Mercurial > repos > iuc > humann2_barplot

annotate humann2_barplot.xml @ 2:fc30f1dec9b9 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2 commit 18fea370966f4b87c8180df4afa0f3b138b75908"
author iuc
date Sat, 25 Jan 2020 18:24:25 -0500
parents efd98a5e8255
children 56cb2b0269d1
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1 <tool id="humann2_barplot" name="Barplot" version="@WRAPPER_VERSION@.0">
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2 <description>stratified HUMAnN2 features</description>
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3 <macros>
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4 <import>humann2_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements">
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7 <requirement type="package" version="2.0.2">matplotlib</requirement>
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8 <requirement type="package" version="1.13.1">numpy</requirement>
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9 <requirement type="package" version="0.19.1">scipy</requirement>
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10 </expand>
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11 <expand macro="version"/>
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12 <command detect_errors="exit_code"><![CDATA[
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13 humann2_barplot
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14 --input '$input'
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15 --focal-feature '$focal_feature'
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16 #if str($top_strata) != ''
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17 --top-strata '$top_strata'
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18 #end if
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19 --sort $sort
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20 --last-metadatum '$last_metadatum'
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21 --focal-metadatum '$focal_metadatum'
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22 #if str($colormap) != ''
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23 --colormap '$'colormap'
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24 #end if
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25 #if str($meta_colormap) != ''
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26 --meta-colormap '$meta_colormap'
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27 #end if
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28 $exclude_unclassified
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29 --scaling '$scaling'
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30 $as_genera
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31 $grid
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32 $remove_zeroes
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33 --width '$width'
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34 --dimensions '$height' '$width'
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35 #if str($ylims) != ''
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36 --ylims '$ylims'
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37 #end if
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38 #if $format == 'png'
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39 --output 'output.png'
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40 #elif $format == 'pdf'
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41 --output 'output.pdf'
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42 #elif $format == 'svg'
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43 --output 'output.svg'
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44 #end if
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45 ]]></command>
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46 <inputs>
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47 <param argument="--input" type="data" format="tsv,tabular" label="HUMAnN2 table with optional metadata"/>
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48 <param name="focal_feature" argument="--focal-feature" type="text" value="" label="Feature ID of interest (give ID not full name)">
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49 <validator type="empty_field" />
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50 </param>
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51 <param name="top_strata" argument="--top-strata" type="integer" value="" optional="true" label="Number of top stratifications to highlight" help="top = highest grand means"/>
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52 <param argument="--sort" type="select" label="Sample sorting methods">
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53 <option value="none">Default</option>
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54 <option value="sum">Sum of stratified values</option>
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55 <option value="dominant">Value of the most dominant stratification</option>
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56 <option value="similarity">Bray-Curtis agreement of relative stratifications</option>
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57 <option value="usimilarity">Bray-Curtis agreement of raw stratifications</option>
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58 <option value="metadata">Given metadata label</option>
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59 </param>
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60 <param name="focal_metadatum" argument="--focal-metadatum" type="text" value="" label="Metadatum to highlight / group by">
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61 <validator type="empty_field" />
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62 </param>
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63 <param name="last_metadatum" argument="--last-metadatum" type="text" value="" label="End of metadata rows">
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64 <validator type="empty_field" />
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65 </param>
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66 <param argument="--colormap" type="text" value="" optional="true" label="Color space for stratifications"/>
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67 <param name="meta_colormap" argument="--meta-colormap" type="text" value="" optional="true" label="Color space for metadata levels"/>
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68 <param name="exclude_unclassified" argument="--exclude-unclassified" type="boolean" truevalue="--exclude-unclassified" falsevalue="" checked="false" label="Do not include the 'unclassified' stratum?"/>
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69 <param argument="--scaling" type="select" label="Scaling options for total bar heights" help="Strata are always proportional to height">
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70 <option value="none">Default</option>
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71 <option value="pseudolog">Total bar heights log-scaled (strata are NOT log scaled)</option>
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72 <option value="normalize">Bars all have height=1 (highlighting relative attribution)</option>
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73 </param>
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74 <param name="as_genera" argument="--as-genera" type="boolean" truevalue="--as-genera" falsevalue="" checked="false" label="Collapse species to genera?"/>
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75 <param argument="--grid" type="boolean" truevalue="--grid" falsevalue="" checked="false" label="Add y-axis grid?"/>
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76 <param name="remove_zeroes" argument="--remove-zeroes" type="boolean" truevalue="--remove-zeroes" falsevalue="" checked="false" label="Do not plot samples with zero sum for this feature?"/>
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77 <param argument="--width" type="integer" value="5" label="Relative width of the plot vs. legend"/>
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78 <param name="height" argument="--dimensions" type="text" value="8" label="Image height in inches"/>
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79 <param name="width" argument="--dimensions" type="text" value="4" label="Image width in inches"/>
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80 <param argument="--ylims" type="text" value="" optional="true" label="Limits of y-axis (2 floats separated with a space)"/>
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81 <param name="format" type="select" label="Format for the output">
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82 <option value="pdf">PDF</option>
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83 <option value="png">PNG</option>
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84 <option value="svg">SVG</option>
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85 </param>
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86 </inputs>
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87 <outputs>
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88 <data format="png" name="barplot_png" from_work_dir="output.png" label="${tool.name} on ${on_string}">
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89 <filter>format == 'png'</filter>
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90 </data>
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91 <data format="pdf" name="barplot_pdf" from_work_dir="output.pdf" label="${tool.name} on ${on_string}">
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92 <filter>format == 'pdf'</filter>
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93 </data>
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94 <data format="svg" name="barplot_svg" from_work_dir="output.svg" label="${tool.name} on ${on_string}">
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95 <filter>format == 'svg'</filter>
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96 </data>
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97 </outputs>
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98 <tests>
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99 <test>
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100 <param name="input" value="hmp_pathabund.txt"/>
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101 <param name="focal_feature" value="ANAGLYCOLYSIS-PWY"/>
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102 <param name="sort" value="none"/>
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103 <param name="last_metadatum" value="STSite"/>
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104 <param name="focal_metadatum" value="STSite"/>
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105 <param name="exclude_unclassified" value=""/>
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106 <param name="scaling" value="none"/>
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107 <param name="as_genera" value=""/>
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108 <param name="grid" value=""/>
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109 <param name="remove_zeroes" value=""/>
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110 <param name="width" value="5"/>
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111 <param name="height" value="8"/>
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112 <param name="width" value="4"/>
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113 <param name="format" value="png"/>
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114 <output name="barplot_png" file="barplot1.png" ftype="png" compare="sim_size"/>
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115 </test>
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116 <test>
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117 <param name="input" value="hmp_pathabund.txt"/>
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118 <param name="focal_feature" value="ANAGLYCOLYSIS-PWY"/>
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119 <param name="sort" value="sum"/>
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120 <param name="last_metadatum" value="STSite"/>
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121 <param name="focal_metadatum" value="STSite"/>
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122 <param name="exclude_unclassified" value=""/>
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123 <param name="scaling" value="none"/>
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124 <param name="as_genera" value=""/>
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125 <param name="grid" value=""/>
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126 <param name="remove_zeroes" value=""/>
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127 <param name="width" value="5"/>
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128 <param name="height" value="8"/>
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129 <param name="width" value="4"/>
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130 <param name="format" value="pdf"/>
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131 <output name="barplot_pdf" file="barplot2.pdf" ftype="pdf" compare="sim_size"/>
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132 </test>
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133 <test>
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134 <param name="input" value="hmp_pathabund.txt"/>
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135 <param name="focal_feature" value="ANAGLYCOLYSIS-PWY"/>
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136 <param name="sort" value="metadata"/>
efd98a5e8255 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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137 <param name="last_metadatum" value="STSite"/>
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138 <param name="focal_metadatum" value="STSite"/>
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139 <param name="exclude_unclassified" value="--exclude-unclassified"/>
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140 <param name="scaling" value="none"/>
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141 <param name="as_genera" value="--as-genera"/>
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142 <param name="grid" value="--grid"/>
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143 <param name="remove_zeroes" value="--remove-zeroes"/>
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144 <param name="width" value="5"/>
efd98a5e8255 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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145 <param name="height" value="8"/>
efd98a5e8255 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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146 <param name="width" value="4"/>
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147 <param name="format" value="svg"/>
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148 <output name="barplot_svg" file="barplot3.svg" ftype="svg" compare="sim_size"/>
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149 </test>
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150 <test>
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151 <param name="input" value="hmp_pathabund.txt"/>
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152 <param name="focal_feature" value="ANAGLYCOLYSIS-PWY"/>
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153 <param name="top_strata" value="12"/>
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154 <param name="sort" value="sum"/>
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155 <param name="last_metadatum" value="STSite"/>
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156 <param name="focal_metadatum" value="STSite"/>
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157 <param name="exclude_unclassified" value=""/>
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158 <param name="scaling" value="normalize"/>
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159 <param name="as_genera" value=""/>
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160 <param name="grid" value=""/>
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161 <param name="remove_zeroes" value=""/>
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162 <param name="width" value="5"/>
efd98a5e8255 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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163 <param name="height" value="8"/>
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164 <param name="width" value="4"/>
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165 <param name="format" value="png"/>
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166 <output name="barplot_png" file="barplot4.png" ftype="png" compare="sim_size"/>
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167 </test>
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168 </tests>
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169 <help><![CDATA[
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170 @HELP_HEADER@
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172 humann2_barplot produces plots of stratified HUMAnN2 features and includes many options for sorting and scaling data
efd98a5e8255 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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174 Here is an example of a HUMAnN2 barplot for a pathway (denitrification) that was preferentially enriched in Human Microbiome Project oral samples relative to other body sites. This figure uses many options from humann2_barplot, including regrouping by genus, pseudolog scaling, and sorting samples by similarity and metadata:
efd98a5e8255 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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176 .. image:: $PATH_TO_IMAGES/731303924-page_DENITRIFICATION-PWY.png
efd98a5e8255 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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177 :width: 800
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178 ]]></help>
efd98a5e8255 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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179 <expand macro="citations"/>
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180 </tool>