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comparison macros.xml @ 42:9531bbe2d8ff draft

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author greg
date Fri, 28 Apr 2017 09:03:02 -0400
parents 8102c8bf2414
children ac9b32bd719c
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41:61977f3f19ea 42:9531bbe2d8ff
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="Process corresponding gene family classification orthogroups CDS fasta files?"> 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">
68 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold"> 68 <param name="scaffold" type="select" label="Gene family scaffold">
69 <options from_data_table="plant_tribes_scaffolds" /> 69 <options from_data_table="plant_tribes_scaffolds" />
70 <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." /> 70 <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." />
71 </param> 71 </param>
72 </xml> 72 </xml>
73 <xml name="param_sequence_type"> 73 <xml name="param_sequence_type">
76 <option value="dna">Nucleotide based</option> 76 <option value="dna">Nucleotide based</option>
77 </param> 77 </param>
78 </xml> 78 </xml>
79 <xml name="cond_alignment_method"> 79 <xml name="cond_alignment_method">
80 <conditional name="alignment_method_cond"> 80 <conditional name="alignment_method_cond">
81 <param name="alignment_method" type="select" force_select="true" label="Select method for multiple sequence alignments"> 81 <param name="alignment_method" type="select" force_select="true" label="Multiple sequence alignment method">
82 <option value="mafft" selected="true">MAFFT algorithm</option> 82 <option value="mafft" selected="true">MAFFT</option>
83 <option value="pasta">PASTA algorithm</option> 83 <option value="pasta">PASTA</option>
84 </param> 84 </param>
85 <when value="mafft" /> 85 <when value="mafft" />
86 <when value="pasta"> 86 <when value="pasta">
87 <param name="pasta_iter_limit" type="integer" value="3" min="1" label="Maximum number of iterations that the PASTA algorithm will execute" /> 87 <param name="pasta_iter_limit" type="integer" value="3" min="1" label="Maximum number of iterations that the PASTA algorithm will execute" />
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="Remove gappy sequences in alignments?"> 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">
99 <conditional name="trim_type_cond"> 99 <conditional name="trim_type_cond">
100 <param name="trim_type" type="select" label="Select process used for trimming"> 100 <param name="trim_type" type="select" label="Trimming method">
101 <option value="gap_trimming" selected="true">Remove gappy sites in alignments (gap trimming)</option> 101 <option value="gap_trimming" selected="true">Gap score based trimming</option>
102 <option value="automated_trimming">Trim alignments using trimAl's ML heuristic trimming approach (automated trimming)</option> 102 <option value="automated_trimming">Automated heuristic trimming</option>
103 </param> 103 </param>
104 <when value="gap_trimming"> 104 <when value="gap_trimming">
105 <param name="gap_trimming" type="float" optional="true" min="0" max="1.0" label="Remove sites in alignments with gaps of" /> 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 with specified gaps?"> 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">
116 <param name="remove_sequences_with_gaps_of" type="float" optional="true" min="0" max="1" label="Remove sequences with gaps of" /> 116 <param name="remove_sequences_with_gaps_of" type="float" optional="true" min="0" max="1" label="Coverage score" />
117 <param name="iterative_realignment" type="integer" optional="true" min="0" label="Maximum number of iterations" /> 117 <param name="iterative_realignment" type="integer" optional="true" min="0" label="Realignment iteration limit" />
118 </when> 118 </when>
119 </conditional> 119 </conditional>
120 </when> 120 </when>
121 </conditional> 121 </conditional>
122 </xml> 122 </xml>
128 title = {Manuscript in preparation}, 128 title = {Manuscript in preparation},
129 year = {None}, 129 year = {None},
130 url = {https://github.com/dePamphilis/PlantTribes},} 130 url = {https://github.com/dePamphilis/PlantTribes},}
131 </citation> 131 </citation>
132 </xml> 132 </xml>
133 <xml name="citations2to4">
134 <citation type="bibtex">
135 @article{Sasidharan2012,
136 journal = {Nucleic Acids Research},
137 author = {2. Sasidharan R, Nepusz T, Swarbreck D, Huala E, Paccanaro A},
138 title = {GFam: a platform for automatic annotation of gene families},
139 year = {2012},
140 pages = {gks631},}
141 </citation>
142 <citation type="bibtex">
143 @article{Li2003,
144 journal = {Genome Research}
145 author = {3. Li L, Stoeckert CJ, Roos DS},
146 title = {OrthoMCL: identification of ortholog groups for eukaryotic genomes},
147 year = {2003},
148 volume = {13},
149 number = {9},
150 pages = {2178-2189},}
151 </citation>
152 <citation type="bibtex">
153 @article{Emms2015,
154 journal = {Genome Biology}
155 author = {4. Emms DM, Kelly S},
156 title = {OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy},
157 year = {2015},
158 volume = {16},
159 number = {1},
160 pages = {157},}
161 </citation>
162 </xml>
163 </macros> 133 </macros>