Mercurial > repos > greg > gene_family_aligner

comparison gene_family_aligner.xml @ 55:259901da9ed5 draft

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author greg
date Wed, 04 Oct 2017 15:05:36 -0400
parents ad8032da13b9
children f782812220e1
comparison
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54:49c4cd22e7cf 55:259901da9ed5
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
9 #set alignment_method_cond = $input_format_cond.alignment_method_cond
10 #set alignment_method = $alignment_method_cond.alignment_method 8 #set alignment_method = $alignment_method_cond.alignment_method
9 #set input_dir = 'input_dir'
10 mkdir $input_dir &&
11 #for $i in $input:
12 #set filename = $i.file_name
13 #set name = $i.name
14 ln -s $filename $input_dir/$name &&
15 #end for
11 GeneFamilyAligner 16 GeneFamilyAligner
12 --alignment_method $alignment_method 17 --alignment_method $alignment_method
13 #if str($alignment_method) == 'pasta': 18 #if str($alignment_method) == 'pasta':
14 --pasta_script_path '$__tool_directory__/run_pasta.py' 19 --pasta_script_path '$__tool_directory__/run_pasta.py'
15 --pasta_iter_limit $alignment_method_cond.pasta_iter_limit 20 --pasta_iter_limit $alignment_method_cond.pasta_iter_limit
16 #end if 21 #end if
17 --num_threads \${GALAXY_SLOTS:-4} 22 --num_threads \${GALAXY_SLOTS:-4}
18 #if str($input_format) == 'ptortho': 23 --orthogroup_faa '$input_dir'
19 --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path' 24 #if str($codon_alignments) == 'yes':
20 #else: 25 --codon_alignments
21 ## str($input_format) == 'ptorthocs'
22 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path'
23 #if str($input_format_cond.codon_alignments) == 'yes':
24 --codon_alignments
25 #end if
26 #end if 26 #end if
27 #set remove_gappy_sequences = $remove_gappy_sequences_cond.remove_gappy_sequences 27 #set remove_gappy_sequences = $remove_gappy_sequences_cond.remove_gappy_sequences
28 #if str($remove_gappy_sequences) == 'yes': 28 #if str($remove_gappy_sequences) == 'yes':
29 #set trim_type_cond = $remove_gappy_sequences_cond.trim_type_cond 29 #set trim_type_cond = $remove_gappy_sequences_cond.trim_type_cond
30 #set trim_type = $trim_type_cond.trim_type 30 #set trim_type = $trim_type_cond.trim_type
45 #end if 45 #end if
46 #end if 46 #end if
47 #end if 47 #end if
48 ]]></command> 48 ]]></command>
49 <inputs> 49 <inputs>
50 <conditional name="input_format_cond"> 50 <param name="input" format="fasta" type="data_collection" collection_type="list" label="Proteins orthogroup fasta files" />
51 <param name="input_format" type="select" label="Classified orthogroup fasta files"> 51 <expand macro="cond_alignment_method" />
52 <option value="ptortho">Proteins orthogroup fasta files</option> 52 <expand macro="param_codon_alignments" />
53 <option value="ptorthocs">Protein and coding sequences orthogroup fasta files</option>
54 </param>
55 <when value="ptortho">
56 <param name="input_ptortho" format="ptortho" type="data" label="Proteins orthogroup fasta files">
57 <validator type="empty_extra_files_path" />
58 </param>
59 <expand macro="cond_alignment_method" />
60 </when>
61 <when value="ptorthocs">
62 <param name="input_ptorthocs" format="ptorthocs" type="data" label="Protein and coding sequences orthogroup fasta files">
63 <validator type="empty_extra_files_path" />
64 </param>
65 <expand macro="cond_alignment_method" />
66 <expand macro="param_codon_alignments" />
67 </when>
68 </conditional>
69 <expand macro="cond_remove_gappy_sequences" /> 53 <expand macro="cond_remove_gappy_sequences" />
70 </inputs> 54 </inputs>
71 <outputs> 55 <outputs>
72 <collection name="primary_faa" type="list" label="${tool.name} (primary orthogroup protein alignments) on ${on_string}"> 56 <collection name="primary_faa" type="list" label="${tool.name} (primary orthogroup protein alignments) on ${on_string}">
73 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_aln_faa" format="fasta" /> 57 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_aln_faa" format="fasta" />
81 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_filtered_aln_faa" format="fasta" /> 65 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_filtered_aln_faa" format="fasta" />
82 <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes'</filter> 66 <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes'</filter>
83 </collection> 67 </collection>
84 <collection name="pristine_faa" type="list" label="${tool.name} (primary orthogroup protein alignments) on ${on_string}"> 68 <collection name="pristine_faa" type="list" label="${tool.name} (primary orthogroup protein alignments) on ${on_string}">
85 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/other_orthogroups_aln" format="fasta" /> 69 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/other_orthogroups_aln" format="fasta" />
86 <filter>input_format_cond['input_format'] == 'ptortho' and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['output_pristine_alignments'] == 'yes'</filter> 70 <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['output_pristine_alignments'] == 'yes'</filter>
87 </collection> 71 </collection>
88 <collection name="primary_fna" type="list" label="${tool.name} (primary orthogroup codon alignments) on ${on_string}"> 72 <collection name="primary_fna" type="list" label="${tool.name} (primary orthogroup codon alignments) on ${on_string}">
89 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_aln_fna" format="fasta" /> 73 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_aln_fna" format="fasta" />
90 <filter>input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes' and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'no'</filter> 74 <filter>codon_alignments == 'yes' and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'no'</filter>
91 </collection> 75 </collection>
92 <collection name="trimmed_fna" type="list" label="${tool.name} (trimmed orthogroup codon alignments) on ${on_string}"> 76 <collection name="trimmed_fna" type="list" label="${tool.name} (trimmed orthogroup codon alignments) on ${on_string}">
93 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_trimmed_aln_fna" format="fasta" /> 77 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_trimmed_aln_fna" format="fasta" />
94 <filter>input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes' and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no'</filter> 78 <filter>codon_alignments == 'yes' and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no'</filter>
95 </collection> 79 </collection>
96 <collection name="filtered_fna" type="list" label="${tool.name} (filtered orthogroup codon alignments) on ${on_string}"> 80 <collection name="filtered_fna" type="list" label="${tool.name} (filtered orthogroup codon alignments) on ${on_string}">
97 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_filtered_aln_fna" format="fasta" /> 81 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_filtered_aln_fna" format="fasta" />
98 <filter>input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes' and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes'</filter> 82 <filter>codon_alignments == 'yes' and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes'</filter>
99 </collection> 83 </collection>
100 <collection name="pristine_fna" type="list" label="${tool.name} (primary orthogroup protein and codon alignments) on ${on_string}"> 84 <collection name="pristine_fna" type="list" label="${tool.name} (primary orthogroup protein and codon alignments) on ${on_string}">
101 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/other_orthogroups_aln" format="fasta" /> 85 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/other_orthogroups_aln" format="fasta" />
102 <filter>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['output_pristine_alignments'] == 'yes'</filter> 86 <filter>codon_alignments == 'yes' and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['output_pristine_alignments'] == 'yes'</filter>
103 </collection> 87 </collection>
104 </outputs> 88 </outputs>
105 <tests> 89 <tests>
106 <test> 90 <test>
107 </test> 91 </test>