Mercurial > repos > iuc > ampvis2_venn

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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 12:59:31 +0000
parents c8999971bab3
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11d29b7b44f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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1 <tool id="ampvis2_venn" name="ampvis2 venn diagram" 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"/>
11d29b7b44f9 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[
11d29b7b44f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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8 Rscript '$rscript'
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9 ]]></command>
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10 <configfiles>
11d29b7b44f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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11 <configfile name="rscript"><![CDATA[
11d29b7b44f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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12 library(ampvis2, quietly = TRUE)
11d29b7b44f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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13 data <- readRDS("$data")
11d29b7b44f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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14 plot <- amp_venn(
11d29b7b44f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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15 data,
11d29b7b44f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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16 #if $group_by
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17 group_by = "$group_by",
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18 #end if
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19 cut_a = $cut_a,
11d29b7b44f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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20 cut_f = $cut_f,
11d29b7b44f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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21 text_size = $text_size,
11d29b7b44f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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22 normalise = $normalise,
11d29b7b44f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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23 ## detailed_output = TRUE seems not supported yet https://github.com/MadsAlbertsen/ampvis2/issues/132
11d29b7b44f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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24 )
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25 ## names(plot)
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26 @OUTPUT_TOKEN@
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27 ]]></configfile>
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28 </configfiles>
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29 <inputs>
11d29b7b44f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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30 <expand macro="rds_metadata_input_macro"/>
3
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31 <expand macro="metadata_select_discrete" argument="group_by" label="Group the data by" help="Currently only supports a maximum of 3 different groups.">
0
11d29b7b44f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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32 <validator type="expression" message="A maximum of 3 different groups is supported"><![CDATA[len(str(value).split(",")) < 4]]></validator>
11d29b7b44f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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33 </expand>
11d29b7b44f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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34 <param argument="cut_a" type="float" value="0.1" min="0" max="100" label="Abundance cutoff (percent)" help="OTU's below this abundance are excluded from the analysis"/>
11d29b7b44f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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35 <param argument="cut_f" type="float" value="80" min="0" max="100" label="Frequency cutoff (percent)" help="OTU's within the top cut_f of the reads are considered a core OTU"/>
11d29b7b44f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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36 <param argument="text_size" type="integer" value="5" min="1" label="Size of the plotted text."/>
11d29b7b44f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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37 <expand macro="normalise_macro"/>
11d29b7b44f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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38 <expand macro="out_format_macro"/>
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39 </inputs>
11d29b7b44f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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40 <outputs>
11d29b7b44f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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41 <expand macro="out_macro"/>
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42 </outputs>
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43 <tests>
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44 <!-- defaults -->
11d29b7b44f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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45 <test expect_num_outputs="1">
11d29b7b44f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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46 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
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47 <output name="plot" value="AalborgWWTPs-venn.pdf" ftype="pdf" compare="sim_size"/>
11d29b7b44f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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48 </test>
11d29b7b44f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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49 <!-- defaults + group_by -->
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50 <test expect_num_outputs="1">
11d29b7b44f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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51 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
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52 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
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53 <param name="group_by" value="Plant"/>
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54 <output name="plot" value="AalborgWWTPs-venn-group.pdf" ftype="pdf" compare="sim_size"/>
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55 </test>
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56 </tests>
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57 <help><![CDATA[
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58 What it does
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59 ============
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60
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61 Calculates the number of "core" OTUs shared by groups given thresholds for how
11d29b7b44f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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62 frequent the OTUs should be above a certain abundance. Also returns the average
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63 abundance of the OTUs in a particular group.
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64
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65 The Galaxy tool calls the `amp_venn
11d29b7b44f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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66 <https://kasperskytte.github.io/ampvis2/reference/amp_venn.html>`_ function
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67 of the ampvis2 package.
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68
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69 @HELP_RELATIVE_ABUNDANCES@
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70
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71 Input
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72 =====
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73
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74 @HELP_RDS_INPUT@
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75
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76 @HELP_METADATA_LIST_INPUT@
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77
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78 Output
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79 ======
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80
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81 A venn diagram in the chosen output format.
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82 ]]></help>
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83 <expand macro="citations"/>
3
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84 </tool>