1 <?xml version="1.0" encoding="US-ASCII" standalone="yes" ?>
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2 <runnerConfig xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="D:/workspace/clusterengine/testsrc/testdata/RunnerConfigSchema.xsd">
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3 <runnerClassName>compbio.runner.mafft.Mafft</runnerClassName>
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4 <options isRequired="false">
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5 <name>Shared 6mers distance calculation</name>
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6 <description>Distance is calculated based on the number of shared 6mers. Default: on</description>
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7 <!-- no optionName here! -->
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8 <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>
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9 <defaultValue>--6merpair</defaultValue>
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11 <options isRequired="true">
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12 <name>Output sequences order</name>
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13 <description>--inputorder - Output order: same as input.
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14 --reorder - Output order: aligned. Default: same as input</description>
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15 <optionNames>--inputorder</optionNames>
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16 <optionNames>--reorder</optionNames>
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17 <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>
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18 <defaultValue>--inputorder</defaultValue>
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20 <options isRequired="false">
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21 <name>Sequence type</name>
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23 --nuc - Assume the sequences are nucleotide.
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24 --amino - Assume the sequences are amino acid. </description>
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25 <optionNames>--amino</optionNames>
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26 <optionNames>--nuc</optionNames>
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27 <optionNames>--auto</optionNames>
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28 <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>
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29 <defaultValue>--auto</defaultValue>
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31 <options isRequired="false">
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32 <name>Pairwise alignment computation method</name>
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35 All pairwise alignments are computed with the Needleman-Wunsch algorithm. More accurate but slower than --6merpair. Suitable for a set of globally alignable sequences. Applicable to up to ~200 sequences. A combination with --maxiterate 1000 is recommended (G-INS-i). Default: off (6mer distance is used)
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37 All pairwise alignments are computed with a local algorithm with the generalized affine gap cost (Altschul 1998). More accurate but slower than --6merpair. Suitable when large internal gaps are expected. Applicable to up to ~200 sequences. A combination with --maxiterate 1000 is recommended (E-INS-i). Default: off (6mer distance is used)
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39 All pairwise alignments are computed with FASTA (Pearson and Lipman 1988). FASTA is required. Default: off (6mer distance is used)
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41 All pairwise alignments are computed with the Smith-Waterman algorithm. More accurate but slower than --6merpair. Suitable for a set of locally alignable sequences. Applicable to up to ~200 sequences. A combination with --maxiterate 1000 is recommended (L-INS-i). Default: off (6mer distance is used)
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43 <optionNames>--fastapair</optionNames>
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44 <optionNames>--genafpair</optionNames>
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45 <optionNames>--localpair</optionNames>
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46 <optionNames>--globalpair</optionNames>
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47 <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>
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49 <options isRequired="false">
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50 <name>FFT approximation</name>
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51 <description>Use / Do not use FFT approximation in group-to-group alignment. Default: off</description>
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52 <optionNames>--nofft</optionNames>
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53 <optionNames>--fft</optionNames>
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54 <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>
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56 <options isRequired="false">
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57 <name>No score</name>
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58 <description>Alignment score is not checked in the iterative refinement stage. Default: off (score is checked)</description>
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59 <optionNames>--noscore</optionNames>
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60 <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>
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62 <options isRequired="false">
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63 <name>Part tree</name>
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65 --parttree - Use a fast tree-building method (PartTree, Katoh and Toh 2007) with the 6mer distance.
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66 --dpparttree - the PartTree algorithm is used with distances based on DP.
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67 Slightly more accurate and slower than --parttree.
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68 --fastaparttree - The PartTree algorithm is used with distances based on FASTA.
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69 Slightly more accurate and slower than --parttree.
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70 All methods recommended for a large number (> ~10,000) of sequences are input.
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72 <optionNames>--dpparttree</optionNames>
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73 <optionNames>--parttree</optionNames>
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74 <optionNames>--fastaparttree</optionNames>
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75 <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>
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77 <prmSeparator> </prmSeparator>
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78 <parameters isRequired="false">
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79 <name>Max iteration number</name>
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80 <description>number cycles of iterative refinement are performed. Default: 0</description>
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81 <optionNames>--maxiterate</optionNames>
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82 <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>
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83 <defaultValue>0</defaultValue>
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85 <type>Integer</type>
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90 <parameters isRequired="false">
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91 <name>Partsize</name>
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92 <description>The number of partitions in the PartTree algorithm. Default: 50</description>
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93 <optionNames>--partsize</optionNames>
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94 <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>
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95 <defaultValue>50</defaultValue>
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97 <type>Integer</type>
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101 <parameters isRequired="false">
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102 <name>Group size</name>
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103 <description>Do not make alignment larger than number sequences. Valid only with the --*parttree options. Default: the number of input sequences</description>
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104 <optionNames>--groupsize</optionNames>
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105 <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>
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106 <defaultValue>20</defaultValue>
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108 <type>Integer</type>
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112 <parameters isRequired="false">
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113 <name>Guide tree rebuild</name>
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114 <description>Guide tree is built number times in the progressive stage. Valid with 6mer distance. Default: 2</description>
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115 <optionNames>--retree</optionNames>
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116 <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>
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117 <defaultValue>2</defaultValue>
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119 <type>Integer</type>
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124 <parameters isRequired="false">
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125 <name>Gap opening penalty</name>
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126 <description>Gap opening penalty at group-to-group alignment. Default: 1.53</description>
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127 <optionNames>--op</optionNames>
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128 <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>
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129 <defaultValue>1.53</defaultValue>
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135 <parameters isRequired="false">
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136 <name>Group-to-group gap extension penalty</name>
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137 <description>Offset value, which works like gap extension penalty, for group-to-group alignment. Deafult: 0.123</description>
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138 <optionNames>--ep</optionNames>
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139 <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>
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140 <defaultValue>0.123</defaultValue>
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146 <parameters isRequired="false">
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147 <name>Gap opening penalty at local pairwise alignment</name>
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148 <description>Gap opening penalty at local pairwise alignment. Valid when the --localpair or --genafpair option is selected. Default: -2.00</description>
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149 <optionNames>--lop</optionNames>
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150 <furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>
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151 <defaultValue>-2.00</defaultValue>
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