Mercurial > repos > greg > gene_family_aligner

comparison gene_family_aligner.xml @ 14:af8dad310c32 draft

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Uploaded
author greg
date Tue, 11 Apr 2017 14:21:35 -0400
parents d7e6201b8d81
children 5a5f80ea6306
comparison
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13:d7e6201b8d81 14:af8dad310c32
36 #end if 36 #end if
37 #set remove_gappy_sequences = $remove_gappy_sequences_cond.remove_gappy_sequences 37 #set remove_gappy_sequences = $remove_gappy_sequences_cond.remove_gappy_sequences
38 #if str($remove_gappy_sequences) == 'yes': 38 #if str($remove_gappy_sequences) == 'yes':
39 #set trim_type_cond = $remove_gappy_sequences_cond.trim_type_cond 39 #set trim_type_cond = $remove_gappy_sequences_cond.trim_type_cond
40 #set trim_type = $trim_type_cond.trim_type 40 #set trim_type = $trim_type_cond.trim_type
41 #if str($trim_type) == 'gap_trimming': 41 #if str($trim_type) == 'gap_trimming' and str($trim_type_cond.gap_trimming):
42 --gap_trimming $trim_type_cond.gap_trimming 42 --gap_trimming $trim_type_cond.gap_trimming
43 #else: 43 #else:
44 ## str($trim_type) == 'automated_trimming' 44 ## str($trim_type) == 'automated_trimming'
45 --automated_trimming 'true' 45 --automated_trimming 'true'
46 #end if 46 #end if
47 #set remove_sequences_with_gaps_cond = $remove_gappy_sequences_cond.remove_sequences_with_gaps_cond 47 #set remove_sequences_with_gaps_cond = $remove_gappy_sequences_cond.remove_sequences_with_gaps_cond
48 #set remove_sequences_with_gaps = $remove_sequences_with_gaps_cond.remove_sequences_with_gaps 48 #set remove_sequences_with_gaps = $remove_sequences_with_gaps_cond.remove_sequences_with_gaps
49 #if str($remove_sequences_with_gaps) == 'yes': 49 #if str($remove_sequences_with_gaps) == 'yes':
50 --remove_sequences $remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of 50 #if str($remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of):
51 --iterative_realignment $remove_sequences_with_gaps_cond.iterative_realignment 51 --remove_sequences $remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of
52 #end if
53 #if str($remove_sequences_with_gaps_cond.iterative_realignment):
54 --iterative_realignment $remove_sequences_with_gaps_cond.iterative_realignment
55 #end if
52 #if $output_codon_alignments: 56 #if $output_codon_alignments:
53 --output '$output_aln_filtered_ca' 57 --output '$output_aln_filtered_ca'
54 --output_dir '$output_aln_filtered_ca.files_path' 58 --output_dir '$output_aln_filtered_ca.files_path'
55 #else: 59 #else:
56 --output '$output_aln_filtered' 60 --output '$output_aln_filtered'
81 <param name="input_format" type="select" label="Select type of data to sub sample"> 85 <param name="input_format" type="select" label="Select type of data to sub sample">
82 <option value="ptortho">Gene family clusters</option> 86 <option value="ptortho">Gene family clusters</option>
83 <option value="ptorthocs">Gene family clusters with corresponding coding sequences</option> 87 <option value="ptorthocs">Gene family clusters with corresponding coding sequences</option>
84 </param> 88 </param>
85 <when value="ptortho"> 89 <when value="ptortho">
86 <param name="input_ptortho" format="ptortho" type="data" label="Gene family clusters" /> 90 <param name="input_ptortho" format="ptortho" type="data" label="Gene family clusters">
91 <validator type="empty_files_path" />
92 </param>
87 <expand macro="cond_alignment_method" /> 93 <expand macro="cond_alignment_method" />
88 </when> 94 </when>
89 <when value="ptorthocs"> 95 <when value="ptorthocs">
90 <param name="input_ptorthocs" format="ptorthocs" type="data" label="Gene family clusters with corresponding coding sequences" /> 96 <param name="input_ptorthocs" format="ptorthocs" type="data" label="Gene family clusters with corresponding coding sequences">
97 <validator type="empty_files_path" />
98 </param>
91 <expand macro="cond_alignment_method" /> 99 <expand macro="cond_alignment_method" />
92 <expand macro="param_codon_alignments" /> 100 <expand macro="param_codon_alignments" />
93 </when> 101 </when>
94 </conditional> 102 </conditional>
95 <expand macro="cond_remove_gappy_sequences" /> 103 <expand macro="cond_remove_gappy_sequences" />