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comparison gene_family_aligner.xml @ 43:fc829bac606b draft

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author greg
date Wed, 06 Sep 2017 09:18:38 -0400
parents 7cb6a832af82
children d02010937c05
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42:7cb6a832af82 43:fc829bac606b
1 <tool id="plant_tribes_gene_family_aligner" name="GeneFamilyAligner" version="@WRAPPER_VERSION@.2"> 1 <tool id="plant_tribes_gene_family_aligner" name="GeneFamilyAligner" version="@WRAPPER_VERSION@.3.0">
2 <description>aligns integrated orthologous gene family clusters</description> 2 <description>aligns integrated 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_aligner" /> 6 <expand macro="requirements_gene_family_aligner" />
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 #set input_format = $input_format_cond.input_format 8 #set input_format = $input_format_cond.input_format
9 #set alignment_method_cond = $input_format_cond.alignment_method_cond 9 #set alignment_method_cond = $input_format_cond.alignment_method_cond
10 #set alignment_method = $alignment_method_cond.alignment_method 10 #set alignment_method = $alignment_method_cond.alignment_method
11 #if str($input_format_cond.input_format) == 'ptortho': 11 GeneFamilyAligner
12 #set output_codon_alignments = False
13 #else if str($input_format_cond.input_format) == 'ptorthocs' and str($input_format_cond.codon_alignments ) == 'no':
14 #set output_codon_alignments = False
15 #else:
16 #set output_codon_alignments = True
17 #end if
18
19 python '$__tool_directory__/gene_family_aligner.py'
20 --alignment_method $alignment_method 12 --alignment_method $alignment_method
21 #if str($alignment_method) == 'pasta': 13 #if str($alignment_method) == 'pasta':
22 --pasta_script_path '$__tool_directory__/run_pasta.py' 14 --pasta_script_path '$__tool_directory__/run_pasta.py'
23 --pasta_iter_limit $alignment_method_cond.pasta_iter_limit 15 --pasta_iter_limit $alignment_method_cond.pasta_iter_limit
24 #end if 16 #end if
27 --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path' 19 --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path'
28 #else: 20 #else:
29 ## str($input_format) == 'ptorthocs' 21 ## str($input_format) == 'ptorthocs'
30 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path' 22 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path'
31 #if str($input_format_cond.codon_alignments) == 'yes': 23 #if str($input_format_cond.codon_alignments) == 'yes':
32 --codon_alignments true 24 --codon_alignments
33 #end if 25 #end if
34 #end if 26 #end if
35 #set remove_gappy_sequences = $remove_gappy_sequences_cond.remove_gappy_sequences 27 #set remove_gappy_sequences = $remove_gappy_sequences_cond.remove_gappy_sequences
36 #if str($remove_gappy_sequences) == 'yes': 28 #if str($remove_gappy_sequences) == 'yes':
37 #set trim_type_cond = $remove_gappy_sequences_cond.trim_type_cond 29 #set trim_type_cond = $remove_gappy_sequences_cond.trim_type_cond
38 #set trim_type = $trim_type_cond.trim_type 30 #set trim_type = $trim_type_cond.trim_type
39 #if str($trim_type) == 'gap_trimming' and str($trim_type_cond.gap_trimming): 31 #if str($trim_type) == 'gap_trimming' and str($trim_type_cond.gap_trimming):
40 --gap_trimming $trim_type_cond.gap_trimming 32 --gap_trimming $trim_type_cond.gap_trimming
41 #else: 33 #else:
42 ## str($trim_type) == 'automated_trimming' 34 ## str($trim_type) == 'automated_trimming'
43 --automated_trimming true 35 --automated_trimming
44 #end if 36 #end if
45 #set remove_sequences_with_gaps_cond = $remove_gappy_sequences_cond.remove_sequences_with_gaps_cond 37 #set remove_sequences_with_gaps_cond = $remove_gappy_sequences_cond.remove_sequences_with_gaps_cond
46 #set remove_sequences_with_gaps = $remove_sequences_with_gaps_cond.remove_sequences_with_gaps 38 #set remove_sequences_with_gaps = $remove_sequences_with_gaps_cond.remove_sequences_with_gaps
47 #if str($remove_sequences_with_gaps) == 'yes': 39 #if str($remove_sequences_with_gaps) == 'yes':
48 #if str($remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of): 40 #if str($remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of):
49 --remove_sequences $remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of 41 --remove_sequences $remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of
50 #end if 42 #end if
51 #if str($remove_sequences_with_gaps_cond.iterative_realignment): 43 #if str($remove_sequences_with_gaps_cond.iterative_realignment):
52 --iterative_realignment $remove_sequences_with_gaps_cond.iterative_realignment 44 --iterative_realignment $remove_sequences_with_gaps_cond.iterative_realignment
53 #end if 45 #end if
54 #if $output_codon_alignments:
55 --output '$output_aln_filtered_ca'
56 --output_dir '$output_aln_filtered_ca.files_path'
57 #else:
58 --output '$output_aln_filtered'
59 --output_dir '$output_aln_filtered.files_path'
60 #end if
61 #else:
62 #if $output_codon_alignments:
63 --output '$output_aln_trimmed_ca'
64 --output_dir '$output_aln_trimmed_ca.files_path'
65 #else:
66 --output '$output_aln_trimmed'
67 --output_dir '$output_aln_trimmed.files_path'
68 #end if
69 #end if 46 #end if
70 #else:
71 #if $output_codon_alignments:
72 --output '$output_aln_ca'
73 --output_dir '$output_aln_ca.files_path'
74 #else:
75 --output '$output_aln'
76 --output_dir '$output_aln.files_path'
77 #end if
78 #end if
79 #if str($output_dataset_collection) == 'yes':
80 --output_dataset_collection dataset_collection
81 #end if 47 #end if
82 ]]></command> 48 ]]></command>
83 <inputs> 49 <inputs>
84 <conditional name="input_format_cond"> 50 <conditional name="input_format_cond">
85 <param name="input_format" type="select" label="Classified orthogroup fasta files"> 51 <param name="input_format" type="select" label="Classified orthogroup fasta files">
105 <option value="no" selected="true">No</option> 71 <option value="no" selected="true">No</option>
106 <option value="yes">Yes</option> 72 <option value="yes">Yes</option>
107 </param> 73 </param>
108 </inputs> 74 </inputs>
109 <outputs> 75 <outputs>
110 <data name="output_aln" format="ptalign" label="${tool.name} (proteins orthogroup alignments) on ${on_string}"> 76 <collection name="primary" type="list" label="${tool.name} (primary proteins orthogroup alignments) on ${on_string}">
111 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'no')) and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'no'</filter> 77 <discover_datasets pattern="__name__" directory="orthogroups_aln" format="fasta" />
112 </data> 78 <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'no'</filter>
113 <data name="output_aln_ca" format="ptalignca" label="${tool.name} (protein and coding sequences orthogroup alignments) on ${on_string}"> 79 </collection>
114 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes')) and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'no'</filter> 80 <collection name="trimmed" type="list" label="${tool.name} (trimmed proteins orthogroup alignments) on ${on_string}">
115 </data> 81 <discover_datasets pattern="__name__" directory="orthogroups_aln" format="fasta" />
116 <data name="output_aln_filtered" format="ptalignfiltered" label="${tool.name} (filtered proteins orthogroup alignments) on ${on_string}"> 82 <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no'</filter>
117 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'no')) and (remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes')</filter> 83 </collection>
118 </data> 84 <collection name="primary_trimmed" type="list" label="${tool.name} (primary proteins orthogroup alignments) on ${on_string}">
119 <data name="output_aln_filtered_ca" format="ptalignfilteredca" label="${tool.name} (filtered protein and coding sequences orthogroup alignments) on ${on_string}"> 85 <discover_datasets pattern="__name__" directory="other_orthogroups_aln" format="fasta" />
120 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes')) and (remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes')</filter> 86 <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no'</filter>
121 </data> 87 </collection>
122 <data name="output_aln_trimmed" format="ptaligntrimmed" label="${tool.name} (trimmed proteins orthogroup alignments) on ${on_string}"> 88 <collection name="filtered" type="list" label="${tool.name} (filtered proteins orthogroup alignments) on ${on_string}">
123 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'no')) and (remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no')</filter> 89 <discover_datasets pattern="__name__" directory="orthogroups_aln" format="fasta" />
124 </data> 90 <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes'</filter>
125 <data name="output_aln_trimmed_ca" format="ptaligntrimmedca" label="${tool.name} (trimmed protein and coding sequences orthogroup alignments) on ${on_string}"> 91 </collection>
126 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes')) and (remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no')</filter> 92 <collection name="primary_filtered" type="list" label="${tool.name} (primary and trimmed proteins orthogroup alignments) on ${on_string}">
127 </data> 93 <discover_datasets pattern="__name__" directory="other_orthogroups_aln" format="fasta" />
128 <collection name="dataset_collection" type="list" label="${tool.name} (dataset collection) on ${on_string}"> 94 <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes'</filter>
129 <discover_datasets pattern="__name__" directory="dataset_collection" format="fasta" />
130 <filter>output_dataset_collection == 'yes'</filter>
131 </collection> 95 </collection>
132 </outputs> 96 </outputs>
133 <tests> 97 <tests>
134 <!-- Test framework does not currently support inputs whose associated extra_files_path contains files to be analyzed. 98 <!-- Test framework does not currently support inputs whose associated extra_files_path contains files to be analyzed.
135 <test> 99 <test>