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annotate BlastAlign.xml @ 3:49017ea906b5 draft

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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
author abims-sbr
date Wed, 17 Jan 2018 08:55:00 -0500
parents 92615a423389
children 9eb5bb56bf41
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1 <tool name="BlastAlign" id="blastalign" version="2.0">
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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 $fasta_out.value == True
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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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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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53
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54 <param name="fasta_out" type="boolean" checked="true" label="Do you want to convert the output phylip in fasta format ? " />
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55 </inputs>
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56
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57 <outputs>
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58 <data format="phylip" name="phy" from_work_dir="out.phy" label="Alignment of ${input.name} in phylip" hidden="True"/>
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59 <data format="nexus" name="nxs" from_work_dir="out.nxs" label="Alignment of ${input.name} in nexus" hidden="True"/>
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60 <data format="fasta" name="fasta" from_work_dir="out.fasta" label="Alignment of ${input.name} in fasta" hidden="True">
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61 <filter>fasta_out == True</filter>
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62 </data>
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63 </outputs>
0
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64
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65 <tests>
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66 <test>
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67 <param name="input" ftype="fasta" value="inputs/locus1_sp2.fasta" />
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68 <section name="advanced_option">
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69 <param name="m" value="95" />
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70 <param name="r" value="" />
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71 <param name="x" value="" />
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72 <param name="n" value="False" />
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73 <param name="s" value="0" />
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74 </section>
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75 <param name="fasta_out" value="True" />
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76 <output name="phy" value="outputs/locus1_sp2.phy" />
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77 <output name="nxs" value="outputs/locus1_sp2.nxs" />
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78 <output name="fasta" value="outputs/locus1_sp2.fasta" />
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79 </test>
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80 <test>
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81 <param name="input" ftype="fasta" value="inputs/locus1_sp3.fasta" />
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82 <section name="advanced_option">
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83 <param name="m" value="95" />
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84 <param name="r" value="" />
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85 <param name="x" value="" />
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86 <param name="n" value="False" />
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87 <param name="s" value="0" />
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88 </section>
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89 <param name="fasta_out" value="True" />
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90 <output name="phy" value="outputs/locus1_sp3.phy" />
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91 <output name="nxs" value="outputs/locus1_sp3.nxs" />
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92 <output name="fasta" value="outputs/locus1_sp3.fasta" />
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93 </test>
3
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94 <test>
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95 <param name="input" ftype="fasta" value="inputs/locus3_sp2.fasta" />
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96 <section name="advanced_option">
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97 <param name="m" value="95" />
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98 <param name="r" value="" />
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99 <param name="x" value="" />
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100 <param name="n" value="False" />
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101 <param name="s" value="0" />
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102 </section>
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103 <param name="fasta_out" value="False" />
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104 <output name="phy" value="outputs/locus3_sp2.phy" />
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105 <output name="nxs" value="outputs/locus3_sp2.nxs" />
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106 </test>
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107 <test>
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108 <param name="input" ftype="fasta" value="inputs/locus8_sp2.fasta" />
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109 <section name="advanced_option">
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110 <param name="m" value="95" />
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111 <param name="r" value="" />
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112 <param name="x" value="" />
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113 <param name="n" value="False" />
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114 <param name="s" value="0" />
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115 </section>
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116 <param name="fasta_out" value="True" />
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117 <output name="phy" value="outputs/locus8_sp2.phy" />
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118 <output name="nxs" value="outputs/locus8_sp2.nxs" />
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119 <output name="fasta" value="outputs/locus8_sp2.fasta" />
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120 </test>
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121
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122 <!--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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123 </tests>
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124
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125 <help>
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126 <![CDATA[
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127
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128 . class:: infomark
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129
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130 **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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131
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132 .. class:: infomark
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133
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134 **Galaxy integration** Julie Baffard and ABiMS Team.
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135
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136 Contact support.abims@sb-roscoff.fr for any questions or concerns about the Galaxy implementation of this tool.
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137
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138 --------
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139
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140 **Description**
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141
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142 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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143
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144 --------
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145
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146 **Parameters**
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147
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148 The choice of several parameters for the blast is possible.
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149
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150 **-m : Proportion of gaps allowed in any one sequence in the final alignement**
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151 integer (between 0 and 100).
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152 By default : 95%, i.e. only removes sequences with extremely short matches.
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153 We find 50 the most useful.
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154
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155 **-r : Name of reference sequence**
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156 text.
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157 Default is searching for best candidate.
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158 If entered, the sequence will be extracted, written to a separate file, and blasted against the original input file.
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159
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160 **-x : Name of sequences to be excluded from the analysis**
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161 text.
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162 names must be comma-separated.
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163
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164 **-n**
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165 If checked : retain original names in output files.
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166 If not checked : output the 15 character name abbreviations (stripped of potentially problematic characters) that is used in the tool.
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167 Default : checked.
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168
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169 **-s : Number of sequences to be used in initial search for reference sequence**
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170 integer (between 0 and total number of sequences).
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171 Default : 0
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172 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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173
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174 --------
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175
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176 <<<<<<< HEAD
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177 **Outputs**
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178
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179 - 'Alignment_{input.name}_phylip' :
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180 the aligned sequences in Phylip format.
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181 =======
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182 ===============
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183 Working Example
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184 ===============
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185
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186 ------------------------------
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187 The input file and its options
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188 ------------------------------
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189
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190 **Input file**
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191
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192 | &gt;Pf210_1/1_1.000_920
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193 | CCGGTGGCCATTTTCTGCACCTCGTGGGTTATTGAGCTGAAAGTGGTTCAGCTCACTGTCTGTTAACAGCCGTGTCGGTCTGAGGGTATCACAGTTAATATAATGAATCAAGAGAAGTTGAAGCAGCTCCAGGCCCAAGTCCGCATCGGAGGAAAGGG
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194 | CACAGCAAGAAGAAAGAAGAAGGTGATTCACAGAACAGCAACAACAGATGACAAGAAACTGCAAAGTACACTGAAGAAATTGGCAGTAAATAATATTCCGGGTATAGAAGAGGTTAACATGATAAAGGATGACGGGCAAGTAATACATTTTACCAATCCGA
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195 | AGGTGCAGGCTTCTCTTCAGTCAAACACATTTGCCATTAATGGCCAAGCCGAAACGAAACAAATCACTGACTTGCTACCCGGTATATTAAATCAGCTGGGGGCTGAAAGTTTAACAAACTTGAAGAAGCTGGCTAAATCTGTGACTGCTGGAGTTGATTC
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196 | TGATAACAAGCAGGATGCAGCAGATATTGATGAAGATGATGATGATGTCCCAGAACTGGTTGAAAACTTTGACGAAGCATCGAAGAATGAGGGGACGTAATTCTTCTCCCACTTTATGCCATGGTAGCATCAATCGTTTTGCTGATGATGGCGTGTTTATAC
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197 | CTACCACCCAGTGTAGATTTGTCCAGACCTGGCTTGTTTGACATTGCTTGTTGGATTTTGCAACAATATCATGATTAGACTGCCTGGCTTTGTGGCCTAAATACTGTATTAAAGTGTCTGTAAAAGGGAAGCAATTTTTCTATTAAGAAGTTATCCACTAGCAT
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198 | ATTGACAGTTTTGCATGTTTGATTTTGTTCCTCGTGCAGGTCAGAACACTGATTGTACAGTGGCTGATTACAGAAAAATTGTATTCAGAGTTAAATAAACACATTATTATCCAAA
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199 | &gt;Pp_17_1/1_1.000_930
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200 | CCGGTGGCCATTTTCTGCACCTCGTGGGTATCTTGGGTTCGATTTGTATCAGCTCCCTATGTAAAATTAAACAAACTTATAACATAGATTGCAGCTGACAATACAATGAACCAAGAAAAATTAAAACAACTCCAAGCCCAGGTGCGCATTGGAGGCAAGGG
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201 | TACAGCAAGAAGAAAGAAGAAGGTCATTCATAGAACAGCAACAACAGATGATAAAAAACTGCAGAGTACATTAAAAAAACTAGCAGTAAATAATATTCCAGGTATAGAAGAGGTTAATATGATAAAAGATGATGGACAGGTAATACATTTTACCAATCCAAAA
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202 | GTACAGGCTTCTCTACAGTCAAACACATTTGCTATTAATGGGCAAGCTGAGACAAAACAAATCACCGAATTGTTGCCTGGTATATTAAATCAGCTGGGAGCAGAAAGTTTAACAAATCTGAAGAAACTGGCTACATCCGTGACTGGTGGAGTTGATTCTGAT
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203 | AACAAGCCAGAAACAGCAGAAATTGATGAAGACGATGATGATGTTCCAGATTTGGTTGAAAACTTTGACGAGGCATCCAAGAATGAAGGAACGTAATTTGTCATTGGTAGATCCTCCCATAGCCTGATTCTTGTGGCTGGCGACAGCTTGTTTATATTTTAC
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204
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205 CCAGTGTAGATTTGTTCAAGAAGGTGTGCTGGCGTTGTTTGAATTTTGTAATAGTACCATGATTTAAATACCCGGTTAACGGCCTACCTGTTATGTAGAAATTGTAGAGAAAAAATTAAATCAATTTTGTATGAACTATAAGCAGCAGCTAATATATTTGCAGTTT
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206 TACATGTTTATCTGTTCATCAGCATGGGTCAGAGAATGACCGTACTTTGCTGGTGATAGAATGCTTGTATTCAAAGTTTAATAAATGGTTGTAAGCCATTTAAAAAAAAAAAAAAA
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207
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208 ----------------
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209 The output files
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210 ----------------
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211
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212 **BlastAlign**
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213
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214 ************************ BlastAlign ************************
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215
2
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216 |
0
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217 | This program takes nucleotide sequences in fasta format and returns a multiple alignment (in Nexus and Phylip formats) using BLASTN
2
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218 |
0
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219 | Input file locus_2_sp_8.fasta has 2 sequences and is 1894 bytes
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220 | (maximum number of sequences that will be used to search for the reference sequence is 770)
2
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221 |
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222 |
0
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223 | BlastAlign finished: it has produced a multiple alignment of 2 sequences and length 720 by aligning to sequence Pf2101/11000920 (proportion of gaps in each sequence is less than 0.95)
3
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224 |
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225 >>>>>>> blastalign bug fix but with no file renaming
0
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226
3
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227 - 'Alignment_{input.name}_nexus' :
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228 the aligned sequences in Nexus format.
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229
3
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230 - 'Alignment_{input_file}_fasta' :
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231 the aligned sequences in Fasta format if the option "fasta format" is checked.
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232
3
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233 ---------
2
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234
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235 Changelog
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236 ---------
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237
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238 **Version 2.0 - 21/04/2017**
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239
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240 - 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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241
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242 **Version 1.0 - 13/04/2017**
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243
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244 - TEST: Add funtional test with planemo
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245 - IMPROVEMENT: Use conda dependencies for blastalign, blast-legacy, perl, python
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246
3
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247 ]]>
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248
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249 </help>
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250
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251 <expand macro="citations" />
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253 </tool>
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254