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comparison phylogenomics_analysis.xml @ 26:e19872abae29 draft

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Uploaded
author greg
date Tue, 10 Jan 2017 09:51:27 -0500
parents 61c90d75c7cd
children ce6108b3063b
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25:61c90d75c7cd 26:e19872abae29
116 #if str($remove_gappy_sequences_cond) == 'yes': 116 #if str($remove_gappy_sequences_cond) == 'yes':
117 #set trim_type_cond = $remove_gappy_sequences_cond.trim_type_cond 117 #set trim_type_cond = $remove_gappy_sequences_cond.trim_type_cond
118 --remove_sequences $remove_gappy_sequences_cond.remove_sequences 118 --remove_sequences $remove_gappy_sequences_cond.remove_sequences
119 #if str($trim_type_cond.trim_type) == 'automated_trimming': 119 #if str($trim_type_cond.trim_type) == 'automated_trimming':
120 --automated_trimming 120 --automated_trimming
121 else: 121 #else:
122 --gap_trimming $trim_type_cond.gap_trimming 122 --gap_trimming $trim_type_cond.gap_trimming
123 #end if 123 #end if
124 #end if 124 #end if
125 #end if 125 #end if
126 #end if 126 #end if
257 <when value="no"/> 257 <when value="no"/>
258 <when value="yes"> 258 <when value="yes">
259 <param name="remove_sequences" type="float" value="0.5" min="0" max="1" label="Remove sequences with gaps of" help="0.5 removes sequences with 50% gaps"/> 259 <param name="remove_sequences" type="float" value="0.5" min="0" max="1" label="Remove sequences with gaps of" help="0.5 removes sequences with 50% gaps"/>
260 <conditional name="trim_type_cond"> 260 <conditional name="trim_type_cond">
261 <param name="trim_type" type="select" label="Select process used for gap trimming"> 261 <param name="trim_type" type="select" label="Select process used for gap trimming">
262 <option value="automated_trimming" selected="true">Trim alignments using trimAl's ML heuristic trimming approach</option> 262 <option value="gap_trimming" selected="true">Nucleotide based</option>
263 <option value="gap_trimming">Nucleotide based</option> 263 <option value="automated_trimming">Trim alignments using trimAl's ML heuristic trimming approach</option>
264 </param> 264 </param>
265 <when value="automated_trimming"/> 265 <when value="automated_trimming"/>
266 <when value="gap_trimming"> 266 <when value="gap_trimming">
267 <param name="gap_trimming" type="float" value="0.1" min="0" max="1.0" label="Remove sites in alignments with gaps of" help="0.1 removes sites with 90% gaps"/> 267 <param name="gap_trimming" type="float" value="0.1" min="0" max="1.0" label="Remove sites in alignments with gaps of" help="0.1 removes sites with 90% gaps"/>
268 </when> 268 </when>