Mercurial > repos > greg > gene_family_phylogeny_builder
comparison macros.xml @ 45:5873a9420e03 draft
Uploaded
| author | greg |
|---|---|
| date | Fri, 08 Sep 2017 10:05:12 -0400 |
| parents | 4dfc191c7e4e |
| children | 9962341547d3 |
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| 44:97a298d2fc36 | 45:5873a9420e03 |
|---|---|
| 65 <param name="scaffold" type="select" label="Gene family scaffold"> | 65 <param name="scaffold" type="select" label="Gene family scaffold"> |
| 66 <options from_data_table="plant_tribes_scaffolds" /> | 66 <options from_data_table="plant_tribes_scaffolds" /> |
| 67 <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." /> | 67 <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." /> |
| 68 </param> | 68 </param> |
| 69 </xml> | 69 </xml> |
| 70 <xml name="param_sequence_type"> | |
| 71 <param name="sequence_type" type="select" label="Sequence type used in the phylogenetic inference (dna)"> | |
| 72 <option value="protein" selected="true">Amino acid based</option> | |
| 73 <option value="dna">Nucleotide based</option> | |
| 74 </param> | |
| 75 </xml> | |
| 76 <xml name="cond_alignment_method"> | 70 <xml name="cond_alignment_method"> |
| 77 <conditional name="alignment_method_cond"> | 71 <conditional name="alignment_method_cond"> |
| 78 <param name="alignment_method" type="select" force_select="true" label="Multiple sequence alignment method"> | 72 <param name="alignment_method" type="select" force_select="true" label="Multiple sequence alignment method"> |
| 79 <option value="mafft" selected="true">MAFFT</option> | 73 <option value="mafft" selected="true">MAFFT</option> |
| 80 <option value="pasta">PASTA</option> | 74 <option value="pasta">PASTA</option> |
| 112 <when value="yes"> | 106 <when value="yes"> |
| 113 <param name="remove_sequences_with_gaps_of" type="float" optional="true" min="0" max="1" label="Coverage score" /> | 107 <param name="remove_sequences_with_gaps_of" type="float" optional="true" min="0" max="1" label="Coverage score" /> |
| 114 <param name="iterative_realignment" type="integer" optional="true" min="0" label="Realignment iteration limit" /> | 108 <param name="iterative_realignment" type="integer" optional="true" min="0" label="Realignment iteration limit" /> |
| 115 </when> | 109 </when> |
| 116 </conditional> | 110 </conditional> |
| 111 <param name="output_pristine_alignments" type="select" display="radio" label="Output non-filtered, non-trimmed alignemnts?" help="In addition to trimmed/filtered alignments"> | |
| 112 <option value="no" selected="true">No</option> | |
| 113 <option value="yes">Yes</option> | |
| 114 </param> | |
| 117 </when> | 115 </when> |
| 118 </conditional> | 116 </conditional> |
| 119 </xml> | 117 </xml> |
| 120 <xml name="citation1"> | 118 <xml name="citation1"> |
| 121 <citation type="bibtex"> | 119 <citation type="bibtex"> |