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annotate BlastAlign.xml @ 7:9c0044eff621 draft

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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 273a9af69b672b2580cd5dec4c0e67a4a96fb0fe
author abims-sbr
date Tue, 27 Feb 2018 08:47:11 -0500
parents e0bea88bb09f
children f19cca5b8632
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1 <tool name="BlastAlign" id="blastalign" version="2.1">
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3 <description>
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4 Align the nucleic acid sequences using BLASTN
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5 </description>
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7 <macros>
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8 <import>macros.xml</import>
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9 </macros>
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11 <requirements>
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12 <expand macro="python_required" />
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13 <requirement type="package" version="1.4">blastalign</requirement>
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14 </requirements>
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16 <stdio>
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17 <exit_code range="1:" level="fatal" />
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18 </stdio>
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20 <command><![CDATA[
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21 ln -s '$input' '$input.element_identifier'".fasta" &&
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23 BlastAlign -i '$input.element_identifier'".fasta"
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24 -m $advanced_option.m
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25 #if $advanced_option.r != ""
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26 -r $advanced_option.r
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27 #end if
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28 #if $advanced_option.x != ""
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29 -x $advanced_option.x
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30 #end if
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31 -n $advanced_option.n
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32 #if $advanced_option.s != 0
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33 -s $advanced_option.s
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34 #end if
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35 &&
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36 ln -s '$input.element_identifier'".fasta.phy" out.phy &&
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37 ln -s '$input.element_identifier'".fasta.nxs" out.nxs
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38 #if $output_format.value == "fasta"
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39 && python $__tool_directory__/scripts/S01_phylip2fasta.py out.phy out.fasta
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40 #end if
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41
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42 ]]></command>
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43 <inputs>
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44 <param name="input" type="data" format="fasta" label="Choose your file" help="A fasta file with nucleotides sequences" />
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45
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46 <section name="advanced_option" title="Blast advanced options" expanded="True">
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47 <param argument="-m" type="integer" value="95" min="0" max="100" label="Proportion of gaps allowed in any one sequence in the final alignement" help="default = 95, i.e. only removing sequences with extremely short matches" />
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48 <param argument="-r" type="text" area="True" size="1x20" label="Choose a reference sequence" help="default is to search for best candidate (if entered, the sequence will be extracted, written to a separate file, and blasted against the original input file)"/>
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49 <param argument="-x" type="text" area="True" size="5x25" label="Choose the sequences to be excluded from this analysis" help="name of comma-separated sequences " />
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50 <param argument="-n" type="boolean" checked="true" truevalue="T" falsevalue="F" label="Retain original names in output files" help="option F is to output the 15 character name abbreviations (stripped of potentially problematic characters) that is used in the program" />
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51 <param argument="-s" type="integer" value="0" min="0" label="Number of sequences to be used in initial search for reference sequence" help="default (= 0) is to find the reference sequence by blasting all sequences against all sequences, only randomly subsampling when it thinks the blast output file might be too large" />
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52 </section>
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54 <param name="output_format" type="select" label="Output format" help="phylip, nexus, or fasta." >
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55 <option value="fasta">fasta</option>
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56 <option value="phylip">phylip</option>
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57 <option value="nexus">nexus</option>
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58 </param>
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59 </inputs>
0
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61 <outputs>
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62 <data format="phylip" name="phy" from_work_dir="out.phy" label="Blastalign on ${input.name} in phylip">
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63 <filter>output_format == "phylip"</filter>
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64 </data>
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65 <data format="nexus" name="nxs" from_work_dir="out.nxs" label="Blastalign on ${input.name} in nexus">
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66 <filter>output_format == "nexus"</filter>
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67 </data>
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68 <data format="fasta" name="fasta" from_work_dir="out.fasta" label="Blastalign on ${input.name} in fasta">
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69 <filter>output_format == "fasta"</filter>
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70 </data>
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71 </outputs>
0
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72
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73 <tests>
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74 <test>
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75 <param name="input" ftype="fasta" value="inputs/locus1_sp2.fasta" />
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76 <section name="advanced_option">
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77 <param name="m" value="95" />
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78 <param name="r" value="" />
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79 <param name="x" value="" />
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80 <param name="n" value="False" />
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81 <param name="s" value="0" />
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82 </section>
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83 <param name="output_format" value="fasta" />
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84 <output name="fasta" value="outputs/locus1_sp2.fasta" />
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85 </test>
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86 <test>
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87 <param name="input" ftype="fasta" value="inputs/locus1_sp3.fasta" />
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88 <section name="advanced_option">
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89 <param name="m" value="95" />
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90 <param name="r" value="" />
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91 <param name="x" value="" />
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92 <param name="n" value="False" />
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93 <param name="s" value="0" />
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94 </section>
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95 <param name="output_format" value="phylip" />
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96 <output name="phy" value="outputs/locus1_sp3.phy" />
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97 </test>
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98 <test>
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99 <param name="input" ftype="fasta" value="inputs/locus3_sp2.fasta" />
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100 <section name="advanced_option">
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101 <param name="m" value="95" />
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102 <param name="r" value="" />
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103 <param name="x" value="" />
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104 <param name="n" value="False" />
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105 <param name="s" value="0" />
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106 </section>
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107 <param name="output_format" value="nexus" />
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108 <output name="nxs" value="outputs/locus3_sp2.nxs" />
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109 </test>
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110 <test>
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111 <param name="input" ftype="fasta" value="inputs/locus8_sp2.fasta" />
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112 <section name="advanced_option">
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113 <param name="m" value="95" />
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114 <param name="r" value="" />
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115 <param name="x" value="" />
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116 <param name="n" value="False" />
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117 <param name="s" value="0" />
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118 </section>
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119 <param name="output_format" value="phylip" />
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120 <output name="phy" value="outputs/locus8_sp2.phy" />
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121 </test>
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122 <test>
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123 <param name="input" ftype="fasta" value="inputs/locus8_sp2.fasta" />
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124 <section name="advanced_option">
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125 <param name="m" value="95" />
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126 <param name="r" value="" />
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127 <param name="x" value="" />
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128 <param name="n" value="False" />
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129 <param name="s" value="0" />
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130 </section>
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131 <param name="output_format" value="fasta" />
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132 <output name="phy" value="outputs/locus8_sp2.fasta" />
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133 </test>
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134
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135 <!--locus10_sp2.fasta locus1_sp3.fasta locus2_sp2.fasta locus3_sp2.fasta locus4_sp2.fasta locus5_sp2.fasta locus6_sp2.fasta locus7_sp2.fasta locus8_sp2.fasta locus9_sp2.fasta-->
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136 </tests>
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137
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138 <help>
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139 <![CDATA[
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140
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141 . class:: infomark
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142
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143 **Authors** BlastAlign has been written by Robert Belshaw and Aris Katzourakis. The scripts of this tool have been written by Eric Fontanillas.
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144
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145 .. class:: infomark
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146
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147 **Galaxy integration** Julie Baffard and ABiMS Team.
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148
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149 Contact support.abims@sb-roscoff.fr for any questions or concerns about the Galaxy implementation of this tool.
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150
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151 --------
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152
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153 **Description**
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154
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155 BlastAlign takes a set of nucleic sequences in a file in fasta format and returns a multiple alignment (in Nexus and Phylip formats) using BLAST+. This Galaxy implementation works with dataset collections, which allows multiple parallels runs of BlastAlign at once on many files.
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156
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157 --------
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158
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159 **Parameters**
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160
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161 The choice of several parameters for the blast is possible.
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162
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163 **-m : Proportion of gaps allowed in any one sequence in the final alignement**
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164 integer (between 0 and 100).
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165 By default : 95%, i.e. only removes sequences with extremely short matches.
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166 We find 50 the most useful.
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167
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168 **-r : Name of reference sequence**
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169 text.
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170 Default is searching for best candidate.
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171 If entered, the sequence will be extracted, written to a separate file, and blasted against the original input file.
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172
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173 **-x : Name of sequences to be excluded from the analysis**
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174 text.
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175 names must be comma-separated.
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176
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177 **-n**
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178 If checked : retain original names in output files.
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179 If not checked : output the 15 character name abbreviations (stripped of potentially problematic characters) that is used in the tool.
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180 Default : checked.
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181
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182 **-s : Number of sequences to be used in initial search for reference sequence**
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183 integer (between 0 and total number of sequences).
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184 Default : 0
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185 Default is finding the reference sequence by blasting all sequences against all sequences, only randomly subsampling when it thinks the blast output file might be too large.
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186
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187 ** Output format :**
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188 The user have the choice between three format (only one is returned per run) : fasta, phylip, and nexus.
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189 --------
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190
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191 **Outputs**
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192
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193 The output format is
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194
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195 - 'Blastalign_on_{input.name}_phylip' :
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196 the aligned sequences in Phylip format.
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197
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198 - 'Blastalign_on_{input.name}_nexus' :
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199 the aligned sequences in Nexus format.
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200
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201 - 'Blastalign_on_{input_file}_fasta' :
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202 the aligned sequences in Fasta format if the option "fasta format" is checked.
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203
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204 ---------
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205
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206 Changelog
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207 ---------
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208
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209 **Version 2.1 - 17/01/2018**
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210
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211 - New parameter "output format"
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212 - Applied some bugfixes and minor improvments
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213
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214 **Version 2.0 - 21/04/2017**
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215
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216 - NEW: BlastAlign will now be launched on one file at once. Although, it will manage a Dataset Collection to deal with numerous files.
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217
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218 **Version 1.0 - 13/04/2017**
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219
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220 - TEST: Add funtional test with planemo
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221 - IMPROVEMENT: Use conda dependencies for blastalign, blast-legacy, perl, python
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222
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223 ]]>
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224
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225 </help>
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226
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227 <expand macro="citations" />
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229 </tool>
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230