Mercurial > repos > iuc > ampvis2_subset_samples

annotate subset_samples.xml @ 4:fa298a49c564 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 12:51:03 +0000
parents 1187994f81a2
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1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
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1 <tool id="ampvis2_subset_samples" name="ampvis2 subset samples" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
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2 <description>by sample metadata</description>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
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3 <macros>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
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4 <import>macros.xml</import>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
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5 </macros>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
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6 <expand macro="header"/>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
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7 <command detect_errors="exit_code"><![CDATA[
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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8 Rscript '$rscript'
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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9 ]]></command>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
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10 <configfiles>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
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11 <configfile name="rscript"><![CDATA[
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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12 library(ampvis2, quietly = TRUE)
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
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13 data <- readRDS("$data")
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
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14 #set vals = 'c("' + '", "'.join(str($vals).split(",")) + '")'
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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15 data <- amp_subset_samples(
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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16 data,
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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17 $invert $var %in% $vals,
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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18 minreads = $minreads
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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19 @RAREFY_TOKEN@,
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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20 normalise = $normalise,
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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21 removeAbsents = $removeAbsents
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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22 )
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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23 saveRDS(data, "$ampvis")
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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24 @SAVE_METADATA_LIST@
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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25 ]]></configfile>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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26 </configfiles>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
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27 <inputs>
1187994f81a2 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"/>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
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29 <expand macro="metadata_select" an="name" argument="var" optional="false" multiple="false" label="Metadata variable"/>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
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30 <param name="vals" type="select" optional="false" multiple="true" label="Metadata value(s)">
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
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31 <options from_dataset="metadata_list">
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
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32 <column name="name" index="1"/>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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33 <column name="value" index="1"/>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
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34 <filter type="param_value" ref="var" column="0"/>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
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35 <filter type="unique_value" column="1"/>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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36 </options>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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37 </param>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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38 <param name="invert" type="boolean" truevalue="!" falsevalue="" checked="false"/>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
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39 <param argument="minreads" type="integer" value="0" min="0" label="Minimum number of reads" help="Per sample. Samples below this value will be removed initially"/>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
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40 <expand macro="rarefy_macro" help="This is done initially, but after filtering based on the minreads value, if set."/>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
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41 <expand macro="normalise_macro"/>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
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42 <param argument="removeAbsents" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true"/>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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43 </inputs>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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44 <outputs>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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45 <data name="ampvis" format="ampvis2"/>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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46 <data name="metadata_list_out" format="tabular" label="${tool.name} on ${on_string}: metadata list"/>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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47 </outputs>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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48 <tests>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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49 <!-- defaults -->
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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50 <test expect_num_outputs="2">
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
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51 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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52 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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53 <param name="var" value="Plant"/>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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54 <param name="vals" value="Aalborg East"/>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
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55 <output name="ampvis" value="AalborgWWTPs-subset_samples.rds" ftype="ampvis2" compare="sim_size"/>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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56 <output name="metadata_list_out" ftype="tabular">
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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57 <assert_contents>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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58 <has_line line="Plant&#9;Aalborg East&#9;FALSE&#9;character"/>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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59 <not_has_text text="Plant&#9;Aalborg West&#9;FALSE&#9;character"/>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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60 <has_n_lines n="85"/>
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61 <has_n_columns n="4"/>
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62 </assert_contents>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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63 </output>
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64 </test>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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65 <!-- test NA values in metadata -->
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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66 <test expect_num_outputs="2">
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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67 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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68 <param name="metadata_list" value="AalborgWWTPs-metadata_NA.list"/>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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69 <param name="var" value="Plant"/>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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70 <param name="vals" value="Aalborg East"/>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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71 <output name="ampvis" value="AalborgWWTPs-subset_samples.rds" ftype="ampvis2" compare="sim_size"/>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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72 <output name="metadata_list_out" ftype="tabular">
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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73 <assert_contents>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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74 <has_line line="Plant&#9;Aalborg East&#9;FALSE&#9;character"/>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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75 <not_has_text text="SampleID&#9;NA&#9;TRUE&#9;character"/>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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76 <has_n_lines n="85"/>
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77 <has_n_columns n="4"/>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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78 </assert_contents>
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79 </output>
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80 </test>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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81 <!-- invert -->
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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82 <test expect_num_outputs="2">
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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83 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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84 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
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85 <param name="var" value="Plant"/>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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86 <param name="vals" value="Aalborg East"/>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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87 <param name="invert" value="true"/>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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88 <output name="ampvis" value="AalborgWWTPs-subset_samples.rds" ftype="ampvis2" compare="sim_size"/>
1187994f81a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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89 <output name="metadata_list_out" ftype="tabular">
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90 <assert_contents>
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91 <not_has_text text="Plant&#9;Aalborg East&#9;FALSE&#9;character"/>
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92 <has_line line="Plant&#9;Aalborg West&#9;FALSE&#9;character"/>
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93 <has_n_lines n="79"/>
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94 <has_n_columns n="4"/>
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95 </assert_contents>
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96 </output>
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97 </test>
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98 </tests>
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99 <help><![CDATA[
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100 What it does
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101 ============
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102
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103 Subsets the data in ampvis2 objects based on metadata and returns the subsetted object.
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104
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105 The Galaxy tool calls the `amp_subset_samples
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106 <https://kasperskytte.github.io/ampvis2/reference/amp_filter_samples.html>`_ function
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107 of the ampvis2 package.
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108
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109 The subset is performed on the metadata by ``subset()`` and the abundance- and taxonomy
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110 tables are then adjusted accordingly.
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111
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112 @HELP_RELATIVE_ABUNDANCES@
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113
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114 Input
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115 =====
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116
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117 @HELP_RDS_INPUT@
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118
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119 @HELP_METADATA_LIST_INPUT@
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120
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121 Output
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122 ======
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123
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124 An ampvis2_rds dataset containing subsetted data and an updated metadata list dataset.
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125
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126 ]]></help>
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127 <expand macro="citations"/>
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128 </tool>