Mercurial > repos > abims-sbr > blastalign

annotate BlastAlign.xml @ 6:e0bea88bb09f draft

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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 76e603ecd0118c8060d972b675a13db858956eb6
author abims-sbr
date Thu, 18 Jan 2018 09:02:24 -0500
parents 0d2da4c020dc
children 9c0044eff621
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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>
0
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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>
0
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56
2
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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>
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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 **Outputs**
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177
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178 - 'Alignment_{input.name}_phylip' :
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179 the aligned sequences in Phylip format.
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180
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181 - 'Alignment_{input.name}_nexus' :
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182 the aligned sequences in Nexus format.
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183
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184 - 'Alignment_{input_file}_fasta' :
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185 the aligned sequences in Fasta format if the option "fasta format" is checked.
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186
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187 ---------
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188
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189 Changelog
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190 ---------
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191
4
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192 **Version 2.1 - 17/01/2018**
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193
9eb5bb56bf41 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 76e603ecd0118c8060d972b675a13db858956eb6
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194 - Applied some bugfixes and minor improvments
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195
2
92615a423389 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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196 **Version 2.0 - 21/04/2017**
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197
92615a423389 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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198 - 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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199
92615a423389 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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200 **Version 1.0 - 13/04/2017**
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201
92615a423389 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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202 - TEST: Add funtional test with planemo
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203 - IMPROVEMENT: Use conda dependencies for blastalign, blast-legacy, perl, python
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204
3
49017ea906b5 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit cf1b9c905931ca2ca25faa4844d45c908756472f
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205 ]]>
2
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206
92615a423389 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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207 </help>
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208
92615a423389 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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209 <expand macro="citations" />
0
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210
aba551b2b79e planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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211 </tool>
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212