Mercurial > repos > rnateam > mafft

comparison mafft.xml @ 1:95526e9e3808 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 c4313fc798bb8d55e27da78a3fa5d9774b95aaf7-dirty
author rnateam
date Fri, 31 Jul 2015 19:00:37 -0400
parents 8817d3a35fac
children 97adbeef2294
comparison
equal deleted inserted replaced
0:8817d3a35fac 1:95526e9e3808
14 </version_command> 14 </version_command>
15 <command> 15 <command>
16 <![CDATA[ 16 <![CDATA[
17 #if $cond_flavour.flavourType != 'custom' 17 #if $cond_flavour.flavourType != 'custom'
18 $cond_flavour.flavourType 18 $cond_flavour.flavourType
19 #else 19 #elif $cond_flavour.flavourType == 'custom'
20 ### full parameter options 20 ### full parameter options
21 mafft 21 mafft
22 #end if 22 #end if
23 23
24 #if $cond_outformat.outputFormat == 'clustalw' 24 ## specify threads to use
25 --thread \${GALAXY_SLOTS:-1}
26
27 #if $outputFormat.value == 'clustalw'
25 --clustalout 28 --clustalout
26 #end if 29 #end if
27 30
28 $inputSequences > 31 $inputSequences >
29 32
30 #if $cond_outformat.outputFormat == 'fasta' 33 #if $outputFormat.value == 'fasta'
31 $outputFasta 34 $outputFasta
32 #else ## $cond_outformat.outputFormat == 'clustalw' 35 #elif $outputFormat.value == 'clustalw'
33 $outputClustalW 36 $outputClustalW
34 #end if 37 #end if
35 ]]> 38 ]]>
36 </command> 39 </command>
37 <inputs> 40 <inputs>
38 <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."/>
39 <conditional name="cond_flavour"> 42 <conditional name="cond_flavour">
40 <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.">
41 <option value="mafft-fftns" selected="true">fftns</option> 44 <option value="mafft-fftns" selected="true">fftns</option>
45 <option value="mafft --auto">auto</option>
42 <option value="mafft-fftnsi">fftnsi</option> 46 <option value="mafft-fftnsi">fftnsi</option>
43 <option value="mafft-nwns">nwns</option> 47 <option value="mafft-nwns">nwns</option>
44 <option value="mafft-nwnsi">nwnsi</option> 48 <option value="mafft-nwnsi">nwnsi</option>
45 <option value="mafft-einsi">einsi</option> 49 <option value="mafft-einsi">einsi</option>
46 <option value="mafft-ginsi">ginsi</option> 50 <option value="mafft-ginsi">ginsi</option>
47 <option value="mafft-linsi">linsi</option> 51 <option value="mafft-linsi">linsi</option>
48 <option value="mafft-qinsi">qinsi</option> 52 <option value="mafft-qinsi">qinsi</option>
49 <option value="mafft-xinsi">xinsi</option> 53 <option value="mafft-xinsi">xinsi</option>
50 <option value="custom">Custom Parameters</option> 54 <!-- <option value="custom">Custom Parameters</option> this should trigger tweaking of all parameters -->
51 </param> 55 </param>
52 <when value="mafft-fftns"/> 56 <when value="mafft-fftns"/>
57 <when value="mafft --auto"/>
53 <when value="mafft-fftnsi"/> 58 <when value="mafft-fftnsi"/>
54 <when value="mafft-nwns"/> 59 <when value="mafft-nwns"/>
55 <when value="mafft-nwnsi"/> 60 <when value="mafft-nwnsi"/>
56 <when value="mafft-einsi"/> 61 <when value="mafft-einsi"/>
57 <when value="mafft-ginsi"/> 62 <when value="mafft-ginsi"/>
58 <when value="mafft-linsi"/> 63 <when value="mafft-linsi"/>
59 <when value="mafft-qinsi"/> 64 <when value="mafft-qinsi"/>
60 <when value="mafft-xinsi"/> 65 <when value="mafft-xinsi"/>
61 <when value="custom"/>
62 </conditional> 66 </conditional>
63 <conditional name="cond_outformat"> 67 <param name="outputFormat" type="select" label="Output format" help="Either FASTA or ClustalW">
64 <param name="outputFormat" type="select" label="Output format" help="Either FASTA or ClustalW"> 68 <option value="fasta" selected="true">FASTA</option>
65 <option value="fasta" selected="true">FASTA</option> 69 <option value="clustalw">ClustalW</option>
66 <option value="clustalw">ClustalW</option> 70 </param>
67 </param>
68 <when value="fasta"/>
69 <when value="clustalw"/>
70 </conditional>
71 </inputs> 71 </inputs>
72 <outputs> 72 <outputs>
73 <data format="fasta" name="outputFasta" label="${tool.name} on ${on_string}"> 73 <data format="fasta" name="outputFasta" label="${tool.name} on ${on_string}">
74 <filter>(cond_outformat['outputFormat'] == 'fasta')</filter> 74 <filter>outputFormat == 'fasta'</filter>
75 </data> 75 </data>
76 <data format="clustal" name="outputClustalW" label="${tool.name} on ${on_string}"> 76 <data format="clustal" name="outputClustalW" label="${tool.name} on ${on_string}">
77 <filter>(cond_outformat['outputFormat'] == 'clustalw')</filter> 77 <filter>outputFormat == 'clustalw'</filter>
78 </data> 78 </data>
79 </outputs> 79 </outputs>
80 <tests> 80 <tests>
81 <test> 81 <test>
82 <param name="inputSequences" value="sample"/> 82 <param name="inputSequences" value="sample.fa"/>
83 <param name="flavourType" value="fftns"/> 83 <param name="flavourType" value="mafft-fftns"/>
84 <param name="outputFormat" value="fasta"/> 84 <param name="outputFormat" value="fasta"/>
85 <output name="outputFasta" file="sample.fftns2"/> 85 <output name="outputFasta" ftype="fasta" file="mafft_fftns_result.aln"/>
86 </test>
87 <test>
88 <param name="inputSequences" value="sample.fa"/>
89 <param name="flavourType" value="mafft-nwns"/>
90 <param name="outputFormat" value="clustalw"/>
91 <output name="outputClustalW" ftype="clustal" file="mafft_nwns_result.aln"/>
86 </test> 92 </test>
87 </tests> 93 </tests>
88 <help> 94 <help>
89 <![CDATA[ 95 <![CDATA[
90 **What it does** 96 **What it does**
137 - mafft --retree 2 --maxiterate 0 --nofft input [> output] 143 - mafft --retree 2 --maxiterate 0 --nofft input [> output]
138 144
139 - 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):
140 146
141 - mafft --retree 1 --maxiterate 0 --nofft --parttree input [> output] 147 - mafft --retree 1 --maxiterate 0 --nofft --parttree input [> output]
142 148
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)
143 ]]> 153 ]]>
144 </help> 154 </help>
145 <citations> 155 <citations>
146 <citation type="doi">10.1093/molbev/mst010</citation> 156 <citation type="doi">10.1093/molbev/mst010</citation>
147 <citation type="doi">10.1093/nar/gkt389</citation>
148 <citation type="doi">10.1093/bioinformatics/bts578</citation>
149 <citation type="doi">10.1093/bioinformatics/btq224</citation>
150 <citation type="doi">10.1007/978-1-59745-251-9_3</citation>
151 <citation type="doi">10.1186/1471-2105-9-212</citation>
152 <citation type="doi">10.1093/bib/bbn013</citation>
153 <citation type="doi">10.1093/bioinformatics/btl592</citation>
154 <citation type="doi">10.1093/nar/gki198</citation>
155 <citation type="doi">10.1093/nar/gkf436</citation>
156 </citations> 157 </citations>
157 </tool> 158 </tool>