Mercurial > repos > iuc > ampvis2_boxplot

annotate boxplot.xml @ 2:de03693b75b1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 09b56ef3e09ad6c5923c88616fea5cbd77d87616
author iuc
date Mon, 18 Dec 2023 09:45:30 +0000
parents 43776659edf4
children 6eae290d762b
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43776659edf4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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1 <tool id="ampvis2_boxplot" name="ampvis2 boxplot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
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2 <description></description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="header"/>
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7 <command detect_errors="exit_code"><![CDATA[
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8 Rscript '$rscript'
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9 ]]></command>
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10 <configfiles>
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11 <configfile name="rscript"><![CDATA[
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12 #if $tax_add
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13 #set ta='c("' + '", "'.join(str($tax_add).split(",")) + '")'
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14 #else
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15 #set ta='NULL'
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16 #end if
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17 library(ampvis2, quietly = TRUE)
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18 d <- readRDS("$data")
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19 plot <- amp_boxplot(
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20 d,
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21 #if $group_by
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22 group_by = "$group_by",
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23 #end if
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24 sort_by = "$sort_by",
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25 plot_type = "$plot_type",
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26 point_size = $point_size,
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27 tax_aggregate = "$tax_aggregate",
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28 tax_add = $ta,
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29 @TAX_SHOW@
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30 tax_empty = "$tax_empty",
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31 ## tax_class = NULL,
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32 ## order_group = NULL,
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33 ## order_y = NULL,
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34 plot_flip = $plot_flip,
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35 plot_log = $plot_log,
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36 #if str($adjust_zero) != ""
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37 adjust_zero = $adjust_zero,
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38 #end if
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39 normalise = $normalise
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40 ## detailed_output = TRUE
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41 )
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42 @OUTPUT_TOKEN@
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43 ]]></configfile>
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44 </configfiles>
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45 <inputs>
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46 <expand macro="rds_metadata_input_macro"/>
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47 <expand macro="metadata_select_discrete" argument="group_by" label="Group the samples" help="by a discrete variable in the metadata"/>
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48 <param argument="sort_by" type="select" label="Sort boxplots by">
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49 <option value="median">Median</option>
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50 <option value="mean">Mean</option>
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51 <option value="total">Total</option>
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52 </param>
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53 <param argument="plot_type" type="select" label="Plot type">
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54 <option value="boxplot">Boxplot</option>
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55 <option value="point">Points</option>
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56 </param>
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57 <param argument="point_size" type="integer" value="1" min="0" label="Point size"/>
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58 <expand macro="taxlevel_macro" argument="tax_aggregate" label="The taxonomic level to aggregate the OTUs">
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59 <option value="Genus" selected="true">Genus</option>
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60 </expand>
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61 <expand macro="taxlevel_macro" argument="tax_add" multiple="true" optional="true" label="Additional taxonomic level(s) to display"/>
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62 <expand macro="tax_show_macro" value="20"/>
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63 <expand macro="tax_empty_macro"/>
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64 <param argument="plot_flip" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Flip the axes of the plot"/>
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65 <param argument="plot_log" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Log10-scale the plot"/>
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66 <param argument="adjust_zero" type="integer" value="" min="1" optional="true" label="Add value to abundances" help="in order to keep abundances of 0 in the calculation of medians"/>
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67 <expand macro="normalise_macro"/>
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68 <expand macro="out_format_macro"/>
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69 </inputs>
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70 <outputs>
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71 <expand macro="out_macro"/>
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72 </outputs>
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73 <tests>
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74 <test>
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75 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
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76 <output name="plot" value="AalborgWWTPs-boxplot.pdf" ftype="pdf"/>
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77 </test>
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78 <test>
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79 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
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80 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
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81 <param name="group_by" value="Plant"/>
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82 <param name="sort_by" value="total"/>
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83 <param name="tax_show" value="5"/>
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84 <param name="plot_flip" value="true"/>
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85 <param name="plot_log" value="true"/>
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86 <param name="adjust_zero" value="100000"/>
43776659edf4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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87 <param name="normalise" value="true"/>
43776659edf4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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88 <output name="plot" value="AalborgWWTPs-boxplot-group.pdf" ftype="pdf"/>
43776659edf4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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89 </test>
43776659edf4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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90 <test>
43776659edf4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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91 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
43776659edf4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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92 <param name="plot_type" value="point"/>
43776659edf4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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93 <param name="point_size" value="5"/>
43776659edf4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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94 <param name="tax_aggregate" value="Order"/>
43776659edf4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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95 <param name="tax_add" value="Phylum"/>
43776659edf4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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96 <output name="plot" value="AalborgWWTPs-boxplot-point.pdf" ftype="pdf"/>
43776659edf4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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97 </test>
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98 </tests>
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99 <help><![CDATA[
43776659edf4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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100 What it does
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101 ============
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102
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103 Generates boxplots of the most abundant taxa.
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104
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105 The Galaxy tool calls the `amp_boxplot
2
de03693b75b1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 09b56ef3e09ad6c5923c88616fea5cbd77d87616
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106 <https://kasperskytte.github.io/ampvis2/reference/amp_boxplot.html>`_ function
0
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107 of the ampvis2 package.
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108
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109 Input
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110 =====
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111
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112 @HELP_RDS_INPUT@
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113
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114 @HELP_METADATA_LIST_INPUT@
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115
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116 Output
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117 ======
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118
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119 Boxplot in the chosen output format.
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120
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121 ]]></help>
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122 <expand macro="citations"/>
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123 </tool>