Mercurial > repos > iuc > ampvis2_otu_network

annotate otu_network.xml @ 4:0eb71454597d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampvis2 commit e0ad9ce8f508215ec6af69be2682a0faf38415da
author iuc
date Mon, 10 Nov 2025 12:58:55 +0000
parents 3ceafc03b9a0
children
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3ceafc03b9a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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1 <tool id="ampvis2_otu_network" name="ampvis2 OTU network plot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
3ceafc03b9a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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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"/>
3ceafc03b9a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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7 <command detect_errors="exit_code"><![CDATA[
3ceafc03b9a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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8 Rscript '$rscript'
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9 ]]></command>
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10 <configfiles>
3ceafc03b9a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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11 <configfile name="rscript"><![CDATA[
3ceafc03b9a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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12 library(ampvis2, quietly = TRUE)
3ceafc03b9a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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13 #if $tax_add
3ceafc03b9a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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14 #set ta='c("' + '", "'.join(str($tax_add).split(",")) + '")'
3ceafc03b9a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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15 #else
3ceafc03b9a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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16 #set ta='NULL'
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17 #end if
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18 data <- readRDS("$data")
3ceafc03b9a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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19 plot <- amp_otu_network(
3ceafc03b9a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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20 data,
3ceafc03b9a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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21 min_abundance = $min_abundance,
3ceafc03b9a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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22 #if $color_by
3ceafc03b9a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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23 color_by = "$color_by",
3ceafc03b9a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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24 #end if
3ceafc03b9a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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25 tax_aggregate = "$tax_aggregate",
3ceafc03b9a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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26 tax_add = $ta,
3ceafc03b9a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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27 @TAX_SHOW@
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28 tax_class = NULL,
3ceafc03b9a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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29 tax_empty = "$tax_empty",
3ceafc03b9a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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30 normalise = $normalise,
3ceafc03b9a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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31 )
3ceafc03b9a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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32 @OUTPUT_TOKEN@
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33 ]]></configfile>
3ceafc03b9a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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34 </configfiles>
3ceafc03b9a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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35 <inputs>
3ceafc03b9a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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36 <expand macro="rds_metadata_input_macro"/>
3ceafc03b9a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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37 <param argument="min_abundance" type="float" value="0" min="0" label="Minimum taxa abundance" help="per sample"/>
3ceafc03b9a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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38 <expand macro="metadata_select" argument="color_by" label="Color the samples by"/>
3ceafc03b9a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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39 <expand macro="taxlevel_macro" argument="tax_aggregate" label="The taxonomic level to aggregate the OTUs">
3ceafc03b9a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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40 <option value="Phylum" selected="true">Phylum</option>
3ceafc03b9a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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41 </expand>
3ceafc03b9a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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42 <expand macro="taxlevel_macro" argument="tax_add" multiple="true" optional="true" label="Additional taxonomic level(s) to display"/>
3ceafc03b9a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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43 <expand macro="tax_show_macro" value="10"/>
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44 <expand macro="tax_empty_macro"/>
3ceafc03b9a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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45 <expand macro="normalise_macro" checked="true"/>
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46 <expand macro="out_format_macro"/>
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47 </inputs>
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48 <outputs>
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49 <expand macro="out_macro"/>
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50 </outputs>
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51 <tests>
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52 <!-- defaults -->
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53 <test expect_num_outputs="1">
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54 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
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55 <output name="plot" value="AalborgWWTPs-otu_network.pdf" ftype="pdf" compare="sim_size"/>
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56 </test>
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57 <!-- defaults color -->
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58 <test expect_num_outputs="1">
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59 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
3ceafc03b9a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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60 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
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61 <param name="color_by" value="Plant"/>
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62 <output name="plot" value="AalborgWWTPs-otu_network-color_by.pdf" ftype="pdf" compare="sim_size"/>
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63 </test>
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64 </tests>
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65 <help><![CDATA[
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66 What it does
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67 ============
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68
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69 Generates network plot of taxa and samples.
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70
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71 The Galaxy tool calls the `amp_otu_network
3ceafc03b9a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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72 <https://kasperskytte.github.io/ampvis2/reference/amp_otu_network.html>`_ function
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73 of the ampvis2 package (based on ggnet2.).
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74
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75 Input
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76 =====
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77
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78 @HELP_RDS_INPUT@
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79
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80 @HELP_METADATA_LIST_INPUT@
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81
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82 Output
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83 ======
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84
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85 An OTU network plot in the chosen output format.
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86 ]]></help>
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87 <expand macro="citations"/>
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88 </tool>