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1 <!--Convert Matrix - developed by Jocelyn Brayet <jocelyn.brayet@curie.fr>
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2 Copyright (C) 2015 Institut Curie
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3
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4 This program is free software: you can redistribute it and/or modify
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5 it under the terms of the GNU General Public License as published by
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6 the Free Software Foundation, either version 3 of the License, or
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7 (at your option) any later version.
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8
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9 This program is distributed in the hope that it will be useful,
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10 but WITHOUT ANY WARRANTY; without even the implied warranty of
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11 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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12 GNU General Public License for more details.
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13
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14 You should have received a copy of the GNU General Public License
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15 along with this program. If not, see <http://www.gnu.org/licenses/>.-->
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16 <tool id="rsat_convert_matrix" name="RSAT Convert Matrix" version="1.0">
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17 <description>Inter-conversions between various formats of PSSM</description>
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18 <requirements>
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38
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19 <requirement type="package" version="0.6">python_suds</requirement>
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22
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20 </requirements>
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21 <command interpreter="python">
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22 convertMatrix_wrapper.py -matrix $matrixFile -outGalaxy $txtFile -server $server -input_form $input_format -output_form $output_format
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23 #if $advanced_parameters.adv_param == "show":
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24 #if $advanced_parameters.return_count_condition.return_count == "yes":
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25 -return counts
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26 -perm $advanced_parameters.return_count_condition.perm
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27 #else:
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28 -return $advanced_parameters.return_count_condition.return
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29 #end if
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30 -rc $advanced_parameters.rc
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31 -decimals $advanced_parameters.decimals
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32 #end if
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33 </command>
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34 <inputs>
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35 <param name="server" type="select" label="RSAT server (if 'Time out' error, change server)" >
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36 <option value="fr_ens" selected="true">RSAT Protists</option>
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37 <option value="fr_mrs" >RSAT Fungis</option>
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38 <option value="fr_ro" >RSAT Metazoa</option>
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39 <option value="fr_mrs_2" >RSAT Teaching</option>
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40 <option value="es" >RSAT Plants</option>
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41 <option value="mx" >RSAT Prokaryotes</option>
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42 </param>
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43 <param name="matrixFile" type="data" format="txt" label="Matrix (or matrices) (TXT file)" />
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44 <param name="input_format" type="select" label="Matrix input format">
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45 <option value="tab" selected="true">tab</option>
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46 <option value="alignace" >alignace</option>
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47 <option value="assembly" >assembly</option>
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48 <option value="cb" >cb</option>
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49 <option value="clustal" >clustal</option>
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50 <option value="consensus" >consensus</option>
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51 <option value="feature" >feature</option>
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52 <option value="gibbs" >gibbs</option>
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53 <option value="infogibbs" >infogibbs</option>
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54 <option value="meme" >meme</option>
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55 <option value="motifsampler" >motifsampler</option>
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56 <option value="transfac" >transfac</option>
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57 <option value="jaspar" >jaspar</option>
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58 </param>
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59 <param name="output_format" type="select" label="Output format">
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60 <option value="transfac" selected="true">transfac</option>
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61 <option value="consensus" >consensus</option>
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62 <option value="tab" >tab</option>
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63 <option value="jaspar" >jaspar</option>
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64 </param>
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65 <conditional name="advanced_parameters" >
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66 <param name="adv_param" type="select" label="Advanced Parameters" help="" >
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67 <option value="hide" selected="true">Hide</option>
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68 <option value="show">Show</option>
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69 </param>
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70 <when value="hide" />
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71 <when value="show">
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72 <conditional name="return_count_condition" >
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73 <param name="return_count" type="select" label="Counts option in output field" help="" >
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74 <option value="yes" selected="true">Yes</option>
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75 <option value="no">No</option>
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76 </param>
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77 <when value="yes">
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78 <param name="perm" type="integer" value="0" label="Permutations" help="" />
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79 </when>
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80 <when value="no">
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81 <param name="return" type="select" display="checkboxes" multiple="True" label="Output fields">
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82 <option value="consensus" selected="true">consensus</option>
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83 <option value="parameters" selected="true">parameters</option>
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84 <option value="info" >info</option>
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85 <option value="frequencies" >frequencies</option>
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86 <option value="logo" >logo</option>
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87 <option value="margins" >margins</option>
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88 <option value="profile" >profile</option>
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89 <option value="sites" >sites</option>
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90 <option value="wdistrib" >wdistrib</option>
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91 <option value="weights" >weights</option>
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92 <validator type="no_options" message="You must select at least one result type." />
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93 </param>
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94 </when>
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95 </conditional>
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96 <param name="rc" type="select" label="Compute reverse complement" help="" >
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97 <option value="0" selected="true">No</option>
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98 <option value="1">Yes</option>
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99 </param>
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100 <param name="decimals" type="select" label="Score decimals" help="" >
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101 <option value="0" >0</option>
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102 <option value="1" selected="true">1</option>
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103 <option value="2">2</option>
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104 </param>
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105 </when>
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106 </conditional>
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107 </inputs>
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108 <outputs>
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109 <data format="txt" name="txtFile" label="RSAT output - convertMatrix results" />
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110 </outputs>
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111 <help>
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112
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113 **What it does**
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114
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115 .. class:: infomark
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116
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117 Convert different types of position-specific scoring matrices (PSSM), and calculate statistical parameters.
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118
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119 ------
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120
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121 *Example with jaspar matrix*::
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122
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123 >matrix1 matrix1
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124 A [ 4 19 0 0 0 0 ]
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125 C [ 16 0 20 0 0 0 ]
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126 G [ 0 1 0 20 0 20 ]
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127 T [ 0 0 0 0 20 0 ]
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128
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129 ------
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130
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131 *Results : tranfac matrix with output fields (consensus, parameters, frequencies and sites)*::
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132
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133 AC m1
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134 XX
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135 ID m1
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136 XX
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137 DE m1 m1; from JASPAR
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138 P0 A C G T
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139 1 4 16 0 0
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140 2 19 0 1 0
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141 3 0 20 0 0
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142 4 0 0 20 0
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143 5 0 0 0 20
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144 6 0 0 20 0
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145 XX
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146 CC program: jaspar
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147 CC matrix.nb: 1
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148 CC min.prior: 0.25
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149 CC alphabet.size: 4
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150 CC max.bits: 2
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151 CC total.information: 6.56407409450406
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152 CC information.per.column: 1.09401234908401
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153 CC max.possible.info.per.col: 1.38629436111989
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154 CC consensus.strict: CACGTG
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155 CC consensus.strict.rc: CACGTG
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156 CC consensus.IUPAC: CACGTG
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157 CC consensus.IUPAC.rc: CACGTG
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158 CC consensus.regexp: CACGTG
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159 CC consensus.regexp.rc: CACGTG
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160 CC residues.content.crude.freq: a:0.1917|c:0.3000|g:0.3417|t:0.1667
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161 CC G+C.content.crude.freq: 0.641666666666667
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162 CC residues.content.corrected.freq: a:0.1944|c:0.2976|g:0.3373|t:0.1706
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163 CC G+C.content.corrected.freq: 0.634920634920635
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164 XX
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165 //
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166 </help>
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167 <citations>
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168 <citation type="bibtex">@article{Medina-Rivera22042015,
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169 author = {Medina-Rivera, Alejandra and Defrance, Matthieu and Sand, Olivier and Herrmann, Carl and Castro-Mondragon, Jaime A. and Delerce, Jeremy and Jaeger, Sébastien and Blanchet, Christophe and Vincens, Pierre and Caron, Christophe and Staines, Daniel M. and Contreras-Moreira, Bruno and Artufel, Marie and Charbonnier-Khamvongsa, Lucie and Hernandez, Céline and Thieffry, Denis and Thomas-Chollier, Morgane and van Helden, Jacques},
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170 title = {RSAT 2015: Regulatory Sequence Analysis Tools},
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171 year = {2015},
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172 doi = {10.1093/nar/gkv362},
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173 URL = {http://nar.oxfordjournals.org/content/early/2015/04/21/nar.gkv362.abstract},
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174 eprint = {http://nar.oxfordjournals.org/content/early/2015/04/21/nar.gkv362.full.pdf+html},
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175 journal = {Nucleic Acids Research}
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176 }</citation>
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177 </citations>
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178 </tool>
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