Mercurial > repos > greg > plant_tribes_gene_family_aligner

comparison gene_family_aligner.xml @ 5:a73c2e65098e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Fri, 25 Aug 2017 13:01:25 -0400
parents d3f8c8b77dbe
children 3384b6a842b0
comparison
equal deleted inserted replaced
4:d3f8c8b77dbe 5:a73c2e65098e
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 78 #end if
79 #set output_dataset_collection = $output_dataset_collection_cond.output_dataset_collection
80 #if str($output_dataset_collection) == 'yes': 79 #if str($output_dataset_collection) == 'yes':
81 --output_dataset_collection dataset_collection 80 --output_dataset_collection dataset_collection
82 #end if 81 #end if
83 ]]></command> 82 ]]></command>
84 <inputs> 83 <inputs>
100 <expand macro="cond_alignment_method" /> 99 <expand macro="cond_alignment_method" />
101 <expand macro="param_codon_alignments" /> 100 <expand macro="param_codon_alignments" />
102 </when> 101 </when>
103 </conditional> 102 </conditional>
104 <expand macro="cond_remove_gappy_sequences" /> 103 <expand macro="cond_remove_gappy_sequences" />
105 <conditional name="output_dataset_collection_cond"> 104 <param name="output_dataset_collection" type="select" display="radio" label="Output additional dataset collection of files?">
106 <param name="output_dataset_collection" type="select" label="Output additional dataset collection of files?"> 105 <option value="no" selected="true">No</option>
107 <option value="no" selected="true">No</option> 106 <option value="yes">Yes</option>
108 <option value="yes">Yes</option> 107 </param>
109 </param>
110 <when value="no" />
111 <when value="yes" />
112 </conditional>
113 </inputs> 108 </inputs>
114 <outputs> 109 <outputs>
115 <data name="output_aln" format="ptalign" label="${tool.name} (proteins orthogroup alignments) on ${on_string}"> 110 <data name="output_aln" format="ptalign" label="${tool.name} (proteins orthogroup alignments) on ${on_string}">
116 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'no')) and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'no'</filter> 111 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'no')) and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'no'</filter>
117 </data> 112 </data>
130 <data name="output_aln_trimmed_ca" format="ptaligntrimmedca" label="${tool.name} (trimmed protein and coding sequences orthogroup alignments) on ${on_string}"> 125 <data name="output_aln_trimmed_ca" format="ptaligntrimmedca" label="${tool.name} (trimmed protein and coding sequences orthogroup alignments) on ${on_string}">
131 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes')) and (remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no')</filter> 126 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes')) and (remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no')</filter>
132 </data> 127 </data>
133 <collection name="dataset_collection" type="list" label="${tool.name} (dataset collection) on ${on_string}"> 128 <collection name="dataset_collection" type="list" label="${tool.name} (dataset collection) on ${on_string}">
134 <discover_datasets pattern="__name__" directory="dataset_collection" format="fasta" /> 129 <discover_datasets pattern="__name__" directory="dataset_collection" format="fasta" />
135 <filter>output_dataset_collection_cond['output_dataset_collection'] == 'yes'</filter> 130 <filter>output_dataset_collection == 'yes'</filter>
136 </collection> 131 </collection>
137 </outputs> 132 </outputs>
138 <tests> 133 <tests>
139 <!-- Test framework does not currently support inputs whose associated extra_files_path contains files to be analyzed. 134 <!-- Test framework does not currently support inputs whose associated extra_files_path contains files to be analyzed.
140 <test> 135 <test>