annotate merge_ampvis2.xml @ 6:5c6edb00ef4a draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit d92935972ac18906154fadf42bd0c008e3c437e2
author iuc
date Fri, 25 Oct 2024 14:12:34 +0000
parents 78ff575ef835
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1 <tool id="ampvis2_merge_ampvis2" name="ampvis2 merge ampvis2 data sets" 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"/>
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7 <command detect_errors="exit_code"><![CDATA[
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8 Rscript '$rscript'
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9 ]]></command>
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10 <configfiles>
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11 <configfile name="rscript"><![CDATA[
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12 library(ampvis2, quietly = TRUE)
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13 merged <- amp_merge_ampvis2(
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14 #for d in $data
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15 readRDS("$d"),
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16 #end for
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17 by_refseq = $by_refseq
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18 )
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19 saveRDS(merged, "$output")
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20 merged
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21 ]]></configfile>
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22 </configfiles>
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23 <inputs>
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24 <expand macro="rds_input_macro" multiple="true"/>
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25 <param argument="by_refseq" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Merge by exact matches between DNA reference sequences" help="The full DNA sequences will then be used as the new names in the output."/>
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26 <!-- TODO refseq_names = NULL, rename_unmatched = TRUE, unmatched_prefix = "unmatched" -->
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27 </inputs>
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28 <outputs>
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29 <data name="output" format="ampvis2"/>
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30 </outputs>
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31 <tests>
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32 <!-- defaults -->
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33 <test expect_num_outputs="1">
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34 <param name="data" value="AalborgWWTPs.2010.rds,AalborgWWTPs.2011.rds" ftype="ampvis2"/>
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35 <output name="output" ftype="ampvis2">
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36 <assert_contents>
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37 <has_size value="70888" delta="1000"/>
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38 </assert_contents>
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39 </output>
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40 <assert_stdout>
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41 <!--check that the merged data has 13 samples-->
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42 <has_text text="13 125 6714 193 1019 475"/>
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43 </assert_stdout>
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44 </test>
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45 </tests>
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46 <help><![CDATA[
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47 What it does
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48 ============
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49
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50 Merge any number of ampvis2 data sets into a single data set.
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51
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52 The Galaxy tool calls the `amp_merge_ampvis2
1
49b97737747d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 09b56ef3e09ad6c5923c88616fea5cbd77d87616
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53 <https://kasperskytte.github.io/ampvis2/reference/amp_merge_ampvis2.html>`_ function
0
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54 of the ampvis2 package.
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55
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56 Input
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57 =====
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58
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59 @HELP_RDS_INPUT@
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60
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61 Details
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62 =======
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63
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64 It's important to ensure that the taxonomy for all OTU's across data sets is
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65 generated in the exact same way with the same database. When **Merge by exact matches between DNA reference sequences** is not checked
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66 it's likewise important to ensure that OTU ID's are not arbitrary between data
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67 sets and that they are corresponding to the same sequences across data sets
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68 (objects). When **Merge by exact matches between DNA reference sequences** is checked the full DNA sequences will be used as the new
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69 OTU ID's.
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70
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71 Currently, phylogenetic trees are not merged.
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72
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73 Output
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74 ======
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75
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76 The merged data set
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77 ]]></help>
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78 <expand macro="citations"/>
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79 </tool>