Mercurial > repos > greg > phylogenomics_analysis

comparison macros.xml @ 105:e0fa1e2105f6 draft

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Uploaded
author greg
date Mon, 27 Mar 2017 11:20:26 -0400
parents 4d78ec10c07e
children 5e5db789406a
comparison
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104:4d78ec10c07e 105:e0fa1e2105f6
126 #end if 126 #end if
127 --bootstrap_replicates $bootstrap_replicates 127 --bootstrap_replicates $bootstrap_replicates
128 #end if 128 #end if
129 --min_orthogroup_size $min_orthogroup_size 129 --min_orthogroup_size $min_orthogroup_size
130 --max_orthogroup_size $max_orthogroup_size 130 --max_orthogroup_size $max_orthogroup_size
131 </token>
132 <token name="@OUTPUT_ALN@">
133 #if str($input_format_cond['options_type_cond']['options_type']) == 'advanced' and ((str($input_format_cond['options_type_cond']['remove_gappy_sequences_cond']['remove_gappy_sequences']) == 'yes' and str($input_format_cond['options_type_cond']['remove_gappy_sequences_cond']['multiple_sequence_alignments_cond']['multiple_sequence_alignments']) == 'yes') or (str($input_format_cond['options_type_cond']['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes') and str($input_format_cond['options_type_cond']['remove_sequences_with_gaps_cond']['multiple_sequence_alignments_cond']['multiple_sequence_alignments']) == 'yes')):
134 --output_aln '$output_aln'
135 --output_aln_dir '$output_aln.files_path'
136 #end if
137 </token>
138 <token name="@OUTPUT_TREE@">
139 #if str($input_format_cond['options_type_cond']['options_type']) == 'advanced' and str($input_format_cond['options_type_cond']['phylogenetic_trees_cond']['phylogenetic_trees']) == 'yes':
140 --output_tree '$output_tree'
141 --output_tree_dir '$output_tree.files_path'
142 #end if
131 </token> 143 </token>
132 <xml name="param_scaffold"> 144 <xml name="param_scaffold">
133 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold"> 145 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold">
134 <options from_data_table="plant_tribes_scaffolds" /> 146 <options from_data_table="plant_tribes_scaffolds" />
135 <validator type="no_options" message="No PlantTribes scaffolds are available. Use the PlantTribes Scaffolds Download Data Manager tool in Galaxy to install and populate the PlantTribes scaffolds data table." /> 147 <validator type="no_options" message="No PlantTribes scaffolds are available. Use the PlantTribes Scaffolds Download Data Manager tool in Galaxy to install and populate the PlantTribes scaffolds data table." />