Mercurial > repos > rnateam > mafft
comparison mafft.xml @ 1:5e48c4621f9f draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit c4313fc798bb8d55e27da78a3fa5d9774b95aaf7-dirty
| author | rnateam |
|---|---|
| date | Fri, 31 Jul 2015 19:02:11 -0400 |
| parents | a4e086689fae |
| children | d71e007323d4 |
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| 0:a4e086689fae | 1:5e48c4621f9f |
|---|---|
| 40 <inputs> | 40 <inputs> |
| 41 <param name="inputSequences" type="data" format="fasta" label="Sequences to align" help="Amino acid or nucleotide sequences in FASTA format."/> | 41 <param name="inputSequences" type="data" format="fasta" label="Sequences to align" help="Amino acid or nucleotide sequences in FASTA format."/> |
| 42 <conditional name="cond_flavour"> | 42 <conditional name="cond_flavour"> |
| 43 <param name="flavourType" type="select" label="MAFFT flavour" help="Run mafft with pre-defined input parameters. Specification of these parameters can be found in the help section."> | 43 <param name="flavourType" type="select" label="MAFFT flavour" help="Run mafft with pre-defined input parameters. Specification of these parameters can be found in the help section."> |
| 44 <option value="mafft-fftns" selected="true">fftns</option> | 44 <option value="mafft-fftns" selected="true">fftns</option> |
| 45 <option value="mafft --auto">auto</option> | |
| 45 <option value="mafft-fftnsi">fftnsi</option> | 46 <option value="mafft-fftnsi">fftnsi</option> |
| 46 <option value="mafft-nwns">nwns</option> | 47 <option value="mafft-nwns">nwns</option> |
| 47 <option value="mafft-nwnsi">nwnsi</option> | 48 <option value="mafft-nwnsi">nwnsi</option> |
| 48 <option value="mafft-einsi">einsi</option> | 49 <option value="mafft-einsi">einsi</option> |
| 49 <option value="mafft-ginsi">ginsi</option> | 50 <option value="mafft-ginsi">ginsi</option> |
| 51 <option value="mafft-qinsi">qinsi</option> | 52 <option value="mafft-qinsi">qinsi</option> |
| 52 <option value="mafft-xinsi">xinsi</option> | 53 <option value="mafft-xinsi">xinsi</option> |
| 53 <!-- <option value="custom">Custom Parameters</option> this should trigger tweaking of all parameters --> | 54 <!-- <option value="custom">Custom Parameters</option> this should trigger tweaking of all parameters --> |
| 54 </param> | 55 </param> |
| 55 <when value="mafft-fftns"/> | 56 <when value="mafft-fftns"/> |
| 57 <when value="mafft --auto"/> | |
| 56 <when value="mafft-fftnsi"/> | 58 <when value="mafft-fftnsi"/> |
| 57 <when value="mafft-nwns"/> | 59 <when value="mafft-nwns"/> |
| 58 <when value="mafft-nwnsi"/> | 60 <when value="mafft-nwnsi"/> |
| 59 <when value="mafft-einsi"/> | 61 <when value="mafft-einsi"/> |
| 60 <when value="mafft-ginsi"/> | 62 <when value="mafft-ginsi"/> |
| 141 - mafft --retree 2 --maxiterate 0 --nofft input [> output] | 143 - mafft --retree 2 --maxiterate 0 --nofft input [> output] |
| 142 | 144 |
| 143 - NW-NS-PartTree-1 (recommended for ~10,000 to ~50,000 sequences; progressive method with the PartTree algorithm): | 145 - NW-NS-PartTree-1 (recommended for ~10,000 to ~50,000 sequences; progressive method with the PartTree algorithm): |
| 144 | 146 |
| 145 - mafft --retree 1 --maxiterate 0 --nofft --parttree input [> output] | 147 - mafft --retree 1 --maxiterate 0 --nofft --parttree input [> output] |
| 146 | 148 |
| 149 **Options:** | |
| 150 | |
| 151 --auto | |
| 152 Automatically selects an appropriate strategy from L-INS-i, FFT-NS-i and FFT-NS-2, according to data size. Default: off (always FFT-NS-2) | |
| 147 ]]> | 153 ]]> |
| 148 </help> | 154 </help> |
| 149 <citations> | 155 <citations> |
| 150 <citation type="doi">10.1093/molbev/mst010</citation> | 156 <citation type="doi">10.1093/molbev/mst010</citation> |
| 151 </citations> | 157 </citations> |