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1 <!--Compare Matrices - 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_compare_matrices" name="RSAT Compare Matrices" version="1.0">
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17 <description>Comparison between two collections of position-specific scoring matrices</description>
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18 <requirements>
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37
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19 <requirement type="package" version="0.6">python_suds</requirement>
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23
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20 </requirements>
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21 <command interpreter="python">
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22 compareMatrices_wrapper.py -matrix_1 $matrixFile_1 -format1 $matrix_format_1 -matrix_2 $matrixFile_2 -format2 $matrix_format_2 -outGalaxy $txtFile -server $server
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23 #if $advanced_parameters.adv_param == "show":
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24 #if $advanced_parameters.allReturn.all_return == "no":
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25 -returnResults $advanced_parameters.allReturn.return
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26 #else:
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27 -returnResults all
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28 #end if
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29 #end if
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30 </command>
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31 <inputs>
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32 <param name="server" type="select" label="RSAT server (if Time out error, change server)" >
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33 <option value="fr_ens" selected="true">RSAT Protists</option>
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34 <option value="fr_mrs" >RSAT Fungis</option>
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35 <option value="fr_ro" >RSAT Metazoa</option>
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36 <option value="fr_mrs_2" >RSAT Teaching</option>
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37 <option value="es" >RSAT Plants</option>
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38 <option value="mx" >RSAT Prokaryotes</option>
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39 </param>
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40 <param name="matrixFile_1" type="data" format="txt" label="Matrix (or matrices) (TXT file)" />
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41 <param name="matrix_format_1" type="select" label="Matrix 1 format" help="" >
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42 <option value="tab" selected="true">tab</option>
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43 <option value="cb" >cb</option>
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44 <option value="transfac" >transfac</option>
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45 <option value="jaspar" >jaspar</option>
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46 <option value="consensus" >consensus</option>
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47 <option value="gibbs" >gibbs</option>
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48 <option value="meme" >meme</option>
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49 <option value="assembly" >assembly</option>
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50 </param>
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51 <param name="matrixFile_2" type="data" format="txt" label="Matrix (or matrices) (TXT file)" />
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52 <param name="matrix_format_2" type="select" label="Matrix 2 format" help="" >
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53 <option value="tab" selected="true">tab</option>
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54 <option value="cb" >cb</option>
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55 <option value="transfac" >transfac</option>
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56 <option value="jaspar" >jaspar</option>
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57 <option value="consensus" >consensus</option>
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58 <option value="gibbs" >gibbs</option>
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59 <option value="meme" >meme</option>
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60 <option value="assembly" >assembly</option>
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61 </param>
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62 <conditional name="advanced_parameters" >
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63 <param name="adv_param" type="select" label="Advanced Parameters" help="" >
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64 <option value="hide" selected="true">Hide</option>
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65 <option value="show">Show</option>
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66 </param>
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67 <when value="hide" />
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68 <when value="show">
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69 <conditional name="allReturn" >
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70 <param name="all_return" type="select" label="All supported output fields, including all metrics" >
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71 <option value="yes" selected="true">Yes</option>
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72 <option value="no">No</option>
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73 </param>
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74 <when value="yes" />
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75 <when value="no">
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76 <param name="return" type="select" display="checkboxes" multiple="True" label="Fields to return">
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77 <option value="offset">offset</option>
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78 <option value="cor">cor</option>
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79 <option value="Ncor" selected="true">Ncor</option>
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80 <option value="cov">cov</option>
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81 <option value="SSD">SSD</option>
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82 <option value="NSW">NSW</option>
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83 <option value="SW">SW</option>
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84 <option value="dEucl">dEucl</option>
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85 <option value="NdEucl">NdEucl</option>
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86 <option value="NsEucl">NsEucl</option>
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87 <option value="dKL">dKL</option>
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88 <option value="matrix_number">matrix_number</option>
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89 <option value="matrix_id">matrix_id</option>
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90 <option value="matrix_name">matrix_name</option>
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91 <option value="matrix_ac">matrix_ac</option>
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92 <option value="width">width</option>
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93 <option value="strand" selected="true">strand</option>
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94 <option value="pos">pos</option>
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95 <option value="consensus">consensus</option>
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96 <option value="offset_rank">offset_rank</option>
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97 <option value="match_rank">match_rank</option>
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98 <option value="offset_rank">offset_rank</option>
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99 <option value="alignments_pairwise">alignments_pairwise</option>
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100 <option value="alignments_1ton">alignments_1ton</option>
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101 <option value="alignments">alignments</option>
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102 </param>
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103 </when>
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104 </conditional>
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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 - compareMatrices 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 Compare two collections of position-specific scoring matrices (PSSM), and return various similarity statistics + matrix alignments (pairwise, one-to-n).
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118
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119 </help>
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120 <citations>
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121 <citation type="bibtex">@article{Medina-Rivera22042015,
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122 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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123 title = {RSAT 2015: Regulatory Sequence Analysis Tools},
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124 year = {2015},
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125 doi = {10.1093/nar/gkv362},
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126 URL = {http://nar.oxfordjournals.org/content/early/2015/04/21/nar.gkv362.abstract},
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127 eprint = {http://nar.oxfordjournals.org/content/early/2015/04/21/nar.gkv362.full.pdf+html},
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128 journal = {Nucleic Acids Research}
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129 }</citation>
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130 </citations>
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131 </tool>
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