Mercurial > repos > abims-sbr > concatphyl

annotate ConcatPhyl.xml @ 2:1f8d039bd241 draft

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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
author abims-sbr
date Wed, 27 Sep 2017 10:03:45 -0400
parents 6d930f037fea
children 0464ec48bc3a
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1 <tool name="ConcatPhyl" id="concatphyl" version="2.0">
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3 <description>
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4 Concatenation and phylogeny
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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="8.2.9">raxml</requirement>
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14 </requirements>
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16 <command><![CDATA[
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17 #set $infiles_filter_assemblies = ""
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18 #for $input_filter_assemblie in $input_filter_assemblies
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19 ln -s '$input_filter_assemblie' '$input_filter_assemblie.element_identifier';
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20 #set $infiles_filter_assemblies = $infiles_filter_assemblies + $input_filter_assemblie.element_identifier + ","
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21 #end for
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22 #set $infiles_filter_assemblies = $infiles_filter_assemblies[:-1]
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23
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24 #set $infiles_alignments = ""
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25 #for $input_alignment in $input_alignments
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26 ln -s '$input_alignment' '$input_alignment.element_identifier';
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27 #set $infiles_alignments = $infiles_alignments + $input_alignment.element_identifier + ","
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28 #end for
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29 #set $infiles_alignments = $infiles_alignments[:-1]
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31 python $__tool_directory__/scripts/S01_concatenate.py
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33 $infiles_filter_assemblies
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34
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35 #if $format.format_run == "nucleic" :
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36 nucleic
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37 #elif $format.format_run == "proteic" :
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38 proteic
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39 #end if
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40
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41 $infiles_alignments
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42 > ${output};
0
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43
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44 raxmlHPC -n galaxy_run
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45 #if $format.format_run == "nucleic" :
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46 ##-q 05_partitions_gene_NUC
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47 -s "03_Concatenation_nuc.phy"
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48 -m $format.base_model
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49 #elif $format.format_run == "proteic" :
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50 ##-q 06_partitions_gene_AA
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51 -s 02_Concatenation_aa.phy
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52 -m $format.base_model$format.aa_search_matrix
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53 #end if
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54
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55 -p $random_seed
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56
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57 #if $number_of_runs !="" and $number_of_runs_bootstop =="":
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58 -N $number_of_runs
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59 -x $rapid_bootstrap_random_seed
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60 #elif ($number_of_runs !="" and $number_of_runs_bootstop !="") or ($number_of_runs =="" and $number_of_runs_bootstop !=""):
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61 -N $number_of_runs_bootstop
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62 -x $rapid_bootstrap_random_seed
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63 #end if
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64
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65 -f $search_algorithm
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66
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67 >> ${output};
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68 ]]>
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69 </command>
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71 <inputs>
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72
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73 <param name="input_filter_assemblies" type="data" format="fasta" multiple="true" label="Files from Filter assemblies" />
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74 <param name="input_alignments" type="data" format="fasta" multiple="true" label="Aligned files without indels" help="nucleic or proteic format according to the analysis you want to do below"/>
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75
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76 <conditional name="format">
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77 <param name="format_run" type="select" label="Which format do you want to use for this tool (concatenation and RAxML run) ? ">
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78 <option value="nucleic">Nucleic format</option>
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79 <option value="proteic">Proteic format</option>
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80 </param>
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81
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82 <when value="nucleic">
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83 <param name="base_model" type="select" label="Substitution Model">
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84 <option value="GTRCAT">GTRCAT</option>
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85 <option value="GTRCATI">GTRCATI</option>
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86 <option value="GTRGAMMA" selected="true">GTRGAMMA</option>
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87 <option value="GTRGAMMAI">GTRGAMMAI</option>
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88 </param>
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89 </when>
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90
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91 <when value="proteic">
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92 <param name="base_model" type="select" label="Substitution Model (-m)">
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93 <option value="PROTCAT" selected="true">PROTCAT</option>
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94 <option value="PROTCATI">PROTCATI</option>
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95 <option value="PROTGAMMA">PROTGAMMA</option>
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96 <option value="PROTGAMMAI">PROTGAMMAI</option>
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97 </param>
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98 <param name="aa_search_matrix" type="select" label="Matrix">
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99 <option value="DAYHOFF" selected="true">DAYHOFF</option>
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100 <option value="JTT">JTT</option>
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101 <option value="WAG">WAG</option>
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102 <option value="BLOSUM62">BLOSUM62</option>
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103 </param>
0
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104 </when>
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105 </conditional>
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106
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107 <param name="random_seed" type="integer" value="1234567890" size="12" label="Random seed used for the parsimony inferences" />
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108
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109 <!-- ## (-N/#) -->
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110 <param name="number_of_runs" type="integer" size="8" value="100"
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111 label="Number of runs" help="Specify the number of
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112 alternative runs (-N|#) on distinct starting trees In combination
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113 with the '-b' option will invoke a multiple boostrap analysis.
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114 You can add the bootstopping criteria by choosing the autoMR,
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115 autoMRE, autoMRE_IGN, or autoFC value in a menu below instead of
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116 providing a number here. Bootstopping will only work in
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117 combination with '-x' or '-b'."
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118 optional="True" />
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119 <param name="number_of_runs_bootstop" type="select" label="Use bootstopping criteria for number of runs" optional="True">
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120 <option value="" selected="yes"></option>
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121 <option value="autoMR">autoMR</option>
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122 <option value="autoMRE">autoMRE</option>
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123 <option value="autoMRE_IGN">autoMRE_IGN</option>
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124 <option value="autoFC">autoFC</option>
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125 </param>
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126
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127 <!-- ## (-f) -->
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128 <param name="search_algorithm" type="select" label="Algorithm to execute" optional="True">
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129 <option value="a" selected="true">Rapid bootstrap and best ML tree search (a)</option>
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130 <option value="A">Compute marginal ancestral states (A)</option>
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131 <option value="b">Draw bipartition information (b)</option>
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132 <option value="c">Check if the alignment can be read (c)</option>
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133 <option value="d">Hill-climbing ML Search (d) (default)</option>
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134 <option value="e">Optimize GAMMA/GAMMAI model/branches (e)</option>
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135 <option value="g">Compute per-site log likelihoods for -z trees (g)</option>
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136 <option value="h">Compute log likelihood test for -t / -z trees (h)</option>
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137 <option value="j">Generate bootstrapped alignment files (j)</option>
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138 <option value="J">Compute SH-like support values for the -t tree (J)</option>
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139 <option value="m">Compare bipartitions between -t and -z trees (m)</option>
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140 <option value="n">Compute log likelihood score for -z trees (n)</option>
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141 <option value="o">Use old slower search algorithm (o)</option>
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142 <option value="p">Stepwise MP addition of new sequences (p)</option>
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143 <option value="q">Fast quartet calculator (q)</option>
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144 <option value="r">Compute pairwise RF distances in -z trees (r)</option>
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145 <option value="s">Split a multi-gene alignment (s)</option>
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146 <option value="S">Compute site-specific placement bias (S)</option>
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147 <option value="t">Randomized tree searches on a fixed starting tree (t)</option>
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148 <option value="T">Final optimization of a ML tree from a bootstrap (T)</option>
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149 <option value="u">Morphological weight calibration using ML on a -t tree (u)</option>
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150 <option value="v">Classify environmental sequences (v)</option>
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151 <option value="w">Compute ELW-test on -z trees (w)</option>
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152 <option value="x">Compute GAMMA model pair-wise ML distances on a tree (x)</option>
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153 <option value="y">Classify environmental sequences into a reference tree (y)</option>
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154 </param>
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155
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156 <!-- ## (-q) -->
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157 <param name="multiple_model" format="txt" type="data" label="Multiple model assignment to alignment partitions" optional="True" help="Specify the file name which contains the assignment of models to alignment partitions for multiple models of substitution. For the syntax of this file please consult the manual." />
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158
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159 <!-- ## (-x) -->
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160 <param name="rapid_bootstrap_random_seed" type="integer" value='12345' size="7" label="Rapid bootstrapping random seed" optional="True" help="Specify a random seed and turn on rapid bootstrapping. CAUTION: unlike in version 7.0.4 RAxML will conduct rapid BS replicates under the model of rate heterogeneity you specified via '-m' and not by default under CAT." />
0
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161
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162 <param name="out" type="select" label="What format of file do you want for your output (concatenation of the sequences) ? ">
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163 <option value="nothing">No output</option>
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164 <option value="fasta">Fasta format</option>
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165 <option value="phylip">Phylip format</option>
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166 <option value="nexus">Nexus format</option>
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167 </param>
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168
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169 <param name="raxml1" type="boolean" label="Do you want the output of RAxML : best tree ? " />
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170 <param name="raxml3" type="boolean" label="Do you want the output of RAxML : bi-partition ? " />
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171 <param name="raxml4" type="boolean" label="Do you want the output of RAxML : bootstrap ? " help="Only if the option 'rapid bootsptrap' is chosen. When you don't want to choose your options, this output is accessible"/>
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172
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173 </inputs>
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174
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175 <outputs>
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176 <data name="output" format="txt" label="Phylogeny"/>
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177
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178 <data name="out_fasta_aa" format="fasta" label="Phylogeny_concatenation_fasta_aa" from_work_dir="02_Concatenation_aa.fas">
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179 <filter>format['format_run'] == "proteic" and out == "fasta"</filter>
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180 </data>
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181
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182 <data name="out_phylip_aa" format="phylip" label="Phylogeny_concatenation_phylip_aa" from_work_dir="02_Concatenation_aa.phy">
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183 <filter>format['format_run'] == "proteic" and out == "phylip"</filter>
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184 </data>
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185
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186 <data name="out_nexus_aa" format="nexus" label="Phylogeny_concatenation_nexus_aa" from_work_dir="02_Concatenation_aa.nex">
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187 <filter>format['format_run'] == "proteic" and out == "nexus"</filter>
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188 </data>
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189
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190 <data name="out_fasta_nuc" format="fasta" label="Phylogeny_concatenation_fasta_nuc" from_work_dir="03_Concatenation_nuc.fas">
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191 <filter>format['format_run'] == "nucleic" and out == "fasta"</filter>
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192 </data>
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193
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194 <data name="out_phylip_nuc" format="phylip" label="Phylogeny_concatenation_phylip_nuc" from_work_dir="03_Concatenation_nuc.phy">
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195 <filter>format['format_run'] == "nucleic" and out == "phylip"</filter>
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196 </data>
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197
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198 <data name="out_nexus_nuc" format="nexus" label="Phylogeny_concatenation_nexus_nuc" from_work_dir="03_Concatenation_nuc.nex">
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199 <filter>format['format_run'] == "nucleic" and out == "nexus"</filter>
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200 </data>
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201
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202 <data name="out_raxml1" format="txt" label="Phylogeny_RAxML_BestTree" from_work_dir="RAxML_bestTree.galaxy_run">
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203 <filter>raxml1 == True</filter>
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204 </data>
2
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205
0
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206 <data name="out_raxml3" format="txt" label="Phylogeny_RAxML_BiPartition" from_work_dir="RAxML_bipartitions.galaxy_run">
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207 <filter>raxml3 == True</filter>
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208 </data>
2
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209
0
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210 <data name="out_raxml4" format="txt" label="Phylogeny_RAxML_BootStrap" from_work_dir="RAxML_bootstrap.galaxy_run">
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211 <filter>raxml4 == True</filter>
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212 </data>
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213 </outputs>
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214
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215 <tests>
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216 <test>
2
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217 <param name="input_filter_assemblies" ftype="fasta" value="input_filter_assemblies/AcAcaud_trinity.fasta,input_filter_assemblies/AmAmphi_trinity.fasta,input_filter_assemblies/ApApomp_trinity.fasta,input_filter_assemblies/PgPgras_trinity.fasta,input_filter_assemblies/PhPhess_trinity.fasta,input_filter_assemblies/ThThelep_trinity.fasta" />
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218 <param name="input_alignments" ftype="fasta" value="input_from_CDS_Search/locus17_sp3_sp3.fasta,input_from_CDS_Search/locus147_sp3_sp3.fasta,input_from_CDS_Search/locus183_sp3_sp3.fasta,input_from_CDS_Search/locus334_sp3_sp3.fasta" />
1f8d039bd241 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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219 <conditional name="format">
0
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220 <param name="format_run" value="nucleic" />
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221 <param name="base_model" value="GTRGAMMA" />
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222 </conditional>
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223 <param name="random_seed" value="1234567890" />
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224 <param name="number_of_runs" value="100" />
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225 <param name="number_of_runs_bootstop" value="" />
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226 <param name="search_algorithm" value="d" />
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227 <!-- <param name="multiple_model" value="" /> -->
2
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228 <param name="rapid_bootstrap_random_seed" value="123456789" />
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229 <param name="out" value="nothing" />
0
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230 <param name="raxml1" value="True" />
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231 <param name="raxml3" value="True" />
2
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232 <param name="raxml4" value="True" />
0
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233 <output name="out_raxml4">
2
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234 <assert_contents>
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235 <has_text text="((Pg,(Am,Th)),(Ph,Ap),Ac);"/>
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236 <has_text text="((Th,(Pg,Am)),(Ph,Ap),Ac);"/>
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237 <has_text text="((Ph,Ap),(Am,(Pg,Th)),Ac);"/>
0
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238 </assert_contents>
2
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239 </output>
0
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240 </test>
2
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241
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242 <test>
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243 <param name="input_filter_assemblies" ftype="fasta" value="input_filter_assemblies/AcAcaud_trinity.fasta,input_filter_assemblies/AmAmphi_trinity.fasta,input_filter_assemblies/ApApomp_trinity.fasta,input_filter_assemblies/PgPgras_trinity.fasta,input_filter_assemblies/PhPhess_trinity.fasta,input_filter_assemblies/ThThelep_trinity.fasta" />
1f8d039bd241 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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244 <param name="input_alignments" ftype="fasta" value="input_from_CDS_Search/locus17_sp3_sp3.fasta,input_from_CDS_Search/locus147_sp3_sp3.fasta,input_from_CDS_Search/locus183_sp3_sp3.fasta,input_from_CDS_Search/locus334_sp3_sp3.fasta" />
1f8d039bd241 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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245 <conditional name="format">
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246 <param name="format_run" value="nucleic" />
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247 <param name="base_model" value="GTRGAMMA" />
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248 </conditional>
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249 <param name="random_seed" value="1234567890" />
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250 <param name="number_of_runs" value="100" />
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251 <param name="number_of_runs_bootstop" value="" />
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252 <param name="search_algorithm" value="a" />
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253 <param name="rapid_bootstrap_random_seed" value="1234567890" />
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254 <param name="out" value="nothing" />
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255 <param name="raxml1" value="True" />
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256 <param name="raxml3" value="True" />
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257 <param name="raxml4" value="True" />
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258 <output name="out_raxml1" value="RAxML_bestTree"/>
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259 <output name="out_raxml3" value="RAxML_bipartitions"/>
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260 </test>
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261
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262 <test>
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263 <param name="input_filter_assemblies" ftype="fasta" value="input_filter_assemblies/AcAcaud_trinity.fasta,input_filter_assemblies/AmAmphi_trinity.fasta,input_filter_assemblies/ApApomp_trinity.fasta,input_filter_assemblies/PgPgras_trinity.fasta,input_filter_assemblies/PhPhess_trinity.fasta,input_filter_assemblies/ThThelep_trinity.fasta" />
1f8d039bd241 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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264 <param name="input_alignments" ftype="fasta" value="input_from_CDS_Search/locus17_sp3_sp3.fasta,input_from_CDS_Search/locus147_sp3_sp3.fasta,input_from_CDS_Search/locus183_sp3_sp3.fasta,input_from_CDS_Search/locus334_sp3_sp3.fasta" />
1f8d039bd241 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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265 <conditional name="format">
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266 <param name="format_run" value="nucleic" />
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267 <param name="base_model" value="GTRGAMMA" />
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268 </conditional>
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269 <param name="random_seed" value="1234567890" />
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270 <param name="number_of_runs" value="100" />
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271 <param name="number_of_runs_bootstop" value="autoMR" />
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272 <param name="search_algorithm" value="a" />
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273 <param name="rapid_bootstrap_random_seed" value="1234567890" />
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274 <param name="out" value="nothing" />
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275 <param name="raxml1" value="True" />
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276 <param name="raxml3" value="True" />
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277 <param name="raxml4" value="True" />
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278 <output name="out_raxml1" value="RAxML_bestTree_test3"/>
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279 <output name="out_raxml3" value="RAxML_bipartitions_test3"/>
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280 </test>
0
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281 </tests>
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282
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283 <help>
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284
2
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285 @HELP_AUTHORS@
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286
0
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287 ============
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288 What it does
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289 ============
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290
2
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291 | This tool takes a 'dataset collection list' containing nucleic fasta sequence files and searches different homologous genes from pairwise comparisons.
0
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292
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293 --------
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294
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295 ==========
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296 Parameters
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297 ==========
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298
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299 | The choice of the format sequences is possible : **proteic** or **nucleic**
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300 |
0
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301
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302 The choice of parameters for the RAxML run is possible :
0
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303
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304 **-m** :
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305 | is the option for the choice of the substitution model.
0
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306 | By default it's GTRGAMMA.
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307 |
0
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308
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309 **-N** :
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310 | is the option for the choice of the number of run
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311 | by default it's 100
2
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312 |
0
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313
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314 **rapid bootstrapping** :
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315 | is the option to have, in addition to the best tree search, the rapid bootstrapping
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316 | this translates by : -x 12345 -f a
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317 | by default, this option is choosen
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318 |
0
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319
2
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320 .. class:: warningmark
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321 | RAxML has some incompatible parameters.
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322 | The search algorithm compatible with boostrapping and giving a besttree file is the one set by default:
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323 | -f a
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324
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325 | The search algorithm compatible with boostrapping and NOT giving a besttree file are:
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326 | -f d
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327 | -f o
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328 | -f t
0
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329 --------
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330
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331 ======
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332 Inputs
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333 ======
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334
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335 --------
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336
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337 =======
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338 Outputs
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339 =======
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340
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341 This tool, produces the following files :
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342
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343 **Phylogeny** :
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344 | is the general output. It gives the information about the concatenation (statistics) and the RAxML run.
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345 |
0
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346
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347 **Phylogeny_concatenation_fasta_aa** :
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348 | is the output which contains the sequences concatenated in fasta format when you choose the option proteic
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349 |
0
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350
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351 **Phylogeny_concatenation_phylip_aa** :
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352 | is the output which contains the sequences concatenated in phylip format when you choose the option proteic
2
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353 |
0
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354
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355 **Phylogeny_concatenation_nexus_aa** :
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356 | is the output which contains the sequences concatenated in nexus format when you choose the option proteic
2
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357 |
0
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358
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359 **Phylogeny_concatenation_fasta_nuc** :
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360 | is the output which contains the sequences concatenated in fasta format when you choose the option nucleic
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361 |
0
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362
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363 **Phylogeny_concatenation_phylip_nuc** :
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364 | is the output which contains the sequences concatenated in phylip format when you choose the option nucleic
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365 | it's this output which is used for the RAxML run
2
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366 |
0
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367
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368 **Phylogeny_concatenation_nexus_nuc** :
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369 | is the output which contains the sequences concatenated in nexus format when you choose the option nucleic
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370 |
0
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371
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372 **Phylogeny_RAxML_BestTree** :
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373 | is the output of RAxML run which contains the Best Tree found
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374 |
0
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375
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376 **Phylogeny_RAxML_BiPartitionBranchLabel** :
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377 | is the output of RAxML run which contains the Best Tree found with supported values as branch labels
2
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378 |
0
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379
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380 **Phylogeny_RAxML_BiPartition** :
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381 | is the output of RAxML run which contains the Best Tree found with supported values
2
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382 |
0
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383
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384 **Phylogeny_RAxML_BootStrap** :
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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385 | is the output of RAxML run which contains all the boostrapped trees
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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386 | the number of boostraped trees depending of the option -N (number of run)
2
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387 |
0
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388
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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389 --------
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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390
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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391 ===============
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392 Working Example
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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393 ===============
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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394
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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395 ---------------------------
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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396 The input files and options
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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397 ---------------------------
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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398
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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399 **Input files**
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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400 | 6 files with 200 nucleic sequences each
2
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401 | a 'dataset collection list' containing 2 locus aligned without indel (in nucleic format)
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402 |
0
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403 **Parameters**
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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404 | option : nucleic
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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405 | no option for the RAxML run, so by default it's : -m GTRGAMMA -N 100 -f a -x 12345
2
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406 |
0
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407
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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408 ----------------
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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409 The output files
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410 ----------------
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411
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412 **Phylogeny** :
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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413
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414 | ******************** CONCATENATION ********************
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415 |
0
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416 | Process nucleotides concatenation:
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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417 | Number of taxa aligned = 6
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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418 | Number of loci concatenated = 2
2
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419 |
0
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420 | Total length of the concatenated sequences [All codon positions] = 504
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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421 | Total length of the concatenated sequences [Codon positions 1 and 2] = 336
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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422 | Total length of the concatenated sequences [Codon position 3] = 168
2
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423 |
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424 |
0
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425 | 
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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426 | ******************** RAxML RUN ********************
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427 | 
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428
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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429 the informations of the RAxML run
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430
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431 | 
2
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432
0
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433 **Phylogeny_concatenation_fasta_nuc** :
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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434
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435 | &gt;Ps
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436
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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437 cgcagttcctcggtgaggcgttgtagttcggcgttcagacggtcagctctctcctcggctgccctgcgagcattcagtgcctcatccatgtcagcttgcatggcggcaatgtctccctccatacggcgcttatctccagtcaaagtggtcacggtgatgttcagctcgttaacacgggatacagcatcgtgcagttcgttttcggcattcttacgagctctctcagatgtctcca
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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438 gaagagatcgaacgtcctccagctccgtttgtagagcgatcctcttcctctcgagtacggtaaccgccgaacgggcttcctcagcactacggcgctcctcctcaatggcaatctccagctccttgaccttggcactgagtcccttgttggccttagatagttcgttgtttgccctcaatgtctcgaccataatccttaacaacaacacactacagccaacaaccttccttgctt
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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439 taccctctttgtctatcttgcataatccagcccat
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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440
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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441 | Ac
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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442
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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443 cgcagttcctcggtgacgcggtgcagctcggcggcgaggcggtctgccctctcctcggccgccctgcgggcgttcagggcctcgtccagatcggcctgcatggcggcgatgtcgccctccatgcggcgcttgtcgccagtcagcgtcgtcaccgtgatgttcagctcgttgacgcgagccgtggcgtcgtgcaactcgttctcggcattcttacgagctcgttcggc
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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444 ggtctccagtagagatctaacatcctccagctctgtttgcaatgcaatcctcttcctctcgagtacagttacagcggaacgggcttcctcagcactgcggtgctcctcctcaatggcaatttccagctccttgaccttggcactaagtcccttgttggccttggacagctcgttgttggctctaagtgtctccacc---------------------------------------------------------
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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445 ------------------------
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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446
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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447 | &gt;Pp
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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448 | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
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449 | ------------------------------------------------------------------------------------------------ataatccttgacgaccacacactgcatccaacaacttttctggccttgccttccttgtctattttacacaaaccagcccat
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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450
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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451 | &gt;Ap
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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452
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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453 cgcagctcctcggtgacgcggtgcagctcggcggcgaggcgatcggctctctcctcggctgccctgcgggcgttcagggcctcatcaaggtcggcctgcatggcggcgatgtcgccctccatgcggcgcttgtcgccggtcagagtcgtcaccgtgatgttcagctcgttgacgcgagccgtggcgtcgtgtagctcgttctcggcattcttacgagctcgttcggc
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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454 ggtctccagtagggatctaacatcctccagctccgtttgcaatgcaatcctcttcctctcgagtacagttacagcggaacgggcttcctcagcactgcggcgctcctcctcaatggcaatttccagctccttgaccttcgcactaagtcccttgttggccttggacagttcgttgttggctctaagtgtctccactataatccttaacaacaacacactgcaaccaacaacctt
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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455 ccgggccttgccttccttgtctatcttgcaaagaccagcccat
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456
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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457 | &gt;Pf
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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458
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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459 ctgagctcctcggtgaggcgctggagctcggagttcaggcggtcggctcgttcctcggcggcgcggcgagcgttcagcgcctcgtccatgtcggcctgcatggcggcgatgtccgcttccatgcggcgcttgtcgcccgtcagagtggtgaccgtgatgttcagctcgttgacacgggccacggcgtcgtgcagctcgttctcggcgttcttgcgagctctctccga
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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460 cgtctccagaagagatcggacgtcctcgagttccgtctgcagggcgatcctcttcctctcgagcacggtaacagcagaacgggcttcctcggcgctacggcgctcttcctcgatggcgatctccagttccttgacctttgcactgagtcccttgttggccttggatagttcgttgttagccctcagtgtctccaccataatccttaacaacaacacactacagccgacaac
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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461 cttccttgctttcccttctttgtcaatcttgcataatccggcccat
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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462
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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463 | &gt;Pg
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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464
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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diff changeset
465 cgcagctcctcggtgagacgctgcagttcggaattcaggcggtccgccctctcttcggcagccctgcgggcgttcagcgcctcgtccatgtcggcctgcatggcggcgatgtcgccctccatgcggcgcttgtcgccggtcagcgtggtcacggtgatgttcagctcgttgacgcgagaaacggcgtcgtgcatctcgttttcggcattcttgcgagctctctccgacg
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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diff changeset
466 tctcaagaagggatcgtacatcctcgagttctgtctggagggcgatcctctttctctcaagcatggtaaccgcggagcgggcttcctcgccactgcggcgttcttcctcgatggtgatctccagttccttaaccttagtactcagtcccttgttggctttggacagttcgttgttcgctcttagtgtctccactataatccttaaccacaacacactacaaccaacaacctttcttgc
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
467 cttgccttccttgtctatcttacacaagccagcccat
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
468
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
469 .. class:: infomark
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
470
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
471 | If you choose the option proteic : you obtain a file with proteic sequences
2
1f8d039bd241 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
472 |
0
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
473 | 
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
474
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
475
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
476 **Phylogeny_concatenation_phylip_nuc** :
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
477
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
478 | 6 504
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
479 | Ps
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
480
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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diff changeset
481 cgcagttcctcggtgaggcgttgtagttcggcgttcagacggtcagctctctcctcggctgccctgcgagcattcagtgcctcatccatgtcagcttgcatggcggcaatgtctccctccatacggcgcttatctccagtcaaagtggtcacggtgatgttcagctcgttaacacgggatacagcatcgtgcagttcgttttcggcattcttacgagctctctcagatgtctcca
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
482 gaagagatcgaacgtcctccagctccgtttgtagagcgatcctcttcctctcgagtacggtaaccgccgaacgggcttcctcagcactacggcgctcctcctcaatggcaatctccagctccttgaccttggcactgagtcccttgttggccttagatagttcgttgtttgccctcaatgtctcgaccataatccttaacaacaacacactacagccaacaaccttccttgctt
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
483 taccctctttgtctatcttgcataatccagcccat
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
484
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
485 | Ac
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
486
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
487 cgcagttcctcggtgacgcggtgcagctcggcggcgaggcggtctgccctctcctcggccgccctgcgggcgttcagggcctcgtccagatcggcctgcatggcggcgatgtcgccctccatgcggcgcttgtcgccagtcagcgtcgtcaccgtgatgttcagctcgttgacgcgagccgtggcgtcgtgcaactcgttctcggcattcttacgagctcgttcggc
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
488 ggtctccagtagagatctaacatcctccagctctgtttgcaatgcaatcctcttcctctcgagtacagttacagcggaacgggcttcctcagcactgcggtgctcctcctcaatggcaatttccagctccttgaccttggcactaagtcccttgttggccttggacagctcgttgttggctctaagtgtctccacc---------------------------------------------------------
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
489 ------------------------
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
490
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
491 | Pp
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
492 | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
493 | ------------------------------------------------------------------------------------------------ataatccttgacgaccacacactgcatccaacaacttttctggccttgccttccttgtctattttacacaaaccagcccat
2
1f8d039bd241 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
494 |
0
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
495 | Ap
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
496
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
497 cgcagctcctcggtgacgcggtgcagctcggcggcgaggcgatcggctctctcctcggctgccctgcgggcgttcagggcctcatcaaggtcggcctgcatggcggcgatgtcgccctccatgcggcgcttgtcgccggtcagagtcgtcaccgtgatgttcagctcgttgacgcgagccgtggcgtcgtgtagctcgttctcggcattcttacgagctcgttcggc
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
498 ggtctccagtagggatctaacatcctccagctccgtttgcaatgcaatcctcttcctctcgagtacagttacagcggaacgggcttcctcagcactgcggcgctcctcctcaatggcaatttccagctccttgaccttcgcactaagtcccttgttggccttggacagttcgttgttggctctaagtgtctccactataatccttaacaacaacacactgcaaccaacaacctt
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
499 ccgggccttgccttccttgtctatcttgcaaagaccagcccat
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
500
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
501 Pf
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
502 ctgagctcctcggtgaggcgctggagctcggagttcaggcggtcggctcgttcctcggcggcgcggcgagcgttcagcgcctcgtccatgtcggcctgcatggcggcgatgtccgcttccatgcggcgcttgtcgcccgtcagagtggtgaccgtgatgttcagctcgttgacacgggccacggcgtcgtgcagctcgttctcggcgttcttgcgagctctctccga
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
503 cgtctccagaagagatcggacgtcctcgagttccgtctgcagggcgatcctcttcctctcgagcacggtaacagcagaacgggcttcctcggcgctacggcgctcttcctcgatggcgatctccagttccttgacctttgcactgagtcccttgttggccttggatagttcgttgttagccctcagtgtctccaccataatccttaacaacaacacactacagccgacaac
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
504 cttccttgctttcccttctttgtcaatcttgcataatccggcccat
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
505
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
506 Pg
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
507 cgcagctcctcggtgagacgctgcagttcggaattcaggcggtccgccctctcttcggcagccctgcgggcgttcagcgcctcgtccatgtcggcctgcatggcggcgatgtcgccctccatgcggcgcttgtcgccggtcagcgtggtcacggtgatgttcagctcgttgacgcgagaaacggcgtcgtgcatctcgttttcggcattcttgcgagctctctccgacg
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
508 tctcaagaagggatcgtacatcctcgagttctgtctggagggcgatcctctttctctcaagcatggtaaccgcggagcgggcttcctcgccactgcggcgttcttcctcgatggtgatctccagttccttaaccttagtactcagtcccttgttggctttggacagttcgttgttcgctcttagtgtctccactataatccttaaccacaacacactacaaccaacaacctttcttgc
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
509 cttgccttccttgtctatcttacacaagccagcccat
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
510
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
511 .. class:: infomark
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
512
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
513 | If you choose the option proteic : you obtain a file with proteic sequences
2
1f8d039bd241 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
514 |
0
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
515 | 
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
516
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
517 **Phylogeny_concatenation_nexus_nuc** :
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
518
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
519 #NEXUS
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
520
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
521 | Begin data;
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
522 | Dimensions ntax=6 nchar=504;
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
523 | Format datatype=dna gap=-;
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
524
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
525 Matrix
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
526
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
527 Ps cgcagttcctcggtgaggcgttgtagttcggcgttcagacggtcagctctctcctcggctgccctgcgagcattcagtgcctcatccatgtcagcttgcatggcggcaatgtctccctccatacggcgcttatctccagtcaaagtggtcacggtgatgttcagctcgttaacacgggatacagcatcgtgcagttcgttttcggcattcttacgagctctctcagatgtct
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
528 ccagaagagatcgaacgtcctccagctccgtttgtagagcgatcctcttcctctcgagtacggtaaccgccgaacgggcttcctcagcactacggcgctcctcctcaatggcaatctccagctccttgaccttggcactgagtcccttgttggccttagatagttcgttgtttgccctcaatgtctcgaccataatccttaacaacaacacactacagccaacaaccttcct
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
529 tgctttaccctctttgtctatcttgcataatccagcccat
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
530
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
531 Ac cgcagttcctcggtgacgcggtgcagctcggcggcgaggcggtctgccctctcctcggccgccctgcgggcgttcagggcctcgtccagatcggcctgcatggcggcgatgtcgccctccatgcggcgcttgtcgccagtcagcgtcgtcaccgtgatgttcagctcgttgacgcgagccgtggcgtcgtgcaactcgttctcggcattcttacgagctcgttc
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
532 ggcggtctccagtagagatctaacatcctccagctctgtttgcaatgcaatcctcttcctctcgagtacagttacagcggaacgggcttcctcagcactgcggtgctcctcctcaatggcaatttccagctccttgaccttggcactaagtcccttgttggccttggacagctcgttgttggctctaagtgtctccacc---------------------------------------------------
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
533 ------------------------------
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
534
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
535 Pp ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
536 -----------------------------------------------------------------------------------------------------ataatccttgacgaccacacactgcatccaacaacttttctggccttgccttccttgtctattttacacaaaccagcccat
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
537
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
538 Ap cgcagctcctcggtgacgcggtgcagctcggcggcgaggcgatcggctctctcctcggctgccctgcgggcgttcagggcctcatcaaggtcggcctgcatggcggcgatgtcgccctccatgcggcgcttgtcgccggtcagagtcgtcaccgtgatgttcagctcgttgacgcgagccgtggcgtcgtgtagctcgttctcggcattcttacgagctcgttc
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
539 ggcggtctccagtagggatctaacatcctccagctccgtttgcaatgcaatcctcttcctctcgagtacagttacagcggaacgggcttcctcagcactgcggcgctcctcctcaatggcaatttccagctccttgaccttcgcactaagtcccttgttggccttggacagttcgttgttggctctaagtgtctccactataatccttaacaacaacacactgcaaccaacaa
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
540 ccttccgggccttgccttccttgtctatcttgcaaagaccagcccat
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
541
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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diff changeset
542 Pf ctgagctcctcggtgaggcgctggagctcggagttcaggcggtcggctcgttcctcggcggcgcggcgagcgttcagcgcctcgtccatgtcggcctgcatggcggcgatgtccgcttccatgcggcgcttgtcgcccgtcagagtggtgaccgtgatgttcagctcgttgacacgggccacggcgtcgtgcagctcgttctcggcgttcttgcgagctctctcc
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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diff changeset
543 gacgtctccagaagagatcggacgtcctcgagttccgtctgcagggcgatcctcttcctctcgagcacggtaacagcagaacgggcttcctcggcgctacggcgctcttcctcgatggcgatctccagttccttgacctttgcactgagtcccttgttggccttggatagttcgttgttagccctcagtgtctccaccataatccttaacaacaacacactacagccgaca
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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diff changeset
544 accttccttgctttcccttctttgtcaatcttgcataatccggcccat
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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diff changeset
545
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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546 Pg cgcagctcctcggtgagacgctgcagttcggaattcaggcggtccgccctctcttcggcagccctgcgggcgttcagcgcctcgtccatgtcggcctgcatggcggcgatgtcgccctccatgcggcgcttgtcgccggtcagcgtggtcacggtgatgttcagctcgttgacgcgagaaacggcgtcgtgcatctcgttttcggcattcttgcgagctctctccg
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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diff changeset
547 acgtctcaagaagggatcgtacatcctcgagttctgtctggagggcgatcctctttctctcaagcatggtaaccgcggagcgggcttcctcgccactgcggcgttcttcctcgatggtgatctccagttccttaaccttagtactcagtcccttgttggctttggacagttcgttgttcgctcttagtgtctccactataatccttaaccacaacacactacaaccaacaacctttc
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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diff changeset
548 ttgccttgccttccttgtctatcttacacaagccagcccat
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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549
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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550 | ;
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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551 | End;
2
1f8d039bd241 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
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552 |
0
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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diff changeset
553
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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diff changeset
554 .. class:: infomark
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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diff changeset
555
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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556 | If you choose the option proteic : you obtain a file with proteic sequences
2
1f8d039bd241 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
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557 |
0
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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diff changeset
558 | 
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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diff changeset
559
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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diff changeset
560 **Phylogeny_RAxML_BestTree** :
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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diff changeset
561
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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diff changeset
562 | ((Ac:0.02889451913999640381,Ap:0.01674414484251282934):0.17730049470177636217,
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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diff changeset
563 | ((Pp:0.23405795780876006984,Pg:0.02012322210145659623):0.14429203507314311561,Pf:0.09977363663005259231):0.04320803212100913365,Ps:0.08351583721596630983):0.0;
2
1f8d039bd241 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
564 |
0
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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diff changeset
565 | 
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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diff changeset
566
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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diff changeset
567
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
568 **Phylogeny_RAxML_BiPartitionBranchLabel** :
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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diff changeset
569
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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diff changeset
570 | (Pg:0.02012322210145659623,(Pf:0.09977363663005259231,(Ps:0.08351583721596630983,
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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diff changeset
571 | (Ac:0.02889451913999640381,Ap:0.01674414484251282934):0.17730049470177636217[89]):0.04320803212100913365[42]):0.14429203507314311561[70],Pp:0.23405795780876006984);
2
1f8d039bd241 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
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572 |
1f8d039bd241 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
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diff changeset
573 |
0
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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diff changeset
574
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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diff changeset
575
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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diff changeset
576 **Phylogeny_RAxML_BiPartition** :
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
577
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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diff changeset
578 (Pg:0.02012322210145659623,(Pf:0.09977363663005259231,(Ps:0.08351583721596630983,
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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diff changeset
579 (Ac:0.02889451913999640381,Ap:0.01674414484251282934)89:0.17730049470177636217)42:0.04320803212100913365)70:0.14429203507314311561,Pp:0.23405795780876006984);
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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diff changeset
580
2
1f8d039bd241 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
581 |
1f8d039bd241 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
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diff changeset
582 |
0
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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diff changeset
583
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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diff changeset
584 **Phylogeny_RAxML_BootStrap** :
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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diff changeset
585
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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diff changeset
586 | ((Ap,Ac),((Pp,Pg),Pf),Ps);
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
587 | ((Ap,Ac),((Pp,Pg),Pf),Ps);
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
588 | (Pf,((Ap,Ac),(Pp,Pg)),Ps);
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
589 | ((Ap,Ac),((Pp,Pg),Pf),Ps);
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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diff changeset
590 | ((Ap,Ac),((Pp,Pg),Pf),Ps);
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
parents:
diff changeset
591 | ((Ap,Ac),((Pp,Pg),Pf),Ps);
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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diff changeset
592 | ((Pp,Pg),(Pf,(Ap,Ac)),Ps);
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
abims-sbr
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diff changeset
593
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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diff changeset
594 ...
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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diff changeset
595
2
1f8d039bd241 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
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diff changeset
596 ---------------------------------------------------
1f8d039bd241 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
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597
1f8d039bd241 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
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598 Changelog
1f8d039bd241 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
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diff changeset
599 ---------
1f8d039bd241 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
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diff changeset
600
1f8d039bd241 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
601 **Version 2.0 - 06/07/2017**
1f8d039bd241 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
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diff changeset
602
1f8d039bd241 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
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diff changeset
603 - NEW: Replace the zip between tools by Dataset Collection
1f8d039bd241 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
604 - Corrected bug : output files were empty due to errors in the command section (incompatible parameters set by default instead of the ones mentioned in the help)
1f8d039bd241 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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diff changeset
605
1f8d039bd241 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
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606
1f8d039bd241 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
parents: 0
diff changeset
607 **Version 1.0 - 13/04/2017**
1f8d039bd241 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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608
1f8d039bd241 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
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diff changeset
609 - Add funtional test with planemo
1f8d039bd241 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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610
1f8d039bd241 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
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diff changeset
611 - Planemo test with conda dependencies for raxml and python
1f8d039bd241 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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612
1f8d039bd241 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
abims-sbr
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613 - Scripts renamed + symlinks to the directory 'scripts'
1f8d039bd241 planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 44a89d5eeb82789bfc643b33c11f391281b6374b
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614
0
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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diff changeset
615 </help>
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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616
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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diff changeset
617 <expand macro="citations" />
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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618
6d930f037fea planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 38545eb765e0df7fcc6b8130e8e5f87cf4481122
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diff changeset
619 </tool>