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annotate rgClustalw.xml @ 3:fac9d3c091cb draft

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author devteam
date Thu, 15 Sep 2022 12:12:19 +0000
parents bed27b5c0f63
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3
fac9d3c091cb planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/clustalw commit fdbbc72ea8880e53b09ca3e60bafa544d5088dbc
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1 <tool id="clustalw" name="ClustalW" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
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2 <description>multiple sequence alignment program for DNA or proteins</description>
3
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command detect_errors="exit_code"><![CDATA[
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8 ln -s '$input' input.fasta &&
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9 clustalw2 -INFILE=input.fasta -OUTFILE='$output' -OUTORDER=$out_order -TYPE=$type_conditional.dnarna
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10 #if $outcontrol.outform == "clustal"
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11 -OUTPUT=CLUSTAL
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12 #if $outcontrol.out_seqnos == "ON"
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13 -SEQNOS=ON
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14 #end if
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15 #end if
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16 #if $outcontrol.outform == "phylip"
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17 -OUTPUT=PHYLIP
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18 #end if
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19 #if $outcontrol.outform == "fasta"
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20 -OUTPUT=FASTA
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21 #end if
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22 #if $range.mode == "part"
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23 -RANGE=${range.seq_range_start},${range.seq_range_end}
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24 #end if
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25 #if $type_conditional.dnarna == 'PROTEIN'
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26 #if $type_conditional.algorithm_conditional.selector == ''
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27 -PWMATRIX=$type_conditional.algorithm_conditional.slow_pairwise_alignments.PWMATRIX
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28 @SLOW_PAIRWISE_ALIGNMENTS@
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29 #else
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30 @FAST_PAIRWISE_ALIGNMENTS@
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31 #end if
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32 -MATRIX=$type_conditional.multiple_alignments.MATRIX
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33 @MULTIPLE_ALIGNMENTS@
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34 #else
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35 #if $type_conditional.algorithm_conditional.selector == ''
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36 -PWDNAMATRIX=$type_conditional.algorithm_conditional.slow_pairwise_alignments.PWDNAMATRIX
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37 @SLOW_PAIRWISE_ALIGNMENTS@
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38 #else
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39 @FAST_PAIRWISE_ALIGNMENTS@
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40 #end if
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41 -DNAMATRIX=$type_conditional.multiple_alignments.DNAMATRIX
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42 @MULTIPLE_ALIGNMENTS@
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43 #end if
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44 -OUTPUTTREE=$tree_calculation.OUTPUTTREE
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45 $tree_calculation.KIMURA
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46 $tree_calculation.TOSSGAPS
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47 ]]></command>
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48 <inputs>
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49 <param name="input" type="data" format="fasta" label="FASTA file" />
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50 <conditional name="type_conditional">
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51 <param name="dnarna" type="select" label="Data type">
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52 <option value="DNA" selected="True">DNA nucleotide sequences</option>
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53 <option value="PROTEIN">Protein sequences</option>
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54 </param>
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55 <when value="DNA">
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56 <expand macro="macro_options" algorithm="PWDNAMATRIX" multiple="DNAMATRIX" label="DNA" default="IUB">
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57 <option value="IUB" selected="true">IUB</option>
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58 <option value="CLUSTALW">CLUSTALW</option>
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59 </expand>
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60 </when>
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61 <when value="PROTEIN">
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62 <expand macro="macro_options" algorithm="PWMATRIX" multiple="MATRIX" label="Protein" default="GONNET">
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63 <option value="BLOSUM">BLOSUM</option>
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64 <option value="PAM">PAM</option>
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65 <option value="GONNET" selected="true">GONNET</option>
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66 <option value="ID">ID</option>
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67 </expand>
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68 </when>
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69 </conditional>
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70 <section name="tree_calculation" title="Tree calculation/BOOTSTRAP options">
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71 <param argument="-OUTPUTTREE" type="select" label="Output tree/distance forma" help="Specify the output format. Default: phylip">
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72 <option value="PHYLIP">PHYLIP</option>
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73 <option value="DIST">DIST</option>
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74 <option value="NJ">NJ</option>
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75 <option value="NEXUS">NEXUS</option>
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76 </param>
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77 <param argument="-KIMURA" type="boolean" truevalue="-KIMURA" falsevalue="" checked="false" label="Use Kimura correction"
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78 help="For small divergence (say inferior 10%) this option makes no difference. For greater divergence, this option corrects for the fact that observed distances underestimate actual evolutionary distances." />
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79 <param argument="-TOSSGAPS" type="boolean" truevalue="-TOSSGAPS" falsevalue="" checked="false" label="Ignore positions with gaps" help="Default: No" />
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80 </section>
2
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81 <conditional name="outcontrol">
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82 <param name="outform" type="select" label="Output alignment format">
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83 <option value="clustal" selected="True">Native Clustal output format</option>
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84 <option value="phylip">PHYLIP format</option>
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85 <option value="fasta">FASTA format</option>
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86 </param>
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87 <when value="fasta" />
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88 <when value="phylip" />
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89 <when value="clustal">
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90 <param name="out_seqnos" type="boolean" truevalue="ON" falsevalue="OFF" label="Show residue numbers in clustal format output" />
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91 </when>
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92 </conditional>
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93 <param name="out_order" type="select" label="Output order">
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94 <option value="ALIGNED">Aligned</option>
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95 <option value="INPUT">Same order as input file</option>
0
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96 </param>
2
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97 <conditional name="range">
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98 <param name="mode" type="select" label="Output complete alignment (or specify part to output)">
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99 <option value="complete">Complete alignment</option>
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100 <option value="part">Only part of the alignment</option>
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101 </param>
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102 <when value="complete" />
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103 <when value="part">
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104 <param name="seq_range_start" type="integer" value="1" label="Start point" help="Sequence range to write" />
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105 <param name="seq_range_end" type="integer" value="99999" label="End point" />
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106 </when>
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107 </conditional>
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108 </inputs>
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109 <outputs>
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110 <data name="output" format="clustal" label="${tool.name} on ${on_string}: ${outcontrol.outform}">
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111 <change_format>
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112 <when input="outcontrol.outform" value="phylip" format="phylip" />
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113 <when input="outcontrol.outform" value="fasta" format="fasta" />
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114 </change_format>
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115 </data>
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116 <data name="dnd" format="nhx" label="${tool.name} on ${on_string}: dnd" from_work_dir="input.dnd" />
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117 </outputs>
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118 <tests>
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119 <test>
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120 <param name="input" value="rgClustal_testin.fasta" />
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121 <param name="outform" value="fasta" />
3
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122 <conditional name="type_conditional">
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123 <param name="dnarna" value="DNA"/>
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124 </conditional>
2
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125 <param name="mode" value="complete" />
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126 <param name="out_order" value="ALIGNED" />
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127 <output name="output" file="rgClustal_testout.fasta" ftype="fasta" />
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128 <output name="dnd" file="rgClustal_testin.dnd" ftype="nhx" />
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129 </test>
3
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130 <!-- Test DNA options-->
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131 <test expect_num_outputs="2">
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132 <param name="input" value="rgClustal_testin.fasta"/>
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133 <param name="out_order" value="ALIGNED"/>
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134 <section name="tree_calculation">
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135 <param name="OUTPUTTREE" value="PHYLIP"/>
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136 <param name="KIMURA" value="true"/>
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137 <param name="TOSSGAPS" value="true"/>
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138 </section>
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139 <conditional name="type_conditional">
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140 <param name="dnarna" value="DNA"/>
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141 <section name="multiple_alignments">
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142 <param name="DNAMATRIX" value="IUB"/>
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143 <param name="GAPOPEN" value="2"/>
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144 <param name="GAPEXT" value="1"/>
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145 <param name="ENDGAPS" value="true"/>
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146 <param name="GAPDIST" value="1"/>
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147 <param name="NOPGAP" value="true"/>
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148 <param name="NOHGAP" value="true"/>
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149 <param name="MAXDIV" value="1"/>
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150 <param name="NEGATIVE" value="true"/>
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151 <param name="TRANSWEIGHT" value="1"/>
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152 </section>
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153 <conditional name="algorithm_conditional">
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154 <param name="selector" value=""/>
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155 <section name="slow_pairwise_alignments">
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156 <param name="PWGAPOPEN" value="2"/>
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157 <param name="PWGAPEXT" value="1"/>
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158 </section>
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159 </conditional>
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160 </conditional>
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161 <output name="output" file="rgClustal_testout02.aln" ftype="clustal"/>
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162 <output name="dnd" file="rgClustal_testout02.dnd" ftype="nhx"/>
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163 </test>
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164 <!-- Test protein options and fast algorithm-->
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165 <test expect_num_outputs="2">
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166 <param name="input" value="rgClustal_testin_prot.fasta"/>
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167 <param name="out_order" value="ALIGNED"/>
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168 <section name="tree_calculation">
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169 <param name="OUTPUTTREE" value="PHYLIP"/>
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170 <param name="KIMURA" value="false"/>
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171 <param name="TOSSGAPS" value="false"/>
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172 </section>
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173 <conditional name="type_conditional">
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174 <param name="dnarna" value="PROTEIN"/>
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175 <section name="multiple_alignments">
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176 <param name="MATRIX" value="BLOSUM"/>
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177 <param name="GAPOPEN" value="3"/>
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178 <param name="GAPEXT" value="1"/>
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179 <param name="ENDGAPS" value="true"/>
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180 <param name="GAPDIST" value="2"/>
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181 <param name="NOPGAP" value="true"/>
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182 <param name="NOHGAP" value="true"/>
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183 <param name="MAXDIV" value="1"/>
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184 <param name="NEGATIVE" value="true"/>
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185 <param name="TRANSWEIGHT" value="1"/>
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186 </section>
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187 <conditional name="algorithm_conditional">
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188 <param name="selector" value="-QUICKTREE"/>
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189 <section name="fast_pairwise_alignments">
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190 <param name="KTUPLE" value="1"/>
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191 <param name="TOPDIAGS" value="1"/>
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192 <param name="WINDOW" value="2"/>
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193 <param name="PAIRGAP" value="2"/>
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194 <param name="SCORE" value="PERCENT"/>
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195 </section>
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196 </conditional>
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197 </conditional>
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198 <output name="output" file="rgClustal_testout03.aln" ftype="clustal"/>
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199 <output name="dnd" file="rgClustal_testout03.dnd" ftype="nhx"/>
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200 </test>
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201 </tests>
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202 <help><![CDATA[
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203 .. class:: infomark
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204
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205 **Note**
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206
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207 This tool allows you to run a multiple sequence alignment with ClustalW_.
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208 You can align DNA or protein sequences in the input file which should be multiple sequences to be aligned in a FASTA file.
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209
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210 The alignments will appear as a clustal format file or optionally, as PHYLIP or FASTA format files in your history. If you choose FASTA as
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211 the output format, you can create a 'Logo' image using the Sequence Logo tool.
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212
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213 If Clustal format is chosen, you have the option of adding basepair counts to the output.
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214
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215 A subsequence of the alignment can be output by setting the Output complete parameter to "Partial" and defining the offset and end of the subsequence to be output.
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216
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217 ----
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218
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219 .. class:: infomark
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220
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221 **Attribution**
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222
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223 The first iteration of this Galaxy wrapper was written by Hans-Rudolf Hotz.
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224
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225 It was modified by Ross Lazarus for the rgenetics project - tests and some additional parameters were added. Cristóbal Gallardo included the remaining parameters.
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226
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227 This wrapper is released licensed under the LGPL_.
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228
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229 .. _ClustalW: http://www.clustal.org/clustal2/
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230
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231 .. _LGPL: https://www.gnu.org/copyleft/lesser.html
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232 ]]></help>
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233 <citations>
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234 <citation type="doi">10.1093/bioinformatics/btm404</citation>
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235 </citations>
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236 </tool>