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annotate mafft.xml @ 0:8817d3a35fac draft

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author rnateam
date Tue, 16 Jun 2015 10:54:16 -0400
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children 95526e9e3808
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1 <tool id="rbc_mafft" name="MAFFT" version="7.221.0">
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2 <description>Multiple alignment program for amino acid or nucleotide sequences</description>
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3 <requirements>
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4 <requirement type="package" version="7.221">mafft</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
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8 <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />
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9 </stdio>
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10 <version_command>
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11 <![CDATA[
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12 mafft --version
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13 ]]>
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14 </version_command>
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15 <command>
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16 <![CDATA[
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17 #if $cond_flavour.flavourType != 'custom'
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18 $cond_flavour.flavourType
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19 #else
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20 ### full parameter options
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21 mafft
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22 #end if
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23
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24 #if $cond_outformat.outputFormat == 'clustalw'
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25 --clustalout
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26 #end if
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27
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28 $inputSequences >
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29
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30 #if $cond_outformat.outputFormat == 'fasta'
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31 $outputFasta
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32 #else ## $cond_outformat.outputFormat == 'clustalw'
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33 $outputClustalW
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34 #end if
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35 ]]>
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36 </command>
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37 <inputs>
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38 <param name="inputSequences" type="data" format="fasta" label="Sequences to align" help="Amino acid or nucleotide sequences in FASTA format."/>
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39 <conditional name="cond_flavour">
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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.">
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41 <option value="mafft-fftns" selected="true">fftns</option>
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42 <option value="mafft-fftnsi">fftnsi</option>
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43 <option value="mafft-nwns">nwns</option>
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44 <option value="mafft-nwnsi">nwnsi</option>
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45 <option value="mafft-einsi">einsi</option>
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46 <option value="mafft-ginsi">ginsi</option>
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47 <option value="mafft-linsi">linsi</option>
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48 <option value="mafft-qinsi">qinsi</option>
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49 <option value="mafft-xinsi">xinsi</option>
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50 <option value="custom">Custom Parameters</option>
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51 </param>
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52 <when value="mafft-fftns"/>
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53 <when value="mafft-fftnsi"/>
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54 <when value="mafft-nwns"/>
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55 <when value="mafft-nwnsi"/>
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56 <when value="mafft-einsi"/>
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57 <when value="mafft-ginsi"/>
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58 <when value="mafft-linsi"/>
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59 <when value="mafft-qinsi"/>
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60 <when value="mafft-xinsi"/>
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61 <when value="custom"/>
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62 </conditional>
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63 <conditional name="cond_outformat">
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64 <param name="outputFormat" type="select" label="Output format" help="Either FASTA or ClustalW">
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65 <option value="fasta" selected="true">FASTA</option>
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66 <option value="clustalw">ClustalW</option>
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67 </param>
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68 <when value="fasta"/>
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69 <when value="clustalw"/>
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70 </conditional>
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71 </inputs>
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72 <outputs>
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73 <data format="fasta" name="outputFasta" label="${tool.name} on ${on_string}">
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74 <filter>(cond_outformat['outputFormat'] == 'fasta')</filter>
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75 </data>
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76 <data format="clustal" name="outputClustalW" label="${tool.name} on ${on_string}">
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77 <filter>(cond_outformat['outputFormat'] == 'clustalw')</filter>
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78 </data>
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79 </outputs>
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80 <tests>
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81 <test>
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82 <param name="inputSequences" value="sample"/>
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83 <param name="flavourType" value="fftns"/>
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84 <param name="outputFormat" value="fasta"/>
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85 <output name="outputFasta" file="sample.fftns2"/>
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86 </test>
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87 </tests>
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88 <help>
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89 <![CDATA[
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90 **What it does**
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91
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92 MAFFT is a multiple sequence alignment program for unix-like operating systems.
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93 It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences),
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94 FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc.
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95
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96 From the MAFFT man page, an overview of the different predefined flavours of the tool.
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97
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98 **Accuracy-oriented methods:**
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99
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100 - L-INS-i (probably most accurate; recommended for <200 sequences; iterative refinement method incorporating local pairwise alignment information):
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101
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102 - mafft --localpair --maxiterate 1000 input [> output]
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103
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104 - G-INS-i (suitable for sequences of similar lengths; recommended for <200 sequences; iterative refinement method incorporating global pairwise alignment information):
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105
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106 - mafft --globalpair --maxiterate 1000 input [> output]
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107
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108 - E-INS-i (suitable for sequences containing large unalignable regions; recommended for <200 sequences):
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109
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110 - mafft --ep 0 --genafpair --maxiterate 1000 input [> output]. For E-INS-i, the --ep 0 option is recommended to allow large gaps.
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111
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112
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113 **Speed-oriented methods:**
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114
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115 - FFT-NS-i (iterative refinement method; two cycles only):
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116
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117 - mafft --retree 2 --maxiterate 2 input [> output]
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118
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119 - FFT-NS-i (iterative refinement method; max. 1000 iterations):
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120
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121 - mafft --retree 2 --maxiterate 1000 input [> output]
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122
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123 - FFT-NS-2 (fast; progressive method):
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124
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125 - mafft --retree 2 --maxiterate 0 input [> output]
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126
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127 - FFT-NS-1 (very fast; recommended for >2000 sequences; progressive method with a rough guide tree):
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128
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129 - mafft --retree 1 --maxiterate 0 input [> output]
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130
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131 - NW-NS-i (iterative refinement method without FFT approximation; two cycles only):
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132
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133 - mafft --retree 2 --maxiterate 2 --nofft input [> output]
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134
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135 - NW-NS-2 (fast; progressive method without the FFT approximation):
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136
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137 - mafft --retree 2 --maxiterate 0 --nofft input [> output]
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138
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139 - NW-NS-PartTree-1 (recommended for ~10,000 to ~50,000 sequences; progressive method with the PartTree algorithm):
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140
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141 - mafft --retree 1 --maxiterate 0 --nofft --parttree input [> output]
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142
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143 ]]>
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144 </help>
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145 <citations>
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146 <citation type="doi">10.1093/molbev/mst010</citation>
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147 <citation type="doi">10.1093/nar/gkt389</citation>
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148 <citation type="doi">10.1093/bioinformatics/bts578</citation>
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149 <citation type="doi">10.1093/bioinformatics/btq224</citation>
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150 <citation type="doi">10.1007/978-1-59745-251-9_3</citation>
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151 <citation type="doi">10.1186/1471-2105-9-212</citation>
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152 <citation type="doi">10.1093/bib/bbn013</citation>
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153 <citation type="doi">10.1093/bioinformatics/btl592</citation>
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154 <citation type="doi">10.1093/nar/gki198</citation>
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155 <citation type="doi">10.1093/nar/gkf436</citation>
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156 </citations>
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157 </tool>