Mercurial > repos > iuc > ampvis2_core

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9fe04d29ea604a152144908dbd20c0754695a025
author iuc
date Sat, 16 Nov 2024 19:58:07 +0000
parents 2bbf288d6334
children
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48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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1 <macros>
6
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2 <token name="@TOOL_VERSION@">2.8.9</token>
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3 <token name="@VERSION_SUFFIX@">0</token>
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4 <token name="@PROFILE@">22.01</token>
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5 <xml name="header">
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6 <xrefs>
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7 <xref type="bio.tools">ampvis</xref>
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8 </xrefs>
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9 <requirements>
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10 <requirement type="package" version="@TOOL_VERSION@">r-ampvis2</requirement>
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11 <requirement type="package" version="2.1.5">r-readr</requirement>
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12 <requirement type="package" version="1.46.0">bioconductor-phyloseq</requirement>
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13 </requirements>
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14 <version_command><![CDATA[
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15 echo $(R --version | grep "R version")", ampvis2 version" $(R --vanilla --slave -e "library(ampvis2, quietly = TRUE); sessionInfo()\$otherPkgs\$ampvis2\$Version" 2> /dev/null | grep -v -i "WARNING: ")
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16 ]]></version_command>
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18 </xml>
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19 <xml name="citations">
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20 <citations>
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21 <citation type="doi">10.1101/299537</citation>
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22 <yield/>
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23 </citations>
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24 </xml>
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25
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26 <xml name="rds_input_macro" token_multiple="false">
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27 <param argument="data" type="data" format="ampvis2" multiple="@MULTIPLE@" label="Ampvis2 RDS dataset" help="Generated with ampvis2: load"/>
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28 </xml>
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29
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30 <xml name="rds_metadata_input_macro" token_metadata_optional="true">
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31 <expand macro="rds_input_macro"/>
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32 <param name="metadata_list" type="data" optional="@METADATA_OPTIONAL@" format="tabular" label="Metadata list">
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33 <validator type="expression" message="The metadatalist file must have 3 columns"><![CDATA[value.metadata.columns == 4]]></validator>
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34 </param>
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35 </xml>
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36
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37 <token name="@SAVE_TAX_LIST@"><![CDATA[
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38 for(level in colnames(data\$tax)){
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39 for(u in unique(data\$tax[level])){
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40 write(paste(u, level, sep="\t"), file="$taxonomy_list_out", append=T)
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41 }
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42 }
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43 ]]></token>
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44
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45 <token name="@SAVE_METADATA_LIST@"><![CDATA[
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46 classes <- sapply(data\$metadata, class)
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47 data\$metadata[is.na(data\$metadata)] <- "NA" ##the comparison below fails if NA values are present, see https://stackoverflow.com/questions/7355187/error-in-if-while-condition-missing-value-where-true-false-needed
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48 for(name in names(data\$metadata)){
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49 ## check if it is the column containing the sample names
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50 ## the additional column in the ist file can the be used
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51 ## to filter SampleIDs from select inputs
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52 ## (check for character columns only .. since data in the column is otherwise converted to the corresponding type .. which fails)
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53 if(classes[[name]] == "character" && all(data\$metadata[[name]] == rownames(data\$metadata))){
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54 sample_names <- TRUE;
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55 }else{
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56 sample_names <- FALSE;
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57 }
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58 for(m in unique(data\$metadata[[name]])){
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59 write(paste(name, m, sample_names, classes[[name]], sep="\t"), file="$metadata_list_out", append=T);
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60 }
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61 }
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62 ]]></token>
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63
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64 <!-- defaults can be set by redefining an on option with selected="true" -->
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65 <xml name="taxlevel_macro" token_argument="" token_multiple="false" token_optional="false" token_label="" token_help="">
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66 <param argument="@ARGUMENT@" type="select" optional="@OPTIONAL@" multiple="@MULTIPLE@" label="@LABEL@" help="@HELP@">
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67 <option value="OTU">OTU/ASV</option>
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68 <option value="Species">Species</option>
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69 <option value="Genus">Genus</option>
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70 <option value="Family">Family</option>
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71 <option value="Order">Order</option>
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72 <option value="Class">Class</option>
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73 <option value="Phylum">Phylum</option>
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74 <option value="Kingdom">Kingdom</option>
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75 <yield/>
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76 </param>
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77 </xml>
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78
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79 <xml name="tax_empty_macro">
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80 <param argument="tax_empty" type="select" label="How to show OTUs without taxonomic information">
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81 <option value="remove">Remove OTUs without taxonomic information</option>
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82 <option value="best" selected="true">Use the best classification possible</option>
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83 <option value="OTU">Display the OTU name</option>
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84 </param>
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85 </xml>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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86
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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87 <token name="@TAX_SHOW@"><![CDATA[
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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88 #if $tax_show_cond.tax_show_sel == "number"
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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89 tax_show = $tax_show_cond.tax_show,
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90 #else
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91 #set tax_show_list='c("' + '", "'.join(str($tax_show_cond.tax_show).split(",")) + '")'
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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92 tax_show = $tax_show_list
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93 #end if
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94 ]]></token>
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95 <xml name="tax_show_macro" token_value="">
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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96 <conditional name="tax_show_cond">
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97 <param name="tax_show_sel" type="select" label="Limit the number of shown taxa">
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98 <option value="number">Select a number of taxa to show</option>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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99 <option value="explicit">Manually select taxa to show</option>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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100 </param>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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101 <when value="number">
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102 <param argument="tax_show" type="integer" value="@VALUE@" min="1" label="Number of taxa to show"/>
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103 </when>
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104 <when value="explicit">
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105 <param name="taxonomy_list" format="tabular" type="data" optional="false" label="Taxonomy list" help="Generated with ampvis2: load"/>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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106 <param argument="tax_show" type="select" multiple="true" optional="false" label="Taxa to show">
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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107 <options from_dataset="taxonomy_list">
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108 <column name="name" index="0"/>
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109 <column name="value" index="0"/>
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110 <!-- TODO filter by tax_aggregate level? -->
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111 </options>
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112 </param>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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113 </when>
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114 </conditional>
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115 </xml>
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116
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117 <xml name="metadata_select" token_quote="__" tokens="argument,label" token_an="argument" token_optional="true" token_multiple="false" token_help="">
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118 <param __AN__="__ARGUMENT__" type="select" optional="__OPTIONAL__" multiple="__MULTIPLE__" label="__LABEL__" help="In order to select values a metadata list needs to be selected first. __HELP__">
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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119 <options from_dataset="metadata_list">
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120 <column name="name" index="0"/>
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121 <column name="value" index="0"/>
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122 <filter type="unique_value" column="0"/>
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123 <yield name="options"/>
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124 </options>
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125 <yield/>
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126 </param>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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127 </xml>
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128
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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129 <xml name="metadata_select_discrete" tokens="argument,label" token_optional="true" token_multiple="false" token_help="">
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130 <expand macro="metadata_select" argument="@ARGUMENT@" optional="@OPTIONAL@" multiple="@MULTIPLE@" label="@LABEL@" help="@HELP@">
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131 <token name="options">
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132 <filter type="static_value" column="3" value="numeric" keep="false"/>
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133 </token>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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134 <yield/>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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135 </expand>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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136 </xml>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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137
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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138 <xml name="metadata_select_numeric" tokens="argument,label" token_optional="true" token_multiple="false" token_help="">
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139 <expand macro="metadata_select" argument="@ARGUMENT@" optional="@OPTIONAL@" multiple="@MULTIPLE@" label="@LABEL@" help="@HELP@">
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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140 <token name="options">
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141 <filter type="static_value" column="3" value="character" keep="false"/>
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142 <filter type="static_value" column="3" value="Date" keep="false"/>
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143 </token>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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144 <yield/>
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145 </expand>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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146 </xml>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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147
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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148 <xml name="metadata_select_date" tokens="argument,label" token_optional="true" token_multiple="false" token_help="">
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149 <expand macro="metadata_select" argument="@ARGUMENT@" optional="@OPTIONAL@" multiple="@MULTIPLE@" label="@LABEL@" help="@HELP@">
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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150 <token name="options">
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151 <filter type="static_value" column="3" value="Date" keep="true"/>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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152 </token>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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153 <yield/>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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154 </expand>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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155 </xml>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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156
3
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157 <!-- metadata_sample_or_variable_select is currently unused (heatmap is documented to allow normalize by
0d30cb9b14cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 5b6fb9641a1320e13aba367c4e7bc52ae064acc6
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diff changeset
158 sample or variable, but only sample seems possible https://github.com/KasperSkytte/ampvis2/issues/168
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diff changeset
159 leaving it for now in case it can be fixed .. then metadata_sample_select could be removed) -->
0
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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160 <xml name="metadata_sample_select" token_argument="">
3
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161 <param argument="@ARGUMENT@" type="select" optional="true">
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162 <options from_dataset="metadata_list">
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163 <column name="name" index="1"/>
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164 <column name="value" index="1"/>
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165 <filter type="static_value" value="TRUE" column="2"/> <!-- filter samples -->
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166 <filter type="unique_value" column="1"/>
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167 </options>
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diff changeset
168 </param>
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parents: 2
diff changeset
169 </xml>
0d30cb9b14cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 5b6fb9641a1320e13aba367c4e7bc52ae064acc6
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170 <xml name="metadata_sample_or_variable_select" token_argument="">
0
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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diff changeset
171 <conditional name="@ARGUMENT@_cond">
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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172 <param name="@ARGUMENT@_sel" type="select">
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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173 <option value="no">No</option>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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174 <option value="variable">Metadata variable</option>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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175 <option value="sample">Specific sample</option>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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176 </param>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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parents:
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177 <when value="no"/>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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178 <when value="variable">
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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179 <expand macro="metadata_select" argument="@ARGUMENT@" label="Metadata variable"/>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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180 </when>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
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181 <when value="sample">
3
0d30cb9b14cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 5b6fb9641a1320e13aba367c4e7bc52ae064acc6
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parents: 2
diff changeset
182 <expand macro="metadata_sample_select"/>
0
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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183 </when>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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184 </conditional>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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185 </xml>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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186
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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187 <xml name="taxonomy_select_macro" token_argument="" token_optional="false" token_multiple="true">
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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188 <param argument="@ARGUMENT@" type="select" optional="@OPTIONAL@" multiple="@MULTIPLE@">
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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189 <options from_dataset="taxonomy_list">
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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190 <column name="name" index="0"/>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
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191 <column name="value" index="0"/>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
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192 <filter type="unique_value" column="0"/>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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193 </options>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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194 <yield/>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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195 </param>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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196 </xml>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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197
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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198 <xml name="facet_scales_macro" token_argument="" token_label="Scales of the facets" token_help="">
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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199 <param argument="@ARGUMENT@" type="select" optional="true" label="@LABEL@" help="@HELP@">
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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200 <option value="fixed">Same scale</option>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
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201 <option value="free">Free scale</option>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
202 <option value="free_x">Free x-scale</option>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
203 <option value="free_y">Free y-scale</option>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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204 </param>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
205 </xml>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
206
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
207 <token name="@OUTPUT_TOKEN@">
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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diff changeset
208 ggsave("$plot",
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
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diff changeset
209 print(plot),
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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diff changeset
210 device="$output_options.out_format"
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
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diff changeset
211 #if str($output_options.plot_width) != ''
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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diff changeset
212 , width = $output_options.plot_width
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
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diff changeset
213 #end if
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
214 #if str($output_options.plot_height) != ''
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
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diff changeset
215 , height = $output_options.plot_height
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
216 #end if
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
217 )
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
218 </token>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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diff changeset
219 <xml name="out_macro" token_name="plot" token_label="">
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
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220 <data name="@NAME@" format="pdf" label="${tool.name} on ${on_string}@LABEL@">
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
221 <yield/>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
222 <change_format>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
223 <when input="output_options.out_format" value="png" format="png" />
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
224 <when input="output_options.out_format" value="svg" format="svg" />
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
225 </change_format>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
226 </data>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
227 </xml>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
228 <xml name="out_format_macro">
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
229 <section name="output_options" title="Output options" expanded="false">
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
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diff changeset
230 <param name="out_format" type="select" label="Output format">
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
231 <option value="pdf" selected="true">PDF</option>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
232 <option value="png">PNG</option>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
233 <option value="svg">SVG</option>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
234 <yield/>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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parents:
diff changeset
235 </param>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
236 <param name="plot_width" type="float" value="" min="1" optional="true" label="Plot width in cm"/>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
237 <param name="plot_height" type="float" value="" min="1" optional="true" label="Plot height in cm"/>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
238 </section>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
239 </xml>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
240
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
241 <token name="@RAREFY_TOKEN@">
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
242 #if str($rarefy) != ""
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
243 , rarefy = $rarefy
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
244 #end if
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
245 </token>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
246 <xml name="rarefy_macro" token_help="">
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
247 <param argument="rarefy" type="integer" optional="true" value="" min="0" label="Rarefy species richness to this value" help="@HELP@"/>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
248 </xml>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
249
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
250 <xml name="normalise_macro" token_checked="false">
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
251 <param argument="normalise" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="@CHECKED@" label="Normalise read counts" help="Transform the OTU read counts to be in percent per sample."/>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
252 </xml>
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
253
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
254 <token name="@HELP_RDS_INPUT@">
48e343a308b0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
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255 An ampvis2 RDS dataset obtained by the ``ampvis2: load`` tool (or ``ampvis2: mergereplicates`` or one of the
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256 ``ampvis2: subset ...`` tools).
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257 </token>
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258 <token name="@HELP_METADATA_LIST_INPUT@">
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259 The metadata list output of the ``ampvis2: load`` tool (or ``ampvis2: mergereplicates`` or the
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260 ``ampvis2: subset sample`` tool). This input is only used for providing
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261 values to the parameters alowing to select metadata variables or values.
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262 </token>
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263
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264 <token name="@HELP_RELATIVE_ABUNDANCES@">
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265 Preserving relative abundances in a subset of larger data
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266 =========================================================
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267
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268 By default the raw read counts in the abundance matrix are normalised
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269 (transformed to percentages) by some ampvis2 plotting tools (for
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270 example ``ampvis2: heatmap``, ``ampvis2: timeseries``, and more).
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271 If this is applied to data generated by one of the ``ampvis2: subset ...`` tools
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272 this means that the relative
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273 abundances shown will be calculated based on the remaining taxa after the
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274 subset, not including the removed taxa, if any. To circumvent this, enable
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275 ``normalise`` when subsetting with the ``ampvis2: subset ...``` tools,
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276 and then disable ``normalise`` in the plotting tool. This will
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277 transform the OTU counts to relative abundances BEFORE the subset.
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278 </token>
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279 </macros>