Mercurial > repos > galaxyp > metaquantome

annotate metaquantome_viz.xml @ 8:a1df90e6e7d4 draft default tip

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author galaxyp
date Fri, 08 Feb 2019 10:36:53 -0500
parents 80ce9ca55697
children
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1 <tool id="metaquantome_viz" name="metaQuantome: visualize" version="@VERSION@.0">
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2 <description>taxonomic analysis, functional analysis, and function-taxonomy analysis results</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <xml name="img_size">
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6 <param argument="--width" type="float" value="" optional="true" label="Image width in inches"/>
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7 <param argument="--height" type="float" value="" optional="true" label="Image height in inches"/>
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8 </xml>
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9 <xml name="common_bar_params">
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10 <param argument="--target_rank" type="text" value="species" label="Taxonomic rank to restrict to in the plot"
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11 help="">
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12 <option value="species">species</option>
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13 <option value="genus" selected="true">genus</option>
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14 <option value="family">family</option>
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15 <option value="order">order</option>
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16 <option value="class">class</option>
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17 <option value="phylum">phylum</option>
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18 <option value="kingdom">kingdom</option>
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19 </param>
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20 <param argument="--meancol" type="text" label="Mean intensity column name"
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21 help="Mean intensity column name for desired experimental condition">
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22 <validator type="empty_field"/>
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23 </param>
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24 <param argument="--nterms" type="integer" value="5" min="1" optional="true" label="Number of taxa or functional terms to display" help="leave blank for all"/>
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25 <param argument="--barcol" type="integer" value="1" min="1" max="6" label="Color for the bar fill">
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26 <help>
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27 The color vector in R is
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28 c("dodgerblue", "darkorange", "yellow2", "red2", "darkviolet", "black"),
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29 so providing a 1 will give the "dodgerblue" color.
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30 These same colors are also used in the heatmap and PCA plot,
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31 so the colors can be tweaked to match.
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32 </help>
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33 </param>
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34 </xml>
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35 </macros>
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36 <expand macro="requirements" />
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37 <command detect_errors="exit_code"><![CDATA[
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38 @MAKE_SAMPS_TSV@
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39 metaquantome viz
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40 @COMMON_PARAMS@
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41 --infile='$infile'
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42 --plottype=$plot.plottype
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43 #if $plot.plottype == 'bar':
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44 #if str($mode_args.mode) in ['t','ft']:
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45 --target_rank='$plot.target_rank'
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46 #end if
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47 --meancol='$plot.meancol'
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48 #if str($plot.nterms) == '':
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49 --nterms='all'
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50 #else
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51 --nterms=$plot.nterms
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52 #end if
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53 --barcol=$plot.barcol
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54 #elif $plot.plottype == 'volcano':
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55 --fc_name='$plot.fc_name'
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56 #if $plot.textannot:
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57 --textannot='$plot.textannot'
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58 #end if
1
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59 $plot.flip_fc
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60 $plot.gosplit
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61 #elif $plot.plottype == 'heatmap':
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62 $plot.filter_to_sig
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63 --alpha=$plot.alpha
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64 #elif $plot.plottype == 'pca':
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65 $plot.calculate_sep
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66 #elif $plot.plottype == 'ft_dist':
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67 --meancol='$plot.meancol'
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68 #if str($plot.nterms) == '':
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69 --nterms='all'
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70 #else
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71 --nterms=$plot.nterms
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72 #end if
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73 --barcol=$plot.barcol
0
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74 --whichway=$plot.whichway
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75 #if $plot.term.id_or_name == 'id':
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76 --id='$plot.term.id'
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77 #else:
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78 --name='$plot.term.name'
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79 #end if
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80 #if str($mode_args.mode) in ['t','ft']:
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81 --target_rank='$plot.target_rank'
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82 #end if
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83 #if $plot.target_onto:
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84 --target_onto=$plot.target_onto
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85 #end if
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86 #end if
1
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87 #if $plot.width:
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88 --width=$plot.width
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89 #end if
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90 #if $plot.height:
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91 --height=$plot.height
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92 #end if
4
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93 --img='outfile.png' &&
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94 mkdir '${ wrapped_outfile.files_path }' &&
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95 cp outfile.png '${ wrapped_outfile.files_path }' &&
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96 ## stylesheet
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97 echo "img {
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98 display: block;
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99 margin-left: auto;
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100 margin-right: auto;
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101 max-width: 75%;
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102 height: auto;
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103 }" > style.css &&
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104 cp style.css '${ wrapped_outfile.files_path }' &&
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105 echo "<!DOCTYPE html>
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106 <html>
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107 <head>
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108 <link rel=\"stylesheet\" type=\"text/css\" href=\"style.css\"/>
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109 </head>
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110 <body>
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111 <img src=\"outfile.png\">
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112 <br>
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113 <p>To download the image, right-click and choose \"Save image as...\"</p>
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114 </body>
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115 </html>" > wrapped_outfile.html &&
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116 cat wrapped_outfile.html
0
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117 ]]></command>
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118 <inputs>
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119 <expand macro="common_params"/>
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120 <param argument="--infile" type="data" format="tabular" label="metaquantome stats or filtered file"
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121 help=""/>
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122 <conditional name="plot">
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123 <param argument="--plottype" type="select" label="Plot type">
3
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124 <option value="bar">Bar Chart (bar)</option>
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125 <option value="volcano">Volcano Plot (volcano)</option>
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126 <option value="heatmap">Heatmap (heatmap)</option>
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127 <option value="pca">Principal Componets Analysis (pca)</option>
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128 <option value="ft_dist">Functional Taxonomic Distribution (ft_dist)</option>
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129 </param>
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130 <when value="bar">
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131 <expand macro="common_bar_params"/>
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132 <expand macro="img_size"/>
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133 </when>
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134 <when value="volcano">
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135 <param argument="--fc_name" type="text" label="Name of the fold change column in the stat dataframe">
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136 <validator type="empty_field"/>
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137 </param>
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138 <param argument="--textannot" type="text" optional="true" label="Name of the annotation column"
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139 help="Provides text annoatation for the plot. Optional, if missing, no text will be plotted."/>
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140 <param argument="--flip_fc" type="boolean" truevalue="--flip_fc" falsevalue="" checked="false"
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141 label="Flip the fold change (i.e., multiply log fold change by -1)"/>
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142 <param argument="--gosplit" type="boolean" truevalue="--gosplit" falsevalue="" checked="false"
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143 label="Make one plot for each of BiologicalProcess, CellularComponent, and MolecularFunction GO term categories."/>
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144 <expand macro="img_size"/>
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145 </when>
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146 <when value="heatmap">
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147 <param argument="--filter_to_sig" type="boolean" truevalue="--filter_to_sig" falsevalue="" checked="false"
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148 label="Only plot significant term" help="Necessitates use of results from `test`"/>
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149 <param argument="--alpha" type="float" value="0.05" min="0.0" max="1.0" label="If filter_to_sig, the q-value significance level"/>
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150 <expand macro="img_size"/>
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151 </when>
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152 <when value="pca">
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153 <param argument="--calculate_sep" type="boolean" truevalue="--calculate_sep" falsevalue="" checked="false"
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154 label="Calculate separation between groups and include in title"/>
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155 <expand macro="img_size"/>
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156 </when>
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157 <when value="ft_dist">
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158 <expand macro="common_bar_params"/>
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159 <param argument="--whichway" type="select" label="which distribution">
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160 <option value="f_dist">functional distribution for a taxon (f_dist)</option>
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161 <option value="t_dist">taxonomic distribution for a function (t_dist)</option>
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162 </param>
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163 <conditional name="term">
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164 <param argument="id_or_name" type="select" label="">
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165 <option value="id">Taxonomic or functional term ID</option>
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166 <option value="name">Taxonomic or functional term name</option>
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167 </param>
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168 <when value="id">
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169 <param argument="--id" type="text" label="Taxonomic or functional term id">
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170 <help>
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171 NCBI taxID or a GO term id (GO:XXXXXXX)
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172 </help>
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173 </param>
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174 </when>
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175 <when value="name">
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176 <param argument="--name" type="text" label="Taxonomic or functional term name">
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177 <help>
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178 Case-sensitive. Should be either a common taxonomic name ("Streptococcus") or functional term ("carbohydrate metabolic process").
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179 </help>
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180 </param>
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181 </when>
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182 </conditional>
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183 <param argument="--target_onto" type="select" optional="false" label="GO category to restrict to">
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184 <option value="bp">Biological Process</option>
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185 <option value="mf">Molecular Function</option>
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186 <option value="cc">Cellular Component</option>
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187 </param>
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188 <expand macro="img_size"/>
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189 </when>
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190 </conditional>
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191 </inputs>
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192 <outputs>
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193 <data format="png" name="outfile" label="${tool.name} on ${on_string} ${plot.plottype}" from_work_dir="outfile.png"/>
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194 <data format="html" name="wrapped_outfile" label="${tool.name} on ${on_string} ${plot.plottype}" from_work_dir="wrapped_outfile.html"/>
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195 </outputs>
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196 <tests>
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197 <test>
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198 <param name="infile" value="tax_filt.tab" ftype="tabular"/>
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199 <param name="mode" value="t" />
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200 <param name="samps_src" value="history" />
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201 <param name="samps_file" value="samples.tab" ftype="tabular"/>
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202 <param name="plottype" value="bar" />
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203 <param name="target_rank" value="genus" />
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204 <param name="meancol" value="NS_mean" />
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205 <param name="nterms" value="3" />
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206 <param name="barcol" value="1" />
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207 <param name="width" value="3" />
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208 <param name="height" value="3" />
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209 <output name="outfile" file="tax_ns.png" ftype="png" compare="sim_size" delta="50000"/>
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210 </test>
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211 </tests>
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212 <help><![CDATA[
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213 metaQuantome viz
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214 ===================
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215
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216 The *viz* module is the final step in the metaQuantome analysis workflow.
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217 The available visualizations are:
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218
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219 - bar plot
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220 - volcano plot
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221 - heatmap
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222 - PCA plot
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223
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224 Please consult the manuscript for full details on each of these plots.
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225
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226 Questions, Comments, Problems, Kudos
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227 --------------------------------------
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228
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229 Please file any issues at https://github.com/galaxyproteomics/tools-galaxyp/issues.
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230 ]]></help>
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231 <expand macro="citations" />
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232 </tool>