Mercurial > repos > greg > gene_family_aligner

comparison gene_family_aligner.xml @ 8:9e68bebb3d7c draft

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Uploaded
author greg
date Mon, 10 Apr 2017 10:55:45 -0400
parents badd2d0f1689
children 43341e97bb08
comparison
equal deleted inserted replaced
7:529f4635ddb4 8:9e68bebb3d7c
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 --remove_sequences $remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of 48 --remove_sequences $remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of
49 --iterative_realignment $remove_sequences_with_gaps_cond.iterative_realignment 49 --iterative_realignment $remove_sequences_with_gaps_cond.iterative_realignment
50 --output '$output_aln_filtered'
51 --output_dir '$output_aln_filtered.files_path'
52 #else:
53 --output '$output_aln_trimmed'
54 --output_dir '$output_aln_trimmed.files_path'
50 #end if 55 #end if
56 #else:
57 --output '$output_aln'
58 --output_dir '$output_aln.files_path'
51 #end if 59 #end if
60 #esle:
61 --output '$output_aln'
62 --output_dir '$output_aln.files_path'
52 #end if 63 #end if
53 --output '$output'
54 --output_dir '$output.files_path'
55 ]]> 64 ]]>
56 </command> 65 </command>
57 <inputs> 66 <inputs>
58 <conditional name="input_format_cond"> 67 <conditional name="input_format_cond">
59 <param name="input_format" type="select" label="Select type of data to sub sample"> 68 <param name="input_format" type="select" label="Select type of data to sub sample">
81 <expand macro="cond_remove_gappy_sequences" /> 90 <expand macro="cond_remove_gappy_sequences" />
82 </when> 91 </when>
83 </conditional> 92 </conditional>
84 </inputs> 93 </inputs>
85 <outputs> 94 <outputs>
86 <data name="output" format="ptalign" label="Aligned gene family sequences on ${on_string}" /> 95 <data name="output_aln" format="ptalign" label="Aligned gene family sequences on ${on_string}">
96 <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>
97 </data>
98 <data name="output_aln_filtered" format="ptalignfiltered" label="Filtered aligned gene family sequences on ${on_string}">
99 <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>
100 </data>
101 <data name="output_aln_trimmed" format="ptaligntrimmed" label="Trimmed aligned gene family sequences on ${on_string}">
102 <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>
103 </data>
87 </outputs> 104 </outputs>
88 <tests> 105 <tests>
89 <!-- Test framework does not currently support inputs whose associated files_path contains files to be analyzed. 106 <!-- Test framework does not currently support inputs whose associated files_path contains files to be analyzed.
90 <test> 107 <test>
91 </test> 108 </test>