Mercurial > repos > iuc > ampvis2_mergereplicates

annotate mergereplicates.xml @ 4:c77bb786712b 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 12:49:23 +0000
parents 2297a352423e
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2297a352423e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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1 <tool id="ampvis2_mergereplicates" name="ampvis2 merge replicates" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
2297a352423e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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2 <description></description>
2297a352423e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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3 <macros>
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4 <import>macros.xml</import>
2297a352423e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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5 </macros>
2297a352423e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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6 <expand macro="header"/>
2297a352423e 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[
2297a352423e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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8 Rscript '$rscript'
2297a352423e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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9 ]]></command>
2297a352423e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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10 <configfiles>
2297a352423e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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11 <configfile name="rscript"><![CDATA[
2297a352423e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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12 library(ampvis2, quietly = TRUE)
2297a352423e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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13 data <- readRDS("$data")
2297a352423e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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14 data <- amp_mergereplicates(
2297a352423e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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15 data,
2297a352423e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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16 merge_var = "$merge_var",
2297a352423e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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17 #if $round != ""
2297a352423e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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18 round = "$round"
2297a352423e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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19 #end if
2297a352423e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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20 )
2297a352423e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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21 saveRDS(data, "$ampvis")
2297a352423e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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22 @SAVE_METADATA_LIST@
2297a352423e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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23 ]]></configfile>
2297a352423e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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24 </configfiles>
2297a352423e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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25 <inputs>
2297a352423e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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26 <expand macro="rds_metadata_input_macro"/>
2297a352423e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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27 <expand macro="metadata_select_discrete" argument="merge_var" label="Variable that defines the sample groups"/>
2297a352423e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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28 <param argument="round" type="select" label="Round decimals after merging" help="If the read counts are integers, any decimals present after merging will be rounded either up or down. Make sure this makes sense if the read counts have been normalised, as it may result in 0's, 1's, and 2's everywhere. ">
2297a352423e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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29 <option value="">Don't round</option>
2297a352423e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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30 <option value="up">up</option>
2297a352423e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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31 <option value="down">down</option>
2297a352423e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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32 </param>
2297a352423e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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33 </inputs>
2297a352423e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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34 <outputs>
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35 <data name="ampvis" format="ampvis2"/>
2297a352423e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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36 <data name="metadata_list_out" format="tabular" label="${tool.name} on ${on_string}: metadata list"/>
2297a352423e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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37 </outputs>
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38 <tests>
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39 <!-- defaults -->
2297a352423e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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40 <test expect_num_outputs="2">
2297a352423e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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41 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
2297a352423e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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42 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
2297a352423e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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43 <param name="merge_var" value="Period"/>
2297a352423e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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44 <output name="ampvis" value="AalborgWWTPs-mergereplicates.rds" ftype="ampvis2" compare="sim_size"/>
2297a352423e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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45 <output name="metadata_list_out">
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46 <assert_contents>
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47 <has_line line="Period&#9;Winter&#9;TRUE&#9;character"/>
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48 <has_n_lines n="13"/>
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49 <has_n_columns n="4"/>
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50 </assert_contents>
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51 </output>
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52 </test>
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53 <!-- defaults -->
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54 <test expect_num_outputs="2">
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55 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
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56 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
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57 <param name="merge_var" value="Period"/>
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58 <param name="round" value="up"/>
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59 <output name="ampvis" value="AalborgWWTPs-mergereplicates.rds" ftype="ampvis2" compare="sim_size"/>
2297a352423e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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60 <output name="metadata_list_out">
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61 <assert_contents>
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62 <has_line line="Period&#9;Winter&#9;TRUE&#9;character"/>
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63 <has_n_lines n="13"/>
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64 <has_n_columns n="4"/>
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65 </assert_contents>
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66 </output>
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67 </test>
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68 </tests>
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69 <help><![CDATA[
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70 What it does
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71 ============
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72
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73 Aggregates read counts in replicate samples by calculating the mean abundances of OTU's
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74
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75 The Galaxy tool calls the `amp_mergereplicates
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76 <https://kasperskytte.github.io/ampvis2/reference/amp_merge_replicates.html>`_ function
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77 of the ampvis2 package.
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78
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79 Input
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80 =====
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81
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82 @HELP_RDS_INPUT@
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83
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84 @HELP_METADATA_LIST_INPUT@
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85
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86 Output
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87 ======
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88
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89 An rank abundance plot in the chosen output format.
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90 ]]></help>
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91 <expand macro="citations"/>
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92 </tool>