annotate PDAUG_Basic_Plots/PDAUG_Basic_Plots.xml @ 6:738ee8fc0ede draft

"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit e8c8198105af7eab636fb2405e5ff335539ca14b"
author jay
date Sun, 31 Jan 2021 02:02:32 +0000
parents 7d247e27ff11
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1 <tool id="pdaug_basic_plots" name="PDAUG Basic Plots" version="0.1.0" python_template_version="3.6">
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2 <description>Basic Plots</description>
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4 <requirements>
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5 <requirement type="package" version="0.25.3">pandas</requirement>
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6 <requirement type="package" version="4.10.0">plotly</requirement>
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7 <requirement type="package" version="1.8.0">wordcloud</requirement>
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8 <requirement type="package" version="3.1.2">matplotlib</requirement>
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9 </requirements>
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10 <stdio>
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11 <exit_code range="1" level="fatal" />
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12 </stdio>
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13 <command detect_errors="exit_code"><![CDATA[
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16 python '$__tool_directory__/PDAUG_Basic_Plots.py' '$SelPlotting.Plot'
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18 #if $SelPlotting.Plot == 'HeatMap'
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19 --InFile '$SelPlotting.InFile'
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20 --IndexColumn '$SelPlotting.IndexColumn'
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21 --x_label '$SelPlotting.x_label'
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22 --y_label '$SelPlotting.y_label'
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23 #end if
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24
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25 #if $SelPlotting.Plot == 'BoxPlot'
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26 --InFile '$SelPlotting.InFile'
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27 --Feature '$SelPlotting.Feature'
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28 --Label '$SelPlotting.Label'
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29 #end if
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30
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31 #if $SelPlotting.Plot == 'ScatterPlot'
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32 --PlotType '$SelPlotting.PlotType.SelectPlot'
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33 #if $SelPlotting.PlotType.SelectPlot == '2D'
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34 -F1 '$SelPlotting.PlotType.Features1'
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35 -F2 '$SelPlotting.PlotType.Features2'
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36 #end if
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37
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38 #if $SelPlotting.PlotType.SelectPlot == '3D'
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39 -F1 '$SelPlotting.PlotType.Features1'
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40 -F2 '$SelPlotting.PlotType.Features2'
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41 -F3 '$SelPlotting.PlotType.Features3'
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42 #end if
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43
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44 -I '$SelPlotting.InFile'
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45 -L '$SelPlotting.Label'
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46
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47 #end if
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48
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49 #if $SelPlotting.Plot == 'WordCloud'
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50 -I '$SelPlotting.InFile'
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51 -D '$SelPlotting.d'
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52 #end if
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53
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54 --htmlOutDir '$output.extra_files_path'
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55 --htmlFname '$output'
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56
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57 ]]></command>
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58
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59 <inputs>
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60
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61 <conditional name='SelPlotting' >
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62
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63 <param name="Plot" type="select" label="Data plotting method" argument="" help="Data plotting method">
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64 <option value="HeatMap">Heat Map</option>
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65 <option value="BoxPlot">Box Plot</option>
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66 <option value="ScatterPlot">Scatter Plot</option>
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67 <option value="WordCloud">Word Cloud</option>
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68 </param>
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69
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70 <when value="HeatMap">
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71 <param name="InFile" type="data" format="tabular" label="Input file" argument= "--InFile" help="Tabular data file"/>
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72 <param name="IndexColumn" type="text" value="Index" label="Index Column" argument= "--IndexColumn" help="Column name that contains index as row/sample names "/>
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73 <param name="x_label" type="text" value="x-axis" label="Label for x-axis" argument= "--x_label" help="A label that describes x axis"/>
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74 <param name="y_label" type="text" value="y-axis" label="Label for y-axis" argument= "--y_label" help="A label that describes y axis"/>
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75 </when>
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76
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77 <when value="BoxPlot">
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78 <param name="InFile" type="data" label="Input file" format="tabular" argument= "--InFile" help="Tabular data file"/>
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79 <param name="Feature" type="text" value="Feature" label="Feature name" argument= "--Features" help="Name of the feature (column name)"/>
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80 <param name="Label" type="text" value="class label" label="Class label column" argument="--Label" help="Name of the column that contains class label" />
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81 </when>
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82
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83 <when value="ScatterPlot">
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84
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85 <param name="InFile" label="Input file" type="data" format="tabular" argument= "--InFile" help="Tabular data file"/>
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87 <conditional name='PlotType' >
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88
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89 <param name="SelectPlot" type="select" label="Scatter Plot type" argument="" help="Scatter Plot type 2D or 3D.">
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90 <option value="2D">2D</option>
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91 <option value="3D">3D</option>
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92 </param>
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93
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94 <when value="2D">
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95 <param name="Features1" type="text" value="feature1" label="First feature" argument= "--RotationX" help="Feature column name"/>
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96 <param name="Features2" type="text" value="feature2" label="Second feature" argument= "--RotationY" help="Feature column name"/>
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97 </when>
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98
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99 <when value="3D">
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100 <param name="Features1" type="text" value="feature1" label="First feature" argument= "--RotationX" help="Feature column name"/>
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101 <param name="Features2" type="text" value="feature2" label="Second feature" argument= "--RotationY" help="Feature column name"/>
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102 <param name="Features3" type="text" value="feature3" label="Third feature" argument= "--FigHight" help="Feature column name"/>
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103 </when>
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104
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105 </conditional>
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106
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107 <param name="Label" type="text" value="class label" label="Class label column" argument="--Label" help="Name of the column that contains class label" />
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108
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109 </when>
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110
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111 <when value="WordCloud" >
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112 <param name="InFile" type="data" format="fasta" label="Input file" argument= "--InFile" help="Fasta file with peptides"/>
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113 <param name="d" type="integer" value="4" argument= "--FragSize" label="Size of ngrams" help="Size of ngrams"/>
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114 </when>
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115
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116 </conditional>
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117 </inputs>
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118
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119 <outputs>
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120 <data name='output' format='html' label="${tool.name} on $on_string - ${SelPlotting.Plot} (webpage)" >
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121 <filter>SelPlotting['Plot'] != "WordCloud"</filter>
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122 </data>
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123
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124 <data name='output1' format='png' label="${tool.name} on $on_string - ${SelPlotting.Plot} (PNG)" from_work_dir="out.png" >
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125 <filter>SelPlotting['Plot'] != "HeatMap"</filter>
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126 <filter>SelPlotting['Plot'] != "BoxPlot"</filter>
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127 <filter>SelPlotting['Plot'] != "ScatterPlot"</filter>
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128 </data>
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129
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130 </outputs>
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131
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132 <tests>
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133
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134 <test>
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135 <param name="Plot" value="HeatMap" />
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136 <param name="InFile" value="test1.tsv"/>
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137 <param name="IndexColumn" value="Algo"/>
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138 <param name="x_label" value="Performance"/>
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139 <param name="y_label" value="Algorithms"/>
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140 <output name="output" file="test1/report_dir/report.html.re" ftype="html" compare="re_match_multiline"/>
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141 </test>
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142
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143 <test>
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144 <param name="Plot" value="BoxPlot" />
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145 <param name="InFile" value="test2.tsv"/>
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146 <param name="Feature" value="a1"/>
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147 <param name="Label" value="class"/>
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148 <output name="output" file="test2/report_dir/report.html.re" ftype="html" compare="re_match_multiline"/>
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149 </test>
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150
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151 <test>
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152 <param name="Plot" value="ScatterPlot" />
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153 <param name="InFile" value="test2.tsv"/>
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154 <param name="SelectPlot" value="2D" />
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155 <param name="Features1" value="a1"/>
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156 <param name="Features2" value="a2"/>
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157 <param name="Label" value="class"/>
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158 <output name="output" file="test3/report_dir/report.html.re" ftype="html" compare="re_match_multiline"/>
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159 </test>
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160
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161 <test>
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162 <param name="Plot" value="ScatterPlot" />
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163 <param name="SelectPlot" value="3D" />
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164 <param name="InFile" value="test2.tsv"/>
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165 <param name="Features1" value="a1"/>
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166 <param name="Features2" value="a2"/>
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167 <param name="Features3" value="a3"/>
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168 <param name="Label" value="class"/>
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169 <output name="output" file="test4/report_dir/report.html.re" ftype="html" compare="re_match_multiline"/>
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170
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171 </test>
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172
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173 <test>
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174 <param name="Plot" value="WordCloud" />
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175 <param name="InFile" value="positive.fasta"/>
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176 <param name="d" value="4" />
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177 <output name="output" value="test5/out.png" ftype="png" compare="sim_size" delta="10000" />
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178 </test>
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179
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180 </tests>
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181
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182 <help><![CDATA[
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183 .. class:: infomark
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184
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185 **What it does**
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186
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187 This tool generates four different types of plots.
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188
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189 * **HeatMap** Takes a data frame as input and returns heatmap.
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190 * **BoxPlot** Takes a descriptor data frame as input and returns a box plot based on the class label.
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191 * **ScatterPlot** Takes a descriptor data frame with the class label as input and compares the scatteredness based on 2D or 3D scatter plot.
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192 * **WordCloud** Calculates the ngrams from the peptide data set and plot a word cloud for ngrams to assess frequency of ngrams visually.
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193
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194 -----
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195
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196 **Inputs**
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197 **1** Heat Map
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198 * **--Infile** Input data frame as a tabular file.
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199 * **--IndexColumn** Number of sequence to be generated.
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200 * **--x_label** Peptide minimum length.
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201 * **--y_label_s** Peptide maximum length.
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202
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203 **2** Box Plot
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204 * **--Infile** Input data frame as a tabular file.
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205 * **--Feature** Feature(column name) to be assessed.
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206 * **--Label** Class label column name.
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207
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208 **3** Scatter Plot
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209 * **--Infile** Input data frame as a tabular file.
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210 * **--PlotType** 2D or 3D scatter plot.
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211 * **--Feature1** First feature column name.
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212 * **--Feature2** Second feature column name.
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213 * **--Feature3** Third feature column name if 3D scatter plot option selected.
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214 * **--Label** CLass label column name.
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215
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216 **4** Word Cloud
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217 * **--Infile** Input fasta file with peptides.
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218 * **--FragSize** ngram size to be calculated.
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220 -----
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221
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222 **Outputs**
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223 * Return report html file with the respective graph]]></help>
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224
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225 <citations>
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226 <citation type="bibtex">
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227
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228
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229 @article{joshi_j_2020,
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230 title = {PDAUG - a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling},
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231 publisher = {GitHub},
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232 journal = {GitHub repository},
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233 url = {https://github.com/jaidevjoshi83/pdaug.git},
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234 author = {Joshi J. and Blankenberg D.},
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235 year = {2020},
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236 }
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237
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238 </citation>
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239
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240 </citations>
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241 </tool>
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242
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243
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246
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248