa "$orthogroup_fna.extra_files_path" 20 --orthogroup_faa "$orthogroup_faa.extra_files_path"
21 --scaffold "$scaffold" 21 --scaffold "$scaffold"
22 --method $method 22 --method $method
23 #if str($options_type.options_type_selector) == 'advanced': 23 #if str($options_type.options_type_selector) == 'advanced':
24 #if str($options_type.multiple_sequence_alignments_cond.multiple_sequence_alignments) == 'yes': 24 #if str($options_type.multiple_sequence_alignments_cond.multiple_sequence_alignments) == 'yes':
25 #set multiple_sequence_alignments_option_cond = $options_type.multiple_sequence_alignments_cond.multiple_sequence_alignments_option_cond 25 #set multiple_sequence_alignments_option_cond = $options_type.multiple_sequence_alignments_cond.multiple_sequence_alignments_option_cond
26 #set multiple_sequence_alignments_option = $multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option 26 #set multiple_sequence_alignments_option = $multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option
27 #set multiple_codon_alignments_cond = $options_type.multiple_sequence_alignments_cond.multiple_codon_alignments_cond 27 #set multiple_codon_alignments_cond = $options_type.multiple_sequence_alignments_cond.multiple_codon_alignments_cond
28 #set multiple_codon_alignments = $multiple_codon_alignments_cond.multiple_codon_alignments 28 #set multiple_codon_alignments = $multiple_codon_alignments_cond.multiple_codon_alignments
29 #set use_corresponding_coding_sequences_cond = $multiple_codon_alignments_cond.use_corresponding_coding_sequences_cond
30 #set use_corresponding_coding_sequences = $use_corresponding_coding_sequences_cond.use_corresponding_coding_sequences
29 #if str($multiple_sequence_alignments_option) == 'create_alignments': 31 #if str($multiple_sequence_alignments_option) == 'create_alignments':
30 --create_alignments 32 --create_alignments
31 #else if str($multiple_sequence_alignments_option) == 'add_alignments': 33 #else if str($multiple_sequence_alignments_option) == 'add_alignments':
32 --add_alignments 34 --add_alignments
33 #else if str($multiple_sequence_alignments_option) == 'pasta_alignments': 35 #else if str($multiple_sequence_alignments_option) == 'pasta_alignments':
34 --pasta_alignments 36 --pasta_alignments
35 --pasta_iter_limit $multiple_sequence_alignments_option_cond.pasta_iter_limit 37 --pasta_iter_limit $multiple_sequence_alignments_option_cond.pasta_iter_limit
36 #end if 38 #end if
37 #if str($multiple_codon_alignments) == 'yes': 39 #if str($multiple_codon_alignments) == 'yes':
38 --codon_alignments 40 --codon_alignments
39 --orthogroup_fna "$orthogroup_fna" 41 #if str($use_corresponding_coding_sequences) == 'yes':
42 --orthogroup_fna
43 #end if
40 --sequence_type $multiple_codon_alignments_cond.sequence_type 44 --sequence_type $multiple_codon_alignments_cond.sequence_type
41 #end if 45 #end if
42 #end if 46 #end if
43 #if str($options_type.phylogenetic_trees_cond.phylogenetic_trees) == 'yes': 47 #if str($options_type.phylogenetic_trees_cond.phylogenetic_trees) == 'yes':
44 #set tree_inference_cond = $options_type.phylogenetic_trees_cond.tree_inference_cond 48 #set tree_inference_cond = $options_type.phylogenetic_trees_cond.tree_inference_cond
71 && ls $src_dir >> $output 75 && ls $src_dir >> $output
72 && mv $src_dir/* $dest_dir 76 && mv $src_dir/* $dest_dir
73 ]]> 77 ]]>
74 </command> 78 </command>
75 <inputs> 79 <inputs>
76 <param name="orthogroup_fna" format="txt" type="data" label="Select sequences classified into gene family clusters"/> 80 <param name="orthogroup_faa" format="txt" type="data" label="Select sequences classified into gene family clusters"/>
77 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold"> 81 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold">
78 <options from_data_table="plant_tribes_scaffolds" /> 82 <options from_data_table="plant_tribes_scaffolds" />
79 <validator type="no_options" message="No PlantTribes scaffolds are available. Use the PlantTribes Scaffolds Download Data Manager tool to install and populate the PlantTribes scaffolds data table."/> 83 <validator type="no_options" message="No PlantTribes scaffolds are available. Use the PlantTribes Scaffolds Download Data Manager tool to install and populate the PlantTribes scaffolds data table."/>
80 </param> 84 </param>
81 <param name="method" type="select" label="Protein clustering method"> 85 <param name="method" type="select" label="Protein clustering method">
117 <when value="yes"> 121 <when value="yes">
118 <param name="sequence_type" type="select" label="Sequence type used in the phylogenetic inference - (dna)"> 122 <param name="sequence_type" type="select" label="Sequence type used in the phylogenetic inference - (dna)">
119 <option value="protein" selected="true">Amino acid based</option> 123 <option value="protein" selected="true">Amino acid based</option>
120 <option value="dna">Nucleotide based</option> 124 <option value="dna">Nucleotide based</option>
121 </param> 125 </param>
126
127
128 <conditional name="use_corresponding_coding_sequences_cond">
129 <param name="use_corresponding_coding_sequences" type="select" label="Use corresponding coding sequences if available?" help="Ignored if 'No' was selected for the 'Create corresponding coding sequences?' option in the GeneFamilyClassifier tool">
130 <option value="no" selected="true">No</option>
131 <option value="yes">Yes</option>
132 </param>
133 <when value="no" />
134 <when value="yes" />
135 </conditional>
136
137
122 </when> 138 </when>
123 <when value="no"/> 139 <when value="no"/>
124 </conditional> 140 </conditional>
125 </when> 141 </when>
126 </conditional> 142 </conditional>