Mercurial > repos > iuc > ampvis2_subset_taxa

annotate subset_taxa.xml @ 6:cf579d6919e8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit cb30e4b8d695e096753fe7cb5056b118b25a87fd
author iuc
date Mon, 26 Aug 2024 16:18:57 +0000
parents 1332619ad9ec
children 20a62b3a3038
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8cb9c749b2fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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1 <tool id="ampvis2_subset_taxa" name="ampvis2 subset data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
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2 <description>by taxonomy</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 '$rscript'
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9 ]]></command>
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10 <configfiles>
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11 <configfile name="rscript"><![CDATA[
8cb9c749b2fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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12 library(ampvis2, quietly = TRUE)
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13 data <- readRDS("$data")
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14 #set tax_vector = 'c("' + '", "'.join(str($tax_vector).split(",")) + '")'
8cb9c749b2fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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15 data <- amp_subset_taxa(
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16 data,
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17 tax_vector = $tax_vector,
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18 normalise = $normalise,
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19 remove = $remove
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20 )
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21 saveRDS(data, "$ampvis")
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22 @SAVE_TAX_LIST@
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23 ]]></configfile>
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24 </configfiles>
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25 <inputs>
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26 <expand macro="rds_input_macro"/>
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27 <!-- add validator -->
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28 <param name="taxonomy_list" type="data" optional="false" format="tabular" label="Taxonomy list" help="Generated with ampvis2: load"/>
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29 <expand macro="taxonomy_select_macro" argument="tax_vector" label="Taxa to keep"/>
8cb9c749b2fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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30 <expand macro="normalise_macro"/>
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31 <param argument="remove" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Remove" help="Selected taxa will be removed instead of being the only ones kept in the data."/>
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32 </inputs>
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33 <outputs>
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34 <data name="ampvis" format="ampvis2"/>
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35 <data name="taxonomy_list_out" format="tabular" label="${tool.name} on ${on_string}: taxonomy list"/>
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36 </outputs>
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37 <tests>
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38 <!-- defaults -->
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39 <test expect_num_outputs="2">
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40 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
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41 <param name="taxonomy_list" value="AalborgWWTPs-taxonomy.list"/>
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42 <param name="tax_vector" value="f__Caldilineaceae,p__Elusimicrobia"/>
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43 <output name="ampvis" value="AalborgWWTPs-subset_taxa.rds" ftype="ampvis2" compare="sim_size"/>
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44 <output name="taxonomy_list_out" ftype="tabular">
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45 <assert_contents>
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46 <has_text text="f__Caldilineaceae"/>
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47 <has_text text="p__Elusimicrobia"/>
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48 </assert_contents>
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49 </output>
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50 </test>
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51 <!-- defaults -->
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52 <test expect_num_outputs="2">
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53 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
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54 <param name="taxonomy_list" value="AalborgWWTPs-taxonomy.list"/>
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55 <param name="tax_vector" value="f__Caldilineaceae,p__Elusimicrobia"/>
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56 <param name="remove" value="true"/>
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57 <output name="ampvis" value="AalborgWWTPs-subset_taxa.rds" ftype="ampvis2" compare="sim_size"/>
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58 <output name="taxonomy_list_out" ftype="tabular">
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59 <assert_contents>
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60 <not_has_text text="f__Caldilineaceae"/>
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61 <not_has_text text="p__Elusimicrobia"/>
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62 </assert_contents>
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63 </output>
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64 </test>
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65 </tests>
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66 <help><![CDATA[
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67 What it does
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68 ============
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69
8cb9c749b2fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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70 Subsets the data in ampvis2 objects based on taxonomy and returns the subsetted object.
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71
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72 The Galaxy tool calls the `amp_subset_taxa
2
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73 <https://kasperskytte.github.io/ampvis2/reference/amp_filter_taxa.html>`_ function
0
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74 of the ampvis2 package.
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75
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76 The taxonomy subset is done by providing a tax_vector of taxa names which are
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77 then matched to the taxonomy table, where all other taxa not matching the
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78 "Taxa to keep" (``tax_vector``) are removed. If "Remove" is enabled, then the
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79 matching taxa are the ones being removed instead. The taxa names
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80 will be matched in all columns of the taxonomy table.
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81
8cb9c749b2fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
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82 @HELP_RELATIVE_ABUNDANCES@
8cb9c749b2fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
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83
8cb9c749b2fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
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84 Input
8cb9c749b2fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
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85 =====
8cb9c749b2fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
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86
8cb9c749b2fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
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87 @HELP_RDS_INPUT@
8cb9c749b2fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
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88
8cb9c749b2fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
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89 @HELP_METADATA_LIST_INPUT@
8cb9c749b2fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
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90
8cb9c749b2fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
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91 Output
8cb9c749b2fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
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92 ======
8cb9c749b2fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
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93
8cb9c749b2fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
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94 An ampvis2_rds dataset containing subsetted data and an updated taxonomy list dataset.
8cb9c749b2fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
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95
8cb9c749b2fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
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96 ]]></help>
8cb9c749b2fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
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97 <expand macro="citations"/>
8cb9c749b2fc "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
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98 </tool>