Mercurial > repos > iuc > ampvis2_core

annotate core.xml @ 4:f8c3dac570f3 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 12:55:24 +0000
parents 6c809af05ff6
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6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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1 <tool id="ampvis2_core" name="ampvis2 core community analysis" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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2 <description></description>
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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3 <macros>
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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4 <import>macros.xml</import>
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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5 </macros>
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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6 <expand macro="header"/>
6c809af05ff6 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[
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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8 Rscript '$rscript'
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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9 ]]></command>
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
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10 <configfiles>
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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11 <configfile name="rscript"><![CDATA[
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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12 library(ampvis2, quietly = TRUE)
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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13 data <- readRDS("$data")
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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14 #set group_by_list='c("' + '", "'.join(str($group_by).split(",")) + '")'
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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15 plot <- amp_core(
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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16 data,
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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17 group_by = $group_by_list,
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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18 core_pct = $core_pct,
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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19 margin_plots = "$margin_plots",
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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20 margin_plot_values_size = $margin_plot_values_size,
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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21 widths = c($widths, 1),
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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22 heights = c(1, $heights)
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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23 )
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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24 @OUTPUT_TOKEN@
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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25 ]]></configfile>
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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26 </configfiles>
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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27 <inputs>
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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28 <expand macro="rds_metadata_input_macro"/>
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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29 <expand macro="metadata_select_discrete" argument="group_by" optional="false" multiple="true" label="Variable(s) which contain the desired grouping of samples" help="Can also be done by sample, just provide the name of the variable containing unique sample ID's"/>
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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30 <param argument="core_pct" type="float" value="80" min="0" max="100" label="Threshold in percent" help="Threshold for defining abundant (a.k.a. core) OTU's for each group"/>
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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31 <param argument="margin_plots" type="select" label="Margin plots to show" help="Margin plots display the cumulative read abundances of all OTU's per group sharing either x or y axis with the main plot">
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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32 <option value="x">Only show x-axis margin plot</option>
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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33 <option value="y">Only show y-axis margin plot</option>
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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34 <option value="xy" selected="true">Show both x and y-axis margin plots</option>
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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35 <option value="">Don't show any margin plots</option>
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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36 </param>
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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37 <param argument="margin_plot_values_size" type="integer" value="3" min="0" label="The size of the values" help="As indicated in the margin plots on top of the bars. Set to 0 to disable."/>
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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38 <param argument="widths" type="integer" value="5" min="1" label="Relative width of the main and y margin plots"/>
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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39 <param argument="heights" type="integer" value="5" min="1" label="Relative widths of the main and x margin plots"/>
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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40 <expand macro="out_format_macro"/>
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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41 </inputs>
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42 <outputs>
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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43 <expand macro="out_macro"/>
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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44 </outputs>
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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45 <tests>
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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46 <!-- defaults -->
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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47 <test expect_num_outputs="1">
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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48 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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49 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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50 <param name="group_by" value="Period"/>
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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51 <output name="plot" value="AalborgWWTPs-core.pdf" ftype="pdf" compare="sim_size"/>
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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52 </test>
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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53 <!--multiple groups + non-default widths / heights-->
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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54 <test expect_num_outputs="1">
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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55 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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56 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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57 <param name="group_by" value="Plant,Period"/>
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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58 <param name="core_pct" value="90"/>
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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59 <param name="widths" value="4"/>
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60 <param name="heights" value="4"/>
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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61 <output name="plot" value="AalborgWWTPs-core-multiple.pdf" ftype="pdf" compare="sim_size"/>
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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62 </test>
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63 </tests>
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64 <help><![CDATA[
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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65 What it does
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66 ============
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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67
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68 Core community plot to investigate how many of the most abundant OTU's comprise
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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69 the "core" of groups of samples, their abundances etc.
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70
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71 The Galaxy tool calls the `amp_core
6c809af05ff6 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_core.html>`_ function
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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73 of the ampvis2 package.
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74
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75 This analysis only makes sense without aggregating OTU's to any taxonomic level,
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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76 or else it will be biased by taxonomy and only be done on OTU's that have been
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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77 classified, which is rarely all.
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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78
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79
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80 @HELP_RELATIVE_ABUNDANCES@
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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81
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82 Input
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83 =====
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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84
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85 @HELP_RDS_INPUT@
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86
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87 @HELP_METADATA_LIST_INPUT@
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88
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89 Output
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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90 ======
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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91
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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92 A core community plot in the chosen output format.
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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93 ]]></help>
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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94 <expand macro="citations"/>
6c809af05ff6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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95 </tool>