Mercurial > repos > greg > gene_family_integrator

comparison macros.xml @ 9:2457321db163 draft

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author greg
date Fri, 28 Apr 2017 13:59:16 -0400
parents 87e2450855c2
children 31042dc87180
comparison
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8:87e2450855c2 9:2457321db163
38 <regex match="Error:"/> 38 <regex match="Error:"/>
39 <regex match="Exception:"/> 39 <regex match="Exception:"/>
40 </stdio> 40 </stdio>
41 </xml> 41 </xml>
42 <xml name="param_codon_alignments"> 42 <xml name="param_codon_alignments">
43 <param name="codon_alignments" type="select" label="Construct orthogroup multiple codon alignments?"> 43 <param name="codon_alignments" type="select" label="Construct orthogroup multiple codon alignments">
44 <option value="yes" selected="true">Yes</option> 44 <option value="yes" selected="true">Yes</option>
45 <option value="no">No</option> 45 <option value="no">No</option>
46 </param> 46 </param>
47 </xml> 47 </xml>
48 <xml name="param_method"> 48 <xml name="param_method">
57 <option value="basic" selected="true">Basic</option> 57 <option value="basic" selected="true">Basic</option>
58 <option value="advanced">Advanced</option> 58 <option value="advanced">Advanced</option>
59 </param> 59 </param>
60 </xml> 60 </xml>
61 <xml name="param_orthogroup_fna"> 61 <xml name="param_orthogroup_fna">
62 <param name="orthogroup_fna" type="select" label="Orthogroups coding sequences?"> 62 <param name="orthogroup_fna" type="select" label="Orthogroups coding sequences">
63 <option value="yes" selected="true">Yes</option> 63 <option value="yes" selected="true">Yes</option>
64 <option value="no">No</option> 64 <option value="no">No</option>
65 </param> 65 </param>
66 </xml> 66 </xml>
67 <xml name="param_scaffold"> 67 <xml name="param_scaffold">
88 </when> 88 </when>
89 </conditional> 89 </conditional>
90 </xml> 90 </xml>
91 <xml name="cond_remove_gappy_sequences"> 91 <xml name="cond_remove_gappy_sequences">
92 <conditional name="remove_gappy_sequences_cond"> 92 <conditional name="remove_gappy_sequences_cond">
93 <param name="remove_gappy_sequences" type="select" label="Alignment post-processing configuration?"> 93 <param name="remove_gappy_sequences" type="select" label="Alignment post-processing configuration">
94 <option value="no" selected="true">No</option> 94 <option value="no" selected="true">No</option>
95 <option value="yes">Yes</option> 95 <option value="yes">Yes</option>
96 </param> 96 </param>
97 <when value="no" /> 97 <when value="no" />
98 <when value="yes"> 98 <when value="yes">
105 <param name="gap_trimming" type="float" optional="true" min="0" max="1.0" label="Gap score" /> 105 <param name="gap_trimming" type="float" optional="true" min="0" max="1.0" label="Gap score" />
106 </when> 106 </when>
107 <when value="automated_trimming" /> 107 <when value="automated_trimming" />
108 </conditional> 108 </conditional>
109 <conditional name="remove_sequences_with_gaps_cond"> 109 <conditional name="remove_sequences_with_gaps_cond">
110 <param name="remove_sequences_with_gaps" type="select" label="Remove sequences?"> 110 <param name="remove_sequences_with_gaps" type="select" label="Remove sequences">
111 <option value="no" selected="true">No</option> 111 <option value="no" selected="true">No</option>
112 <option value="yes">Yes</option> 112 <option value="yes">Yes</option>
113 </param> 113 </param>
114 <when value="no" /> 114 <when value="no" />
115 <when value="yes"> 115 <when value="yes">