Mercurial > repos > greg > plant_tribes_gene_family_aligner

comparison gene_family_aligner.xml @ 2:2810338344a1 draft

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author greg
date Tue, 01 Aug 2017 14:25:22 -0400
parents 7ba9469800b9
children a54d1ecdf5b3
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1:ab1f0bab96f3 2:2810338344a1
14 #set output_codon_alignments = False 14 #set output_codon_alignments = False
15 #else: 15 #else:
16 #set output_codon_alignments = True 16 #set output_codon_alignments = True
17 #end if 17 #end if
18 18
19 python $__tool_directory__/gene_family_aligner.py 19 python '$__tool_directory__/gene_family_aligner.py'
20 --alignment_method $alignment_method 20 --alignment_method $alignment_method
21 #if str($alignment_method) == 'pasta': 21 #if str($alignment_method) == 'pasta':
22 --pasta_script_path '$__tool_directory__/run_pasta.py' 22 --pasta_script_path '$__tool_directory__/run_pasta.py'
23 --pasta_iter_limit $alignment_method_cond.pasta_iter_limit 23 --pasta_iter_limit $alignment_method_cond.pasta_iter_limit
24 #end if 24 #end if
27 --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path' 27 --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path'
28 #else: 28 #else:
29 ## str($input_format) == 'ptorthocs' 29 ## str($input_format) == 'ptorthocs'
30 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path' 30 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path'
31 #if str($input_format_cond.codon_alignments) == 'yes': 31 #if str($input_format_cond.codon_alignments) == 'yes':
32 --codon_alignments 'true' 32 --codon_alignments true
33 #end if 33 #end if
34 #end if 34 #end if
35 #set remove_gappy_sequences = $remove_gappy_sequences_cond.remove_gappy_sequences 35 #set remove_gappy_sequences = $remove_gappy_sequences_cond.remove_gappy_sequences
36 #if str($remove_gappy_sequences) == 'yes': 36 #if str($remove_gappy_sequences) == 'yes':
37 #set trim_type_cond = $remove_gappy_sequences_cond.trim_type_cond 37 #set trim_type_cond = $remove_gappy_sequences_cond.trim_type_cond
38 #set trim_type = $trim_type_cond.trim_type 38 #set trim_type = $trim_type_cond.trim_type
39 #if str($trim_type) == 'gap_trimming' and str($trim_type_cond.gap_trimming): 39 #if str($trim_type) == 'gap_trimming' and str($trim_type_cond.gap_trimming):
40 --gap_trimming $trim_type_cond.gap_trimming 40 --gap_trimming $trim_type_cond.gap_trimming
41 #else: 41 #else:
42 ## str($trim_type) == 'automated_trimming' 42 ## str($trim_type) == 'automated_trimming'
43 --automated_trimming 'true' 43 --automated_trimming true
44 #end if 44 #end if
45 #set remove_sequences_with_gaps_cond = $remove_gappy_sequences_cond.remove_sequences_with_gaps_cond 45 #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 46 #set remove_sequences_with_gaps = $remove_sequences_with_gaps_cond.remove_sequences_with_gaps
47 #if str($remove_sequences_with_gaps) == 'yes': 47 #if str($remove_sequences_with_gaps) == 'yes':
48 #if str($remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of): 48 #if str($remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of):
73 --output_dir '$output_aln_ca.files_path' 73 --output_dir '$output_aln_ca.files_path'
74 #else: 74 #else:
75 --output '$output_aln' 75 --output '$output_aln'
76 --output_dir '$output_aln.files_path' 76 --output_dir '$output_aln.files_path'
77 #end if 77 #end if
78 #end if
79 #set output_dataset_collection = $output_dataset_collection_cond.output_dataset_collection
80 #if str($output_dataset_collection) == 'yes':
81 --output_dataset_collection dataset_collection
78 #end if 82 #end if
79 ]]></command> 83 ]]></command>
80 <inputs> 84 <inputs>
81 <conditional name="input_format_cond"> 85 <conditional name="input_format_cond">
82 <param name="input_format" type="select" label="Classified orthogroup fasta files"> 86 <param name="input_format" type="select" label="Classified orthogroup fasta files">
96 <expand macro="cond_alignment_method" /> 100 <expand macro="cond_alignment_method" />
97 <expand macro="param_codon_alignments" /> 101 <expand macro="param_codon_alignments" />
98 </when> 102 </when>
99 </conditional> 103 </conditional>
100 <expand macro="cond_remove_gappy_sequences" /> 104 <expand macro="cond_remove_gappy_sequences" />
105 <conditional name="output_dataset_collection_cond">
106 <param name="output_dataset_collection" type="select" label="Output additional dataset collection of files?">
107 <option value="no" selected="true">No</option>
108 <option value="yes">Yes</option>
109 </param>
110 <when value="no" />
111 <when value="yes" />
112 </conditional>
101 </inputs> 113 </inputs>
102 <outputs> 114 <outputs>
103 <data name="output_aln" format="ptalign" label="${tool.name} (proteins orthogroup alignments) on ${on_string}"> 115 <data name="output_aln" format="ptalign" label="${tool.name} (proteins orthogroup alignments) on ${on_string}">
104 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'no')) and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'no'</filter> 116 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'no')) and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'no'</filter>
105 </data> 117 </data>
116 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'no')) and (remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no')</filter> 128 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'no')) and (remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no')</filter>
117 </data> 129 </data>
118 <data name="output_aln_trimmed_ca" format="ptaligntrimmedca" label="${tool.name} (trimmed protein and coding sequences orthogroup alignments) on ${on_string}"> 130 <data name="output_aln_trimmed_ca" format="ptaligntrimmedca" label="${tool.name} (trimmed protein and coding sequences orthogroup alignments) on ${on_string}">
119 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes')) and (remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no')</filter> 131 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes')) and (remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no')</filter>
120 </data> 132 </data>
133 <collection name="dataset_collection" type="list" label="${tool.name} (dataset collection) on ${on_string}">
134 <discover_datasets pattern="__name__" directory="dataset_collection" format="fasta" />
135 <filter>output_dataset_collection_cond['output_dataset_collection'] == 'yes'</filter>
136 </collection>
121 </outputs> 137 </outputs>
122 <tests> 138 <tests>
123 <!-- Test framework does not currently support inputs whose associated extra_files_path contains files to be analyzed. 139 <!-- Test framework does not currently support inputs whose associated extra_files_path contains files to be analyzed.
124 <test> 140 <test>
125 </test> 141 </test>
154 170
155 - **Coverage score** - minimum fraction of sites without gaps for a sequence in a multiple sequence alignment. The score is restricted to the range 0.0 - 1.0. Zero value has no effect. 171 - **Coverage score** - minimum fraction of sites without gaps for a sequence in a multiple sequence alignment. The score is restricted to the range 0.0 - 1.0. Zero value has no effect.
156 172
157 - **Realignment iteration limit** - number of iterations to perform trimming, removal of sequences, and realignment of orthogroup sequences. Zero value has no effect. 173 - **Realignment iteration limit** - number of iterations to perform trimming, removal of sequences, and realignment of orthogroup sequences. Zero value has no effect.
158 174
175 * **Output additional dataset collection of files** - selecting 'Yes' will produce an additional output dataset collection whose elements are copies of the directories of files (these elements can be viewed with visualization tools).
176
159 .. _trimAl: http://trimal.cgenomics.org 177 .. _trimAl: http://trimal.cgenomics.org
160 178
161 </help> 179 </help>
162 <citations> 180 <citations>
163 <expand macro="citation1" /> 181 <expand macro="citation1" />