Mercurial > repos > greg > gene_family_phylogeny_builder

comparison gene_family_phylogeny_builder.xml @ 2:4ce0f6af1a5e draft

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Uploaded
author greg
date Tue, 11 Apr 2017 13:04:27 -0400
parents e5523659847a
children 09a1b1b5aa0d
comparison
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1:e5523659847a 2:4ce0f6af1a5e
6 <expand macro="requirements_gene_family_phylogeny_builder" /> 6 <expand macro="requirements_gene_family_phylogeny_builder" />
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
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 tree_inference_cond = $phylogenetic_trees_cond.tree_inference_cond
12 #set tree_inference = $tree_inference_cond.tree_inference 11 #set tree_inference = $tree_inference_cond.tree_inference
13 #if str($tree_inference) == 'raxml': 12 #if str($tree_inference) == 'raxml':
14 #set rooting_order_file_cond = $tree_inference_cond.rooting_order_file_cond 13 #set rooting_order_file_cond = $tree_inference_cond.rooting_order_file_cond
15 #set rooting_order_file = $rooting_order_file_cond.rooting_order_file 14 #set rooting_order_file = $rooting_order_file_cond.rooting_order_file
16 #if str($rooting_order_file) == 'yes': 15 #if str($rooting_order_file) == 'yes':
69 <option value="ptaligntrimmed">Trimmed aligned gene family sequences</option> 68 <option value="ptaligntrimmed">Trimmed aligned gene family sequences</option>
70 <option value="ptaligntrimmedca">Trimmed aligned gene family sequences with codon alignments</option> 69 <option value="ptaligntrimmedca">Trimmed aligned gene family sequences with codon alignments</option>
71 </param> 70 </param>
72 <when value="ptalign"> 71 <when value="ptalign">
73 <param name="input_ptalign" format="ptalign" type="data" label="Aligned gene family sequences"> 72 <param name="input_ptalign" format="ptalign" type="data" label="Aligned gene family sequences">
74 <!-- <validator type="empty_files_path" /> --> 73 <validator type="empty_files_path" />
75 </param> 74 </param>
76 </when> 75 </when>
77 <when value="ptalignca"> 76 <when value="ptalignca">
78 <param name="input_ptalignca" format="ptalignca" type="data" label="Aligned gene family sequences with codon alignments"> 77 <param name="input_ptalignca" format="ptalignca" type="data" label="Aligned gene family sequences with codon alignments">
79 <!-- <validator type="empty_files_path" /> --> 78 <validator type="empty_files_path" />
80 </param> 79 </param>
81 <expand macro="param_sequence_type" /> 80 <expand macro="param_sequence_type" />
82 </when> 81 </when>
83 <when value="ptalignfiltered"> 82 <when value="ptalignfiltered">
84 <param name="input_ptalignfiltered" format="ptalignfiltered" type="data" label="Filtered aligned gene family sequences"> 83 <param name="input_ptalignfiltered" format="ptalignfiltered" type="data" label="Filtered aligned gene family sequences">
85 <!-- <validator type="empty_files_path" /> --> 84 <validator type="empty_files_path" />
86 </param> 85 </param>
87 </when> 86 </when>
88 <when value="ptalignfilteredca"> 87 <when value="ptalignfilteredca">
89 <param name="input_ptalignfilteredca" format="ptalignfilteredca" type="data" label="Filtered aligned gene family sequences with codon alignments"> 88 <param name="input_ptalignfilteredca" format="ptalignfilteredca" type="data" label="Filtered aligned gene family sequences with codon alignments">
90 <!-- <validator type="empty_files_path" /> --> 89 <validator type="empty_files_path" />
91 </param> 90 </param>
92 <expand macro="param_sequence_type" /> 91 <expand macro="param_sequence_type" />
93 </when> 92 </when>
94 <when value="ptaligntrimmed"> 93 <when value="ptaligntrimmed">
95 <param name="input_ptaligntrimmed" format="ptaligntrimmed" type="data" label="Trimmed aligned gene family sequences"> 94 <param name="input_ptaligntrimmed" format="ptaligntrimmed" type="data" label="Trimmed aligned gene family sequences">
96 <!-- <validator type="empty_files_path" /> --> 95 <validator type="empty_files_path" />
97 </param> 96 </param>
98 </when> 97 </when>
99 <when value="ptaligntrimmedca"> 98 <when value="ptaligntrimmedca">
100 <param name="input_ptaligntrimmedca" format="ptaligntrimmedca" type="data" label="Trimmed aligned gene family sequences with codon alignments"> 99 <param name="input_ptaligntrimmedca" format="ptaligntrimmedca" type="data" label="Trimmed aligned gene family sequences with codon alignments">
101 <!-- <validator type="empty_files_path" /> --> 100 <validator type="empty_files_path" />
102 </param> 101 </param>
103 <expand macro="param_sequence_type" /> 102 <expand macro="param_sequence_type" />
104 </when> 103 </when>
105 </conditional> 104 </conditional>
106 <expand macro="param_scaffold" /> 105 <expand macro="param_scaffold" />