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comparison gene_family_phylogeny_builder.xml @ 38:d818f553ce5a draft

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author greg
date Thu, 08 Jun 2017 10:13:26 -0400
parents a9f6d08ee79e
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37:b07dca8c7bfd 38:d818f553ce5a
2 <description>builds phylogenetic trees of aligned orthologous gene family clusters</description> 2 <description>builds phylogenetic trees of aligned orthologous gene family clusters</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements_gene_family_phylogeny_builder" /> 6 <expand macro="requirements_gene_family_phylogeny_builder" />
7 <command detect_errors="exit_code"> 7 <command detect_errors="exit_code"><![CDATA[
8 <![CDATA[ 8 #set input_format = $input_format_cond.input_format
9 #set input_format = $input_format_cond.input_format 9 #set tree_inference = $tree_inference_cond.tree_inference
10 #set tree_inference = $tree_inference_cond.tree_inference 10 #if str($tree_inference) == 'raxml':
11 #if str($tree_inference) == 'raxml': 11 #set rooting_order_file_cond = $tree_inference_cond.rooting_order_file_cond
12 #set rooting_order_file_cond = $tree_inference_cond.rooting_order_file_cond 12 #set rooting_order_file = $rooting_order_file_cond.rooting_order_file
13 #set rooting_order_file = $rooting_order_file_cond.rooting_order_file 13 #if str($rooting_order_file) == 'yes':
14 #if str($rooting_order_file) == 'yes': 14 #set rooting_order = $rooting_order_file_cond.rooting_order
15 #set rooting_order = $rooting_order_file_cond.rooting_order 15 #end if
16 #end if 16 #set bootstrap_replicates = $tree_inference_cond.bootstrap_replicates
17 #set bootstrap_replicates = $tree_inference_cond.bootstrap_replicates 17 #end if
18 #end if 18
19 19 python $__tool_directory__/gene_family_phylogeny_builder.py
20 python $__tool_directory__/gene_family_phylogeny_builder.py 20 #if str($input_format) == 'ptalign':
21 #if str($input_format) == 'ptalign': 21 --orthogroup_aln '$input_format_cond.input_ptalign.extra_files_path'
22 --orthogroup_aln '$input_format_cond.input_ptalign.extra_files_path' 22 --alignment_type 'aln'
23 --alignment_type 'aln' 23 --sequence_type 'protein'
24 --sequence_type 'protein' 24 #else if str($input_format) == 'ptalignca':
25 #else if str($input_format) == 'ptalignca': 25 --orthogroup_aln '$input_format_cond.input_ptalignca.extra_files_path'
26 --orthogroup_aln '$input_format_cond.input_ptalignca.extra_files_path' 26 --alignment_type 'aln'
27 --alignment_type 'aln' 27 --sequence_type $input_format_cond.sequence_type
28 --sequence_type $input_format_cond.sequence_type 28 #else if str($input_format) == 'ptalignfiltered':
29 #else if str($input_format) == 'ptalignfiltered': 29 --orthogroup_aln '$input_format_cond.input_ptalignfiltered.extra_files_path'
30 --orthogroup_aln '$input_format_cond.input_ptalignfiltered.extra_files_path' 30 --alignment_type 'filter'
31 --alignment_type 'filter' 31 --sequence_type 'protein'
32 --sequence_type 'protein' 32 #else if str($input_format) == 'ptalignfilteredca':
33 #else if str($input_format) == 'ptalignfilteredca': 33 --orthogroup_aln '$input_format_cond.input_ptalignfilteredca.extra_files_path'
34 --orthogroup_aln '$input_format_cond.input_ptalignfilteredca.extra_files_path' 34 --alignment_type 'filter'
35 --alignment_type 'filter' 35 --sequence_type $input_format_cond.sequence_type
36 --sequence_type $input_format_cond.sequence_type 36 #else if str($input_format) == 'ptaligntrimmed':
37 #else if str($input_format) == 'ptaligntrimmed': 37 --orthogroup_aln '$input_format_cond.input_ptaligntrimmed.extra_files_path'
38 --orthogroup_aln '$input_format_cond.input_ptaligntrimmed.extra_files_path' 38 --alignment_type 'trim'
39 --alignment_type 'trim' 39 --sequence_type 'protein'
40 --sequence_type 'protein' 40 #else if str($input_format) == 'ptaligntrimmedca':
41 #else if str($input_format) == 'ptaligntrimmedca': 41 --orthogroup_aln '$input_format_cond.input_ptaligntrimmedca.extra_files_path'
42 --orthogroup_aln '$input_format_cond.input_ptaligntrimmedca.extra_files_path' 42 --alignment_type 'trim'
43 --alignment_type 'trim' 43 --sequence_type $input_format_cond.sequence_type
44 --sequence_type $input_format_cond.sequence_type 44 #end if
45 #end if 45 --scaffold '$scaffold.fields.path'
46 --scaffold '$scaffold.fields.path' 46 --config_dir '$scaffold.fields.path'
47 --config_dir '$scaffold.fields.path' 47 --method $method
48 --method $method 48 --tree_inference $tree_inference
49 --tree_inference $tree_inference 49 #if str($tree_inference) == 'raxml':
50 #if str($tree_inference) == 'raxml': 50 #if str($rooting_order_file) == 'yes':
51 #if str($rooting_order_file) == 'yes': 51 --rooting_order '$rooting_order'
52 --rooting_order '$rooting_order' 52 ## No else block needed here because the default rooting_order
53 ## No else block needed here because the default rooting_order 53 ## configuration will be used if the --rooting_order flag is missing.
54 ## configuration will be used if the --rooting_order flag is missing. 54 #end if
55 #end if 55 --bootstrap_replicates $bootstrap_replicates
56 --bootstrap_replicates $bootstrap_replicates 56 --output_phylip '$output_phylip'
57 --output_phylip '$output_phylip' 57 --output_phylip_dir '$output_phylip.files_path'
58 --output_phylip_dir '$output_phylip.files_path' 58 #end if
59 #end if 59 --min_orthogroup_size $min_orthogroup_size
60 --min_orthogroup_size $min_orthogroup_size 60 --max_orthogroup_size $max_orthogroup_size
61 --max_orthogroup_size $max_orthogroup_size 61 --num_threads \${GALAXY_SLOTS:-4}
62 --num_threads \${GALAXY_SLOTS:-4} 62 #set output_pttree_dir = $output_pttree_dir_cond.output_pttree_dir
63 #set output_pttree_dir = $output_pttree_dir_cond.output_pttree_dir 63 #if str($output_pttree_dir) == 'yes':
64 #if str($output_pttree_dir) == 'yes': 64 --output_tree '$output_tree'
65 --output_tree '$output_tree' 65 --output_tree_dir '$output_tree.files_path'
66 --output_tree_dir '$output_tree.files_path' 66 #end if
67 #end if 67 ]]></command>
68 ]]>
69 </command>
70 <inputs> 68 <inputs>
71 <conditional name="input_format_cond"> 69 <conditional name="input_format_cond">
72 <param name="input_format" type="select" label="Orthogroup alignments"> 70 <param name="input_format" type="select" label="Orthogroup alignments">
73 <option value="ptalign">Proteins orthogroup alignments</option> 71 <option value="ptalign">Proteins orthogroup alignments</option>
74 <option value="ptalignca">Protein and coding sequences orthogroup alignments</option> 72 <option value="ptalignca">Protein and coding sequences orthogroup alignments</option>
154 <data name="output_phylip" format="ptphylip" label="${tool.name} (orthogroup phylip multiple sequence alignments) on ${on_string}"> 152 <data name="output_phylip" format="ptphylip" label="${tool.name} (orthogroup phylip multiple sequence alignments) on ${on_string}">
155 <filter>tree_inference_cond['tree_inference'] == 'raxml'</filter> 153 <filter>tree_inference_cond['tree_inference'] == 'raxml'</filter>
156 </data> 154 </data>
157 </outputs> 155 </outputs>
158 <tests> 156 <tests>
157 <!-- Test framework does not currently support inputs whose associated extra_files_path contains files to be analyzed.
159 <test> 158 <test>
160 </test> 159 </test>
160 -->
161 </tests> 161 </tests>
162 <help> 162 <help>
163 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary 163 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary
164 analyses of genome-scale gene families and transcriptomes. This tool performs gene family phylogenetic inference of 164 analyses of genome-scale gene families and transcriptomes. This tool performs gene family phylogenetic inference of
165 multiple sequence alignments produced by the GeneFamilyAligner tool. 165 multiple sequence alignments produced by the GeneFamilyAligner tool.