Mercurial > repos > rnateam > mafft

comparison mafft.xml @ 2:d71e007323d4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit ef7eb622ae8ea3a2a5aa5f5d2c9eaf41367bfef9-dirty
author rnateam
date Tue, 04 Aug 2015 04:01:23 -0400
parents 5e48c4621f9f
children a681631ccee6
comparison
equal deleted inserted replaced
1:5e48c4621f9f 2:d71e007323d4
1 <tool id="rbc_mafft" name="MAFFT" version="7.221.0"> 1 <tool id="rbc_mafft" name="MAFFT" version="7.221.1">
2 <description>Multiple alignment program for amino acid or nucleotide sequences</description> 2 <description>Multiple alignment program for amino acid or nucleotide sequences</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="7.221">mafft</requirement> 4 <requirement type="package" version="7.221">mafft</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
21 mafft 21 mafft
22 #end if 22 #end if
23 23
24 ## specify threads to use 24 ## specify threads to use
25 --thread \${GALAXY_SLOTS:-1} 25 --thread \${GALAXY_SLOTS:-1}
26
27 $adjustdirection
26 28
27 #if $outputFormat.value == 'clustalw' 29 #if $outputFormat.value == 'clustalw'
28 --clustalout 30 --clustalout
29 #end if 31 #end if
30 32
62 <when value="mafft-ginsi"/> 64 <when value="mafft-ginsi"/>
63 <when value="mafft-linsi"/> 65 <when value="mafft-linsi"/>
64 <when value="mafft-qinsi"/> 66 <when value="mafft-qinsi"/>
65 <when value="mafft-xinsi"/> 67 <when value="mafft-xinsi"/>
66 </conditional> 68 </conditional>
69 <param name="adjustdirection" type="select" display="radio" label="Direction of nucleotide sequences" help="Generate reverse complement sequences, as necessary, and align them together with the remaining sequences">
70 <option value="--adjustdirection">adjust direction</option>
71 <option value=" " selected="true">do not adjust direction</option>
72 </param>
67 <param name="outputFormat" type="select" label="Output format" help="Either FASTA or ClustalW"> 73 <param name="outputFormat" type="select" label="Output format" help="Either FASTA or ClustalW">
68 <option value="fasta" selected="true">FASTA</option> 74 <option value="fasta" selected="true">FASTA</option>
69 <option value="clustalw">ClustalW</option> 75 <option value="clustalw">ClustalW</option>
70 </param> 76 </param>
71 </inputs> 77 </inputs>
148 154
149 **Options:** 155 **Options:**
150 156
151 --auto 157 --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) 158 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)
159 --adjustdirection
160 Generate reverse complement sequences, as necessary, and align them together with the remaining sequences. In the case of protein alignment, these options are just ignored.
153 ]]> 161 ]]>
154 </help> 162 </help>
155 <citations> 163 <citations>
156 <citation type="doi">10.1093/molbev/mst010</citation> 164 <citation type="doi">10.1093/molbev/mst010</citation>
157 </citations> 165 </citations>