Mercurial > repos > greg > gene_family_aligner

comparison gene_family_aligner.xml @ 12:19529df59e9d draft

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Uploaded
author greg
date Mon, 10 Apr 2017 14:43:28 -0400
parents 5ad5d4204edf
children d7e6201b8d81
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11:a2b29eb5459d 12:19529df59e9d
8 <command> 8 <command>
9 <![CDATA[ 9 <![CDATA[
10 #set input_format = $input_format_cond.input_format 10 #set input_format = $input_format_cond.input_format
11 #set alignment_method_cond = $input_format_cond.alignment_method_cond 11 #set alignment_method_cond = $input_format_cond.alignment_method_cond
12 #set alignment_method = $alignment_method_cond.alignment_method 12 #set alignment_method = $alignment_method_cond.alignment_method
13 #if str($input_format_cond.input_format) == 'ptortho':
14 #set output_codon_alignments == False
15 #else if str($input_format_cond.input_format) == 'ptorthocs' and str($input_format_cond.codon_alignments ) == 'no':
16 #set output_codon_alignments == False
17 #else:
18 #set output_codon_alignments == True
19 #end if
13 20
14 python $__tool_directory__/gene_family_aligner.py 21 python $__tool_directory__/gene_family_aligner.py
15 --alignment_method $alignment_method 22 --alignment_method $alignment_method
16 #if str($alignment_method) == 'pasta': 23 #if str($alignment_method) == 'pasta':
17 --pasta_script_path '$__tool_directory__/run_pasta.py' 24 --pasta_script_path '$__tool_directory__/run_pasta.py'
25 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path' 32 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path'
26 #if str($input_format_cond.codon_alignments) == 'yes': 33 #if str($input_format_cond.codon_alignments) == 'yes':
27 --codon_alignments 'true' 34 --codon_alignments 'true'
28 #end if 35 #end if
29 #end if 36 #end if
30 #if str($options_type_cond.options_type) == 'advanced': 37 #set remove_gappy_sequences = $remove_gappy_sequences_cond.remove_gappy_sequences
31 #set remove_gappy_sequences_cond = $options_type_cond.remove_gappy_sequences_cond 38 #if str($remove_gappy_sequences) == 'yes':
32 #set remove_gappy_sequences = $remove_gappy_sequences_cond.remove_gappy_sequences 39 #set trim_type_cond = $remove_gappy_sequences_cond.trim_type_cond
33 #if str($remove_gappy_sequences) == 'yes': 40 #set trim_type = $trim_type_cond.trim_type
34 #set trim_type_cond = $remove_gappy_sequences_cond.trim_type_cond 41 #if str($trim_type) == 'gap_trimming':
35 #set trim_type = $trim_type_cond.trim_type 42 --gap_trimming $trim_type_cond.gap_trimming
36 #if str($trim_type) == 'gap_trimming': 43 #else:
37 --gap_trimming $trim_type_cond.gap_trimming 44 ## str($trim_type) == 'automated_trimming'
45 --automated_trimming 'true'
46 #end if
47 #set remove_sequences_with_gaps_cond = $remove_gappy_sequences_cond.remove_sequences_with_gaps_cond
48 #set remove_sequences_with_gaps = $remove_sequences_with_gaps_cond.remove_sequences_with_gaps
49 #if str($remove_sequences_with_gaps) == 'yes':
50 --remove_sequences $remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of
51 --iterative_realignment $remove_sequences_with_gaps_cond.iterative_realignment
52 #if $output_codon_alignments:
53 --output '$output_aln_filtered_ca'
54 --output_dir '$output_aln_filtered_ca.files_path'
38 #else: 55 #else:
39 ## str($trim_type) == 'automated_trimming' 56 --output '$output_aln_filtered'
40 --automated_trimming 'true' 57 --output_dir '$output_aln_filtered.files_path'
41 #end if
42 #set remove_sequences_with_gaps_cond = $remove_gappy_sequences_cond.remove_sequences_with_gaps_cond
43 #set remove_sequences_with_gaps = $remove_sequences_with_gaps_cond.remove_sequences_with_gaps
44 #if str($remove_sequences_with_gaps) == 'yes':
45 --remove_sequences $remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of
46 --iterative_realignment $remove_sequences_with_gaps_cond.iterative_realignment
47 #if str($input_format) == 'ptortho' or (str($input_format) == 'ptorthocs' and str($input_format_cond.codon_alignments) == 'no'):
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
54 #else:
55 #if str($input_format) == 'ptortho' or (str($input_format) == 'ptorthocs' and str($input_format_cond.codon_alignments) == 'no'):
56 --output '$output_aln_trimmed'
57 --output_dir '$output_aln_trimmed.files_path'
58 #else:
59 --output '$output_aln_trimmed_ca'
60 --output_dir '$output_aln_trimmed_ca.files_path'
61 #end if
62 #end if 58 #end if
63 #else: 59 #else:
64 #if str($input_format) == 'ptortho' or (str($input_format) == 'ptorthocs' and str($input_format_cond.codon_alignments) == 'no'): 60 #if $output_codon_alignments:
65 --output '$output_aln' 61 --output '$output_aln_trimmed_ca'
66 --output_dir '$output_aln.files_path' 62 --output_dir '$output_aln_trimmed_ca.files_path'
67 #else: 63 #else:
68 --output '$output_aln_ca' 64 --output '$output_aln_trimmed'
69 --output_dir '$output_aln_ca.files_path' 65 --output_dir '$output_aln_trimmed.files_path'
70 #end if 66 #end if
71 #end if 67 #end if
72 #esle: 68 #else:
73 #if str($input_format) == 'ptortho' or (str($input_format) == 'ptorthocs' and str($input_format_cond.codon_alignments) == 'no'): 69 #if $output_codon_alignments:
70 --output '$output_aln_ca'
71 --output_dir '$output_aln_ca.files_path'
72 #else:
74 --output '$output_aln' 73 --output '$output_aln'
75 --output_dir '$output_aln.files_path' 74 --output_dir '$output_aln.files_path'
76 #else:
77 --output '$output_aln_ca'
78 --output_dir '$output_aln_ca.files_path'
79 #end if 75 #end if
80 #end if 76 #end if
81 ]]> 77 ]]>
82 </command> 78 </command>
83 <inputs> 79 <inputs>
94 <param name="input_ptorthocs" format="ptorthocs" type="data" label="Gene family clusters with corresponding coding sequences" /> 90 <param name="input_ptorthocs" format="ptorthocs" type="data" label="Gene family clusters with corresponding coding sequences" />
95 <expand macro="cond_alignment_method" /> 91 <expand macro="cond_alignment_method" />
96 <expand macro="param_codon_alignments" /> 92 <expand macro="param_codon_alignments" />
97 </when> 93 </when>
98 </conditional> 94 </conditional>
99 <conditional name="options_type_cond"> 95 <expand macro="cond_remove_gappy_sequences" />
100 <expand macro="param_options_type" />
101 <when value="basic" />
102 <when value="advanced">
103 <expand macro="cond_remove_gappy_sequences" />
104 </when>
105 </conditional>
106 </inputs> 96 </inputs>
107 <outputs> 97 <outputs>
108 <data name="output_aln" format="ptalign" label="Aligned gene family sequences on ${on_string}"> 98 <data name="output_aln" format="ptalign" label="Aligned gene family sequences on ${on_string}">
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> 99 <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>
110 </data> 100 </data>
111 <data name="output_aln_ca" format="ptalignca" label="Aligned gene family sequences with codon alignments on ${on_string}"> 101 <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> 102 <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>
113 </data> 103 </data>
114 <data name="output_aln_filtered" format="ptalignfiltered" label="Filtered aligned gene family sequences on ${on_string}"> 104 <data name="output_aln_filtered" format="ptalignfiltered" label="Filtered aligned gene family sequences on ${on_string}">
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> 105 <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>
116 </data> 106 </data>
117 <data name="output_aln_filtered_ca" format="ptalignfilteredca" label="Filtered aligned gene family sequences with codon alignments on ${on_string}"> 107 <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> 108 <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>
119 </data> 109 </data>
120 <data name="output_aln_trimmed" format="ptaligntrimmed" label="Trimmed aligned gene family sequences on ${on_string}"> 110 <data name="output_aln_trimmed" format="ptaligntrimmed" label="Trimmed aligned gene family sequences on ${on_string}">
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> 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'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no')</filter>
122 </data> 112 </data>
123 <data name="output_aln_trimmed_ca" format="ptaligntrimmedca" label="Trimmed aligned gene family sequences with codon alignments on ${on_string}"> 113 <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> 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'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no')</filter>
125 </data> 115 </data>
126 </outputs> 116 </outputs>
127 <tests> 117 <tests>
128 <!-- Test framework does not currently support inputs whose associated files_path contains files to be analyzed. 118 <!-- Test framework does not currently support inputs whose associated files_path contains files to be analyzed.
129 <test> 119 <test>