Mercurial > repos > proteore > proteore_heatmap_visualization

annotate heatmap.xml @ 2:99207b432ebc draft

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planemo upload commit c599cfc156c77626df2b674bdfbd437b9f664ab9
author proteore
date Thu, 13 Dec 2018 04:14:21 -0500
parents 4651551b48e4
children 07748b0136bb
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1 <tool id="heatmap" name="HeatMap" version="2018.12.12">
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2 <description></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 a file (uto table)" help="" />
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25 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file have 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 to be used for heatmap building">
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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 data columns to use for the heatmap separated by commas" help="For example : c3,c5,c7"/>
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33 </when>
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34 <when value="cols_range">
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35 <param name="cols" type="text" label="Enter a range of data columns to use for the heatmap, first and last column separated bay ':'" help="For example : c2:c7"/>
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36 </when>
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37 </conditional>
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38 <param name="rownames" type="text" value="c1" label="Enter the column to use for row labels" help="for example : c1"/>
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39 <param name="distance" type="select" label="Distance measurement method" value="euclidean">
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40 <option value="euclidean" selected="true">Euclidean</option>
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41 <option value="pearson" selected="true">Pearson</option>
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42 <option value="spearman">Spearman</option>
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43 <option value="kendall">Kendall</option>
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44 <option value="maximum">Maximum</option>
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45 <option value="manhattan">Manhattan</option>
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46 <option value="canberra">Canberra</option>
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47 <option value="binary">Binary</option>
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48 <option value="minkowski">Minkowski</option>
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49 </param>
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50 <param name="clustering" type="select" label="Clustering method" value="average">
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51 <option value="ward.D">Ward</option>
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52 <option value="ward.D2">Ward2</option>
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53 <option value="single">Single linkage (nearest neighbor)</option>
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54 <option value="complete">Complete linkage (farthest neighbor</option>
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55 <option value="average" selected="true">Group average linkage (UPGMA)</option>
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56 <option value="mcquitty">Simple average method (WPGMA)</option>
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57 <!--option value="median">Median (WPGMC)</option>
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58 <option value="centroid">Centroid (UPGMC)</option-->
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59 </param>
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60 <param name="dendrogram" type="select" label="Apply clustering on :" value="both">
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61 <option value="row">Rows</option>
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62 <option value="column">Columns</option>
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63 <option value="both" selected="true">Rows and columns</option>
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64 <option value="none">None</option>
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65 </param>
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66 <param type="integer" name="angle_col" label="Angle of column labels" value="0" min="-90" max="90" />
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67 <param name="output_type" type="select" label="Choose the output format">
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68 <option value="html">html</option>
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69 <option value="pdf">pdf</option>
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70 <option value="jpeg">jpeg</option>
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71 <option value="png">png</option>
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72 </param>
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73
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74 </inputs>
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75 <outputs>
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76 <data name="output" format="html">
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77 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.html" ext="html" visible="true" assign_primary_output="true"/>
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78 <filter>output_type=="html"</filter>
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79 </data>
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80 <data name="pdf" format="pdf">
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81 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.pdf" ext="pdf" visible="true" assign_primary_output="true"/>
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82 <filter>output_type=="pdf"</filter>
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83 </data>
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84 <data name="jpeg" format="jpg">
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85 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.jpg" ext="jpg" visible="true" assign_primary_output="true"/>
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86 <filter>output_type=="jpeg"</filter>
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87 </data>
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88 <data name="png" format="png">
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89 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.png" ext="png" visible="true" assign_primary_output="true"/>
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90 <filter>output_type=="png"</filter>
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91 </data>
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92 </outputs>
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93 <tests>
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94 <test>
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95 <output name="output" file="heatmap.html"/>
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96 </test>
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97 </tests>
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98 <help><![CDATA[
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99
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100 This tool creates a heatmap from a tsv file (tab delimited).
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101
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102 Input file must have a column for rows labels and colums with numeric data to be used for clustering.
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103
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104 See table below for an example input file
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105
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106 .. csv-table:: Example file
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107 :header: "Uniprot","iBAQ_CTR1","iBAQ_CTR2","iBAQ_CTR3","iBAQ_pTCN1","iBAQ_pTCN2","iBAQ_pTCN3"
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108
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109
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110 "Q49AN9",17.4091970440807,16.0474907255521,14.9687330755858,21.8454060245779,18.9468529040903,21.2330797498008
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111 "O00148",14.1001686145694,14.806777888004,15.3555560564928,17.2942797505583,18.2106568817514,16.9479095182613
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112 "F5H6E2",15.0235503328855,16.6142578028388,20.5969569088489,14.6615767253835,17.9752549753108,20.4023495267791
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113 "E9PPW7",18.0770953690935,15.312218369812,13.8048301075204,17.5522130063356,15.9664520099065,15.1597932646987
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114 "O00483",17.4188205774495,16.783665086968,15.1589556127476,19.7398973660168,20.8648965533665,20.1781898785682
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115 "O00571",12.9049717044645,16.717296441372,13.8708732177805,19.8879681981565,21.0815521014477,17.4710040202845
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116
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117 ~
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118
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119 You can choose the columns to be used to create the heatmap.
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120
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121 You can add manually each colums of interest or enter a range of columns to use.
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122
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123 You then entered the column number of the column you want to be used for the rows labels .
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124
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125 If you have long string in your header, you might want to incline the column labels for better reading.
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126
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127 Default output is html, it allows you to zoom and have row an column labels of a cell by passing your cursor on it.
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128
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129 You can select pdf, jpeg or png if you want a static output.
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130
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131 -----
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132
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133 .. class:: infomark
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134
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135 **Authors**
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136
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137 David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
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138
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139 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform
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140
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141 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
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142
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143 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool.
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144
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145 ]]></help>
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146 <citations>
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147 <citation type="bibtex">
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148 @misc{renameTODO,
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149 author = {LastTODO, FirstTODO},
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150 year = {TODO},
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151 title = {TODO},
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152 url = {https://plot.ly/r/},
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153 }</citation>
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154 <citation type="bibtex">
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155 @misc{renameTODO,
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156 author = {LastTODO, FirstTODO},
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157 year = {TODO},
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158 title = {TODO},
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159 url = {https://cran.r-project.org/package=heatmaply},
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160 }</citation>
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161 </citations>
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162 </tool>