Mercurial > repos > rnateam > mafft

annotate mafft.xml @ 5:15974dd17515 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mafft commit fc3727b1b39cd5654a523d03e0df2b9ac87ddcda
author rnateam
date Tue, 20 Sep 2016 09:30:47 -0400
parents f0606dfd5195
children aaefa93c2dd2
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1 <tool id="rbc_mafft" name="MAFFT" version="7.221.3">
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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 #elif $cond_flavour.flavourType == 'custom'
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20 ### full parameter options
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21 mafft
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22 $cond_flavour.distance_method
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23 --retree $cond_flavour.retree
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24 --maxiterate $cond_flavour.iterations
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25 #end if
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26
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27 ## specify threads to use
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28 --thread \${GALAXY_SLOTS:-1}
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29
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30 $datatype
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31 --ep $ep
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32 --op $op
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33 $adjustdirection
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34
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35 #if $matrix_condition.matrix == "BLOSUM"
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36 --bl ${matrix_condition.BLOSUM}
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37 #elif $matrix_condition.matrix == "PAM"
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38 --jtt ${matrix_condition.PAM}
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39 #end if
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40
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41 $reorder
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42 $getTree
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43 $outputFormat
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44 $inputSequences > $outputAlignment;
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45
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46 #if $getTree == "--treeout"
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47 mv ${inputSequences}.tree $outputTree;
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48 #end if
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49 ]]>
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50 </command>
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51 <inputs>
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52 <param name="inputSequences" type="data" format="fasta" label="Sequences to align" help="Amino acid or nucleotide sequences in FASTA format."/>
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53 <param name="datatype" type="select" label="Data type">
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54 <option value="">Auto detection</option>
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55 <option value="--nuc">Nucleic acids</option>
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56 <option value="--amino">Amino acids</option>
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57 </param>
0
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58 <conditional name="cond_flavour">
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59 <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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60 <option value="mafft --auto">auto</option>
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61 <option value="mafft-fftns" selected="true">fftns</option>
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62 <option value="mafft-fftnsi">fftnsi</option>
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63 <option value="mafft-nwns">nwns</option>
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64 <option value="mafft-nwnsi">nwnsi</option>
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65 <option value="mafft-einsi">einsi</option>
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66 <option value="mafft-ginsi">ginsi</option>
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67 <option value="mafft-linsi">linsi</option>
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68 <option value="mafft-qinsi">qinsi</option>
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69 <option value="mafft-xinsi">xinsi</option>
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70 <option value="custom">Custom Parameters</option>
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71 </param>
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72 <when value="mafft-fftns"/>
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73 <when value="mafft --auto"/>
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74 <when value="mafft-fftnsi"/>
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75 <when value="mafft-nwns"/>
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76 <when value="mafft-nwnsi"/>
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77 <when value="mafft-einsi"/>
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78 <when value="mafft-ginsi"/>
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79 <when value="mafft-linsi"/>
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80 <when value="mafft-qinsi"/>
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81 <when value="mafft-xinsi"/>
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82 <when value="custom">
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83 <param name="distance_method" type="select" display="radio" label="Distance method" help="Distance method must be chosen regarding your data">
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84 <option value="--6merpair" selected="true">Shared 6mers distance (fastest)</option>
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85 <option value="--globalpair">Global alignment (Needleman-Wunsch)</option>
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86 <option value="--localpair">Local alignment (Smith-Waterman)</option>
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87 <option value="--genafpair">Local, affine gap cost</option>
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88 </param>
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89 <param name="retree" type="integer" value="2" min="1" max="100" label="Guide tree is built this number of times in the progressive stage." help="Valid with 6mer distance" />
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90 <param name="iterations" type="integer" value="0" min="0" max="1000" label="Maximum number of iterations" help="1000 for maximum quality" />
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91 </when>
0
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92 </conditional>
3
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93 <param name="ep" type="float" value="0.123" label="Gap extend penalty" help="Offset value, which works like gap extension penalty, for group-to-group alignment. For E-INS-i, 0 is recommended to allow large gaps" />
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94 <param name="op" type="float" value="1.53" label="Gap opening penalty" help="1.53 default value" />
2
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95 <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">
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96 <option value="--adjustdirection">adjust direction</option>
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97 <option value=" " selected="true">do not adjust direction</option>
3
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98 </param>
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99 <conditional name="matrix_condition">
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100 <param name="matrix" type="select" label="Matrix selection" display="radio" help="Usefull only for amino acids" >
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101 <option value="">No matrix</option>
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102 <option value="BLOSUM">BLOSUM</option>
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103 <option value="PAM">PAM</option>
2
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104 </param>
3
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105 <when value=""/>
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106 <when value="BLOSUM">
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107 <param name="BLOSUM" type="select" display="radio" label="Coefficient of the BLOSUM matrix">
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108 <option value="30">30</option>
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109 <option value="45">45</option>
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110 <option value="62" selected="true">62</option>
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111 <option value="80">80</option>
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112 </param>
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113 </when>
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114 <when value="PAM">
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115 <param name="PAM" type="integer" value="80" min="1" max="350" label="Coefficient of the PAM matrix" />
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116 </when>
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117 </conditional>
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118 <param name="reorder" type="boolean" truevalue="--reorder" falsevalue="" checked="False" label="Reorder output?" />
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119 <param name="getTree" type="boolean" truevalue="--treeout" falsevalue="" checked="False" label="Display alignment tree ?" />
0
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120 <param name="outputFormat" type="select" label="Output format" help="Either FASTA or ClustalW">
3
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121 <option value="" selected="true">FASTA</option>
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122 <option value="--clustalout">ClustalW</option>
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123 <option value="--phylipout">Phylip</option>
0
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124 </param>
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125 </inputs>
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126 <outputs>
3
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127 <data format="fasta" name="outputAlignment" label="${tool.name} on ${on_string}">
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128 <change_format>
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129 <when input="outputFormat" value="--clustalout" format="clustal"/>
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130 <when input="outputFormat" value="--phylipout" format="phylip"/>
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131 </change_format>
0
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132 </data>
3
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133 <data name="outputTree" format="txt" label="${tool.name} Guide Tree">
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134 <filter>getTree == True</filter>
0
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135 </data>
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136 </outputs>
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137 <tests>
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138 <test>
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139 <param name="inputSequences" value="sample.fa"/>
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140 <param name="flavourType" value="mafft-fftns"/>
3
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141 <param name="outputFormat" value=""/>
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142 <output name="outputAlignment" ftype="fasta" file="mafft_fftns_result.aln"/>
0
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143 </test>
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144 <test>
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145 <param name="inputSequences" value="sample.fa"/>
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146 <param name="flavourType" value="mafft-nwns"/>
3
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147 <param name="outputFormat" value="--clustalout"/>
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148 <output name="outputAlignment" ftype="clustal" file="mafft_nwns_result.aln"/>
0
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149 </test>
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150 </tests>
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151 <help>
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152 <![CDATA[
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153 **What it does**
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154
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155 MAFFT is a multiple sequence alignment program for unix-like operating systems.
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156 It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences),
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157 FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc.
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158
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159 From the MAFFT man page, an overview of the different predefined flavours of the tool.
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160
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161 **Accuracy-oriented methods:**
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162
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163 - L-INS-i (probably most accurate; recommended for <200 sequences; iterative refinement method incorporating local pairwise alignment information):
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164
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165 - mafft --localpair --maxiterate 1000 input [> output]
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166
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167 - 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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168
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169 - mafft --globalpair --maxiterate 1000 input [> output]
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170
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171 - E-INS-i (suitable for sequences containing large unalignable regions; recommended for <200 sequences):
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172
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173 - 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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174
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175
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176 **Speed-oriented methods:**
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177
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178 - FFT-NS-i (iterative refinement method; two cycles only):
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179
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180 - mafft --retree 2 --maxiterate 2 input [> output]
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181
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182 - FFT-NS-i (iterative refinement method; max. 1000 iterations):
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183
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184 - mafft --retree 2 --maxiterate 1000 input [> output]
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185
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186 - FFT-NS-2 (fast; progressive method):
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187
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188 - mafft --retree 2 --maxiterate 0 input [> output]
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189
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190 - FFT-NS-1 (very fast; recommended for >2000 sequences; progressive method with a rough guide tree):
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191
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192 - mafft --retree 1 --maxiterate 0 input [> output]
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193
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194 - NW-NS-i (iterative refinement method without FFT approximation; two cycles only):
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195
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196 - mafft --retree 2 --maxiterate 2 --nofft input [> output]
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197
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198 - NW-NS-2 (fast; progressive method without the FFT approximation):
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199
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200 - mafft --retree 2 --maxiterate 0 --nofft input [> output]
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201
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202 - NW-NS-PartTree-1 (recommended for ~10,000 to ~50,000 sequences; progressive method with the PartTree algorithm):
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203
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204 - mafft --retree 1 --maxiterate 0 --nofft --parttree input [> output]
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205
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206 **Options:**
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207
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208 --auto
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209 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)
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210 --adjustdirection
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211 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.
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212 --op
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213 Gap opening penalty, default: 1.53
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214 --ep
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215 Offset (works like gap extension penalty), default: 0.0
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216 --maxiterate
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217 Maximum number of iterative refinement, default: 0
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218 --clustalout
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219 Output: clustal format, default: fasta
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220 --thread
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221 Number of threads (if unsure, --thread -1)
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222 --retree number
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223 Guide tree is built number times in the progressive stage. Valid with 6mer distance. Default: 2
0
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224 ]]>
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225 </help>
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226 <citations>
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227 <citation type="doi">10.1093/molbev/mst010</citation>
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228 </citations>
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229 </tool>