Mercurial > repos > proteore > proteore_heatmap_visualization
annotate heatmap.xml @ 6:0fd68acd3e31 draft default tip
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author | proteore |
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date | Fri, 24 Jan 2020 10:31:48 -0500 |
parents | 9ccb5122bffb |
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1 <tool id="heatmap" name="HeatMap" version="2020.01.23"> |
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2 <description>(clustering and visualization)</description> |
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3 <requirements> |
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4 <requirement type="package" version="4.7.1">r-plotly</requirement> |
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5 <requirement type="package" version="0.14.1">r-heatmaply</requirement> |
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6 <requirement type="package" version="2.1.1">phantomjs</requirement> |
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7 <requirement type="package" version="2.2.1">pandoc</requirement> |
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8 </requirements> |
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9 <command detect_errors="exit_code"><![CDATA[ |
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10 Rscript $__tool_directory__/heatmap_viz.R |
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11 --input='$file' |
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12 --output="$file.name" |
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13 --type='$output_type' |
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14 --cols='$select_data_columns.cols' |
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15 --row_names="$rownames" |
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16 --header='$header' |
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17 --col_text_angle='$angle_col' |
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18 --dist="$distance" |
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19 --clust="$clustering" |
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20 --dendrogram="$dendrogram" |
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21 |
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22 ]]></command> |
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23 <inputs> |
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24 <param name="file" type="data" format="txt,tabular" label="Select your file (table)" help="" /> |
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25 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your file contain a header?" /> |
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26 <conditional name="select_data_columns"> |
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27 <param name="enter_cols" type="select" label="Select columns or a range of columns containing expression values"> |
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28 <option value="cols_number">Select columns to be used one by one</option> |
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29 <option value="cols_range">Select a range of columns to be used</option> |
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30 </param> |
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31 <when value="cols_number"> |
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32 <param name="cols" type="text" label="Enter column number (separated by a comma)" help="For example : c3,c5,c7"> |
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33 <validator type="regex" message="Please enter column numbers, for example: 'c1,c3' for first and third columns">^([c]{0,1}[0-9]+[,]*)+$</validator> |
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34 </param> |
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35 </when> |
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36 <when value="cols_range"> |
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37 <param name="cols" type="text" label="Enter a range of column number, first and last column separated by ':'" help="For example : c2:c7"> |
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38 <validator type="regex" message="Please enter first and last column numbers separated by ':', for example: 'c2:c7' for all colums from the second to the 7th">^[c]{0,1}[0-9]+:[c]{0,1}[0-9]+$</validator> |
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39 </param> |
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40 </when> |
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41 </conditional> |
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42 <param name="rownames" type="text" value="c1" label="Enter column number containing row labels" help="for example : c1 if labels are in column n°1"> |
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43 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator> |
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44 </param> |
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45 <param type="integer" name="angle_col" label="Angle of column labels" value="0" min="-90" max="90" /> |
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46 <param name="clustering" type="select" label="Clustering method" value="average"> |
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47 <option value="ward.D">Ward</option> |
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48 <option value="ward.D2">Ward2</option> |
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49 <option value="single">Single linkage (nearest neighbor)</option> |
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50 <option value="complete">Complete linkage (farthest neighbor)</option> |
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51 <option value="average" selected="true">Group average linkage (UPGMA)</option> |
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52 <option value="mcquitty">Simple average method (WPGMA)</option> |
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53 <!--option value="median">Median (WPGMC)</option> |
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54 <option value="centroid">Centroid (UPGMC)</option--> |
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55 </param> |
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56 <param name="distance" type="select" label="Distance measurement method" value="euclidean"> |
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57 <option value="euclidean" selected="true">Euclidean</option> |
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58 <option value="pearson" selected="true">Pearson</option> |
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59 <option value="spearman">Spearman</option> |
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60 <option value="kendall">Kendall</option> |
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61 <option value="maximum">Maximum</option> |
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62 <option value="manhattan">Manhattan</option> |
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63 <option value="canberra">Canberra</option> |
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64 <option value="binary">Binary</option> |
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65 <option value="minkowski">Minkowski</option> |
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66 </param> |
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67 <param name="dendrogram" type="select" label="Apply clustering on :" value="both"> |
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68 <option value="row">Rows</option> |
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69 <option value="column">Columns</option> |
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70 <option value="both" selected="true">Rows and columns</option> |
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71 <option value="none">None</option> |
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72 </param> |
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73 |
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74 <param name="output_type" type="select" label="Select output format"> |
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75 <option value="html">html</option> |
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76 <option value="pdf">pdf</option> |
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77 <!--option value="jpeg">jpeg</option--> |
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78 <!--option value="png">png</option--> |
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79 </param> |
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80 |
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81 </inputs> |
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82 <outputs> |
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83 <data name="output" format="html"> |
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84 <discover_datasets pattern="(?P<designation>.+)\.html" ext="html" visible="true" assign_primary_output="true"/> |
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85 <filter>output_type=="html"</filter> |
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86 </data> |
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87 <data name="pdf" format="pdf"> |
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88 <discover_datasets pattern="(?P<designation>.+)\.pdf" ext="pdf" visible="true" assign_primary_output="true"/> |
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89 <filter>output_type=="pdf"</filter> |
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90 </data> |
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91 <data name="jpeg" format="jpg"> |
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92 <discover_datasets pattern="(?P<designation>.+)\.jpg" ext="jpg" visible="true" assign_primary_output="true"/> |
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93 <filter>output_type=="jpeg"</filter> |
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94 </data> |
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95 <data name="png" format="png"> |
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96 <discover_datasets pattern="(?P<designation>.+)\.png" ext="png" visible="true" assign_primary_output="true"/> |
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97 <filter>output_type=="png"</filter> |
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98 </data> |
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99 </outputs> |
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100 <tests> |
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101 <test> |
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102 <output name="output" file="heatmap.html"/> |
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103 </test> |
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104 </tests> |
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105 <help><![CDATA[ |
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106 **Description** |
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107 |
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108 This tool allows users to generate, cluster and visualize expression-based heat maps from transcriptomic, proteomic and metabolomic experiments. |
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109 It is based on heatmaply, an R package for easily creating interactive cluster heatmaps (see reference below) |
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110 |
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111 ----- |
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112 |
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113 **Input** |
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114 |
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115 A file (tab-delimited) having a column with labels (e.g. a gene name, Uniprot accession number...) and colums with numerical value (intensities) for clustering. |
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116 See table below for an example input file |
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117 |
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118 .. csv-table:: example of input file |
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119 :header: "Uniprot","iBAQ_CTR1","iBAQ_CTR2","iBAQ_CTR3","iBAQ_pTCN1","iBAQ_pTCN2","iBAQ_pTCN3" |
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120 |
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121 |
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122 "Q49AN9",17.4091970440807,16.0474907255521,14.9687330755858,21.8454060245779,18.9468529040903,21.2330797498008 |
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123 "O00148",14.1001686145694,14.806777888004,15.3555560564928,17.2942797505583,18.2106568817514,16.9479095182613 |
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124 "F5H6E2",15.0235503328855,16.6142578028388,20.5969569088489,14.6615767253835,17.9752549753108,20.4023495267791 |
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125 "E9PPW7",18.0770953690935,15.312218369812,13.8048301075204,17.5522130063356,15.9664520099065,15.1597932646987 |
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126 "O00483",17.4188205774495,16.783665086968,15.1589556127476,19.7398973660168,20.8648965533665,20.1781898785682 |
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127 "O00571",12.9049717044645,16.717296441372,13.8708732177805,19.8879681981565,21.0815521014477,17.4710040202845 |
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128 |
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129 ----- |
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130 |
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131 **Parameters** |
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132 |
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133 "Select columns or a range of columns containing expression values": choose the columns to use to perform clustering and to create the heatmap. |
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134 You can enter specific column number (e.g. c2,c5 will create a heatmap for column 2 and 5 corresponding to condition from the example file above ) or a range of columns to use (e.g. c2:c7 will consider all replicates of each condition in the example above)). |
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135 |
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136 "Enter column number containing row labels": enter the column number containing the rows labels (e.g. "c1" in the example above). |
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137 |
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138 "Angle of column labels": In case of long label name, you might want to incline the column labels for practical display. |
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139 |
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140 "Clustering method": methods for computing hierarchical clustering (six available) |
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141 |
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142 "Distance measurement method": function used to compute the distance (dissimilarity) between both rows and columns (nine available). The options "pearson", "spearman" and "kendall" can |
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143 be used to use correlation-based clustering. |
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144 |
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145 ----- |
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146 |
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147 **Output** |
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148 |
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149 Default output is html; it allows browsing the heatmap in an interactive way (of note: for large file, display and interactivity can be altered), pdf format are proposed for static output. |
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150 |
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151 ----- |
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152 |
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153 .. class:: infomark |
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154 |
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155 **Authors** |
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156 Galili T, O'Callaghan A, Sidi J, Sievert C. heatmaply: an R package for creating interactive cluster heatmaps for online publishing. Bioinformatics. 2018. 34(9):1600-1602. doi: 10.1093/bioinformatics/btx657. PubMed PMID: 29069305 |
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157 |
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158 ----- |
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159 |
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160 .. class:: infomark |
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161 |
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162 **Galaxy integration** |
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163 |
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164 David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR |
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165 |
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166 Sandra Dérozier, Olivier Rué, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR |
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167 |
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168 This work has been partially funded through the French National Agency for Research (ANR) IFB project. |
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169 |
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170 Help: contact@proteore.org for any questions or concerns about this tool. |
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171 |
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172 ]]></help> |
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173 </tool> |