Mercurial > repos > greg > gene_family_aligner

comparison gene_family_aligner.xml @ 10:5ad5d4204edf draft

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author greg
date Mon, 10 Apr 2017 13:36:27 -0400
parents 43341e97bb08
children 19529df59e9d
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9:43341e97bb08 10:5ad5d4204edf
42 #set remove_sequences_with_gaps_cond = $remove_gappy_sequences_cond.remove_sequences_with_gaps_cond 42 #set remove_sequences_with_gaps_cond = $remove_gappy_sequences_cond.remove_sequences_with_gaps_cond
43 #set remove_sequences_with_gaps = $remove_sequences_with_gaps_cond.remove_sequences_with_gaps 43 #set remove_sequences_with_gaps = $remove_sequences_with_gaps_cond.remove_sequences_with_gaps
44 #if str($remove_sequences_with_gaps) == 'yes': 44 #if str($remove_sequences_with_gaps) == 'yes':
45 --remove_sequences $remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of 45 --remove_sequences $remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of
46 --iterative_realignment $remove_sequences_with_gaps_cond.iterative_realignment 46 --iterative_realignment $remove_sequences_with_gaps_cond.iterative_realignment
47 --output '$output_aln_filtered' 47 #if str($input_format) == 'ptortho' or (str($input_format) == 'ptorthocs' and str($input_format_cond.codon_alignments) == 'no'):
48 --output_dir '$output_aln_filtered.files_path' 48 --output '$output_aln_filtered'
49 --output_dir '$output_aln_filtered.files_path'
50 #else:
51 --output '$output_aln_filtered_ca'
52 --output_dir '$output_aln_filtered_ca.files_path'
53 #end if
49 #else: 54 #else:
50 --output '$output_aln_trimmed' 55 #if str($input_format) == 'ptortho' or (str($input_format) == 'ptorthocs' and str($input_format_cond.codon_alignments) == 'no'):
51 --output_dir '$output_aln_trimmed.files_path' 56 --output '$output_aln_trimmed'
57 --output_dir '$output_aln_trimmed.files_path'
58 #else:
59 --output '$output_aln_trimmed_ca'
60 --output_dir '$output_aln_trimmed_ca.files_path'
61 #end if
52 #end if 62 #end if
53 #else: 63 #else:
64 #if str($input_format) == 'ptortho' or (str($input_format) == 'ptorthocs' and str($input_format_cond.codon_alignments) == 'no'):
65 --output '$output_aln'
66 --output_dir '$output_aln.files_path'
67 #else:
68 --output '$output_aln_ca'
69 --output_dir '$output_aln_ca.files_path'
70 #end if
71 #end if
72 #esle:
73 #if str($input_format) == 'ptortho' or (str($input_format) == 'ptorthocs' and str($input_format_cond.codon_alignments) == 'no'):
54 --output '$output_aln' 74 --output '$output_aln'
55 --output_dir '$output_aln.files_path' 75 --output_dir '$output_aln.files_path'
76 #else:
77 --output '$output_aln_ca'
78 --output_dir '$output_aln_ca.files_path'
56 #end if 79 #end if
57 #esle:
58 --output '$output_aln'
59 --output_dir '$output_aln.files_path'
60 #end if 80 #end if
61 ]]> 81 ]]>
62 </command> 82 </command>
63 <inputs> 83 <inputs>
64 <conditional name="input_format_cond"> 84 <conditional name="input_format_cond">
84 </when> 104 </when>
85 </conditional> 105 </conditional>
86 </inputs> 106 </inputs>
87 <outputs> 107 <outputs>
88 <data name="output_aln" format="ptalign" label="Aligned gene family sequences on ${on_string}"> 108 <data name="output_aln" format="ptalign" label="Aligned gene family sequences on ${on_string}">
89 <filter>options_type_cond['options_type'] == 'basic' or (options_type_cond['options_type'] == 'advanced' and options_type_cond['remove_gappy_sequences_cond']['remove_gappy_sequences'] == 'no')</filter> 109 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'no')) and (options_type_cond['options_type'] == 'basic' or (options_type_cond['options_type'] == 'advanced' and options_type_cond['remove_gappy_sequences_cond']['remove_gappy_sequences'] == 'no'))</filter>
110 </data>
111 <data name="output_aln_ca" format="ptalignca" label="Aligned gene family sequences with codon alignments on ${on_string}">
112 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes')) and (options_type_cond['options_type'] == 'basic' or (options_type_cond['options_type'] == 'advanced' and options_type_cond['remove_gappy_sequences_cond']['remove_gappy_sequences'] == 'no'))</filter>
90 </data> 113 </data>
91 <data name="output_aln_filtered" format="ptalignfiltered" label="Filtered aligned gene family sequences on ${on_string}"> 114 <data name="output_aln_filtered" format="ptalignfiltered" label="Filtered aligned gene family sequences on ${on_string}">
92 <filter>options_type_cond['options_type'] == 'advanced' and options_type_cond['remove_gappy_sequences_cond']['remove_gappy_sequences'] == 'yes' and options_type_cond['remove_gappy_sequences_cond']['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes'</filter> 115 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'no')) and (options_type_cond['options_type'] == 'advanced' and options_type_cond['remove_gappy_sequences_cond']['remove_gappy_sequences'] == 'yes' and options_type_cond['remove_gappy_sequences_cond']['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes'</filter>
116 </data>
117 <data name="output_aln_filtered_ca" format="ptalignfilteredca" label="Filtered aligned gene family sequences with codon alignments on ${on_string}">
118 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes')) and (options_type_cond['options_type'] == 'advanced' and options_type_cond['remove_gappy_sequences_cond']['remove_gappy_sequences'] == 'yes' and options_type_cond['remove_gappy_sequences_cond']['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes'</filter>
93 </data> 119 </data>
94 <data name="output_aln_trimmed" format="ptaligntrimmed" label="Trimmed aligned gene family sequences on ${on_string}"> 120 <data name="output_aln_trimmed" format="ptaligntrimmed" label="Trimmed aligned gene family sequences on ${on_string}">
95 <filter>options_type_cond['options_type'] == 'advanced' and options_type_cond['remove_gappy_sequences_cond']['remove_gappy_sequences'] == 'yes' and options_type_cond['remove_gappy_sequences_cond']['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no'</filter> 121 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'no')) and (options_type_cond['options_type'] == 'advanced' and options_type_cond['remove_gappy_sequences_cond']['remove_gappy_sequences'] == 'yes' and options_type_cond['remove_gappy_sequences_cond']['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no')</filter>
122 </data>
123 <data name="output_aln_trimmed_ca" format="ptaligntrimmedca" label="Trimmed aligned gene family sequences with codon alignments on ${on_string}">
124 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes')) and (options_type_cond['options_type'] == 'advanced' and options_type_cond['remove_gappy_sequences_cond']['remove_gappy_sequences'] == 'yes' and options_type_cond['remove_gappy_sequences_cond']['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no')</filter>
96 </data> 125 </data>
97 </outputs> 126 </outputs>
98 <tests> 127 <tests>
99 <!-- Test framework does not currently support inputs whose associated files_path contains files to be analyzed. 128 <!-- Test framework does not currently support inputs whose associated files_path contains files to be analyzed.
100 <test> 129 <test>