Mercurial > repos > iuc > ampvis2_load

annotate load.xml @ 1:dc0840e31406 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 40ca64669b0f8c875835fcf41ce91e6adb391283"
author iuc
date Thu, 07 Apr 2022 14:06:41 +0000
parents 474bbc45ddd9
children 8d77d277996e
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474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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1 <tool id="ampvis2_load" name="ampvis2 load" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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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 #if $otutable.ext.startswith("biom")
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9 ln -s '$otutable' otutable.biom &&
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10 #else
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11 ln -s '$otutable' otutable.tsv &&
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12 #end if
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13 #if $taxonomy
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14 ln -s '$taxonomy' taxonomy.tsv &&
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15 #end if
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16 Rscript '$rscript'
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17 ]]></command>
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18 <configfiles>
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19 <configfile name="rscript"><![CDATA[
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20 library(ampvis2, quietly = TRUE)
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21 library(readr, quietly = TRUE)
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22 ## 'manually' load metadata treating all columns as character
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23 ## giving colClasses to amp_load seems not possible
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24 #if $metadata
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25 metadata <- read.table("$metadata", header = TRUE, sep = "\t", colClasses = "character")
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26 #end if
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27 data <- amp_load(
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28 #if $otutable.ext.startswith("biom")
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29 otutable = "otutable.biom",
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30 #else
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31 otutable = "otutable.tsv",
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32 #end if
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33 #if $metadata
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34 metadata = metadata,
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35 #end if
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36 #if $taxonomy
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37 taxonomy = "taxonomy.tsv",
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38 #end if
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39 #if $fasta
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40 fasta = "$fasta",
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41 #end if
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42 #if $tree
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43 tree = "$tree",
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44 #end if
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45 pruneSingletons = $pruneSingletons
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46 )
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47 ## try to guess column types with plyr::type.convert
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48 #if $guess_column_types
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49 data\$metadata <- readr::type_convert(data\$metadata, guess_integer=TRUE)
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50 #end if
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51 saveRDS(data, "$ampvis")
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52 ## write metadata list for biom input or if metadata is given
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53 #if "metadata" in $write_lists
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54 @SAVE_METADATA_LIST@
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55 #end if
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56
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57 #if "tax" in $write_lists
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58 @SAVE_TAX_LIST@
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59 #end if
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60 ## print overview of the data to stdout
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61 data
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62 ]]></configfile>
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63 </configfiles>
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64 <inputs>
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65 <param argument="otutable" type="data" format="tabular,biom1,biom2" label="OTU table"/>
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66 <param argument="metadata" type="data" format="tsv" optional="true" label="Sample metadata">
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67 <validator type="expression" message="Table must have at least 1 column"><![CDATA[value.metadata.columns > 0]]></validator>
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68 <!-- TODO in future versions this might change https://github.com/MadsAlbertsen/ampvis2/pull/134
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69 if so, then also adapt help text and test data -->
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70 <validator type="expression" message="First column must be named SampleID"><![CDATA[value.metadata.column_names[0] == "SampleID"]]></validator>
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71 </param>
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72 <param name="guess_column_types" type="boolean" checked="true" label="Guess metadata column types" help="See help"/>
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73 <param argument="taxonomy" type="data" format="tabular" optional="true" label="Taxonomy table"/>
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74 <param argument="fasta" type="data" format="fasta" optional="true" label="Fasta file"/>
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75 <param argument="tree" type="data" format="newick" optional="true" label="Phylogenetic tree"/>
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76 <param argument="pruneSingletons" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Remove singleton OTUs"/>
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77 <param name="write_lists" type="select" optional="true" multiple="true" label="Output list data sets" help="Needed by most downstream tools. Select if the inputs contain taxonomic / metadata information.">
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78 <option value="tax" selected="true">Taxonomy list</option>
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79 <option value="metadata" selected="true">Metadata list</option>
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80 </param>
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81 </inputs>
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82 <outputs>
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83 <data name="ampvis" format="ampvis2"/>
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diff changeset
84 <data name="metadata_list_out" format="tabular" label="${tool.name} on ${on_string}: metadata list">
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
85 <filter>write_lists and "metadata" in write_lists</filter>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
86 </data>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
87 <data name="taxonomy_list_out" format="tabular" label="${tool.name} on ${on_string}: taxonomy list">
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
88 <filter>write_lists and "tax" in write_lists</filter>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
89 </data>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
90 </outputs>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
91 <tests>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
92 <!-- load otu table + metadata + taxonomy -->
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
93 <test expect_num_outputs="3">
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
94 <param name="otutable" value="AalborgWWTPs.otu.csv"/>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
95 <param name="metadata" value="AalborgWWTPs.tsv" ftype="tsv"/>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
96 <param name="taxonomy" value="AalborgWWTPs.tax"/>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
97 <output name="ampvis" value="AalborgWWTPs.rds" ftype="ampvis2" compare="sim_size"/>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
98 <output name="metadata_list_out" value="AalborgWWTPs-metadata.list"/>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
99 <output name="taxonomy_list_out" value="AalborgWWTPs-taxonomy.list"/>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
100 <assert_stdout>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
101 <has_text text="575.79"/>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
102 <has_text text="SampleID, Plant, Date, Year, Period"/>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
103 <has_text text="200(100%) 194(97%) 177(88.5%) 170(85%) 152(76%) 113(56.5%) 2(1%)"/>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
104 </assert_stdout>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
105 </test>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
106 <!-- load otu table + metadata + taxonomy + tree + fasta -->
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
107 <test expect_num_outputs="3">
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
108 <param name="otutable" value="AalborgWWTPs.otu.csv"/>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
109 <param name="metadata" value="AalborgWWTPs.tsv" ftype="tsv"/>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
110 <param name="taxonomy" value="AalborgWWTPs.tax"/>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
111 <param name="fasta" value="AalborgWWTPs.fa" ftype="fasta"/>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
112 <param name="tree" value="AalborgWWTPs.nwk" ftype="newick"/>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
113 <output name="ampvis" value="AalborgWWTPs-complete.rds" ftype="ampvis2" compare="sim_size"/>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
114 <output name="metadata_list_out" value="AalborgWWTPs-metadata.list"/>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
115 <output name="taxonomy_list_out" value="AalborgWWTPs-taxonomy.list"/>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
116 <assert_stdout>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
117 <has_text text="575.79"/>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
118 <has_text text="SampleID, Plant, Date, Year, Period"/>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
119 <has_text text="200(100%) 194(97%) 177(88.5%) 170(85%) 152(76%) 113(56.5%) 2(1%)"/>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
120 </assert_stdout>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
121 </test>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
122 <!-- test biom 1/2 input (taken from https://github.com/biocore/biom-format/tree/master/examples)
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
123 metadata seems not to be loaded from a biom file https://github.com/MadsAlbertsen/ampvis2/issues/129
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
124 taxonomy is loaded from all but 1
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
125 -->
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
126 <test>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
127 <param name="otutable" value="rich-dense.biom" ftype="biom1"/>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
128 <output name="ampvis" ftype="ampvis2">
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
129 <assert_contents>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
130 <has_size value="748"/>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
131 </assert_contents>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
132 </output>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
133 <assert_stdout>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
134 <has_text text="4.5"/>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
135 <has_text text="SampleID, BarcodeSequence, LinkerPrimerSequence, BODY_SITE, Description"/>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
136 <has_text text="5(100%) 5(100%) 5(100%) 5(100%) 5(100%) 5(100%) 1(20%)"/>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
137 </assert_stdout>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
138 </test>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
139 <test>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
140 <param name="otutable" value="rich-sparse.biom" ftype="biom1"/>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
141 <output name="ampvis" ftype="ampvis2">
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
142 <assert_contents>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
143 <has_size value="751"/>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
144 </assert_contents>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
145 </output>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
146 <assert_stdout>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
147 <has_text text="4.5"/>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
148 <has_text text="SampleID, BarcodeSequence, LinkerPrimerSequence, BODY_SITE, Description"/>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
149 <has_text text="5(100%) 5(100%) 5(100%) 5(100%) 5(100%) 5(100%) 1(20%)"/>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
150 </assert_stdout>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
151 </test>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
152 <test>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
153 <param name="otutable" value="min_sparse_otu_table_hdf5.biom" ftype="biom2"/>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
154 <output name="ampvis" ftype="ampvis2">
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
155 <assert_contents>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
156 <has_size value="395"/>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
157 </assert_contents>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
158 </output>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
159 <assert_stdout>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
160 <has_text text="4.5"/>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
161 <!-- input file seems to miss metadata check that no metadata & taxonomy is loaded (ampvis2 adds dummy metadata) -->
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
162 <has_text text="SampleID, DummyVariable"/>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
163 <has_text text="0(0%) 0(0%) 0(0%) 0(0%) 0(0%) 0(0%) 0(0%)"/>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
164 </assert_stdout>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
165 </test>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
166 <test>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
parents:
diff changeset
167 <param name="otutable" value="rich_sparse_otu_table_hdf5.biom" ftype="biom2"/>
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168 <output name="ampvis" ftype="ampvis2">
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169 <assert_contents>
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170 <has_size value="753"/>
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171 </assert_contents>
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172 </output>
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173 <assert_stdout>
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174 <has_text text="4.5"/>
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175 <has_text text="SampleID, BODY_SITE, BarcodeSequence, Description, LinkerPrimerSequence"/>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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176 <has_text text="5(100%) 5(100%) 5(100%) 5(100%) 5(100%) 5(100%) 1(20%)"/>
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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177 </assert_stdout>
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178 </test>
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179 </tests>
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180 <help><![CDATA[
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181
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182 What it does
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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183 ============
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184
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185 This tool reads an OTU-table and corresponding sample metadata, and returns
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186 a RDS data set for use in all ampvis2 tools. It is therefore required to load
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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187 data with this tool before any other ampvis2 tools can be used.
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188
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189 The Galaxy tool calls the `amp_load <https://madsalbertsen.github.io/ampvis2/reference/amp_load.html>`_
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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190 function of the ampvis2 package. This function validates and corrects the
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191 provided data frames in different ways to make it suitable for the rest of the
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192 ampvis2 tools. It is important that the provided data sets match the
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193 requirements as described in the following to work properly.
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194
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195 Input
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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196 =====
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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197
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198 **The OTU-table**
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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199
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200 contains information about the OTUs, their read counts in each sample, and
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201 optionally their assigned taxonomy. The OTU table can be given as
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202
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203 - Tabular data set
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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204 - BIOM version (1 and 2)
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205
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iuc
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206 Metadata and taxonomy in the tabular or BIOM files that are given via the
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
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207 ``OTU table`` parameter can is overwritten if by data presented via the
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
iuc
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208 ``Sample metadata`` or ``Taxonomy table`` parameters.
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209
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210 If given in tabular format the provided OTU-table must be a table with the
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211 following requirements:
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212
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213 - The rows are OTU IDs and the columns are samples.
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214 - The OTU ID's are expected to be in a column called "OTU", "ASV", or "#OTU ID".
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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215 - The column names of the table are the sample IDs, exactly matching those in
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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216 the metadata
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217 - The last 7 columns are optionally the corresponding taxonomy assigned to the
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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218 OTUs, named "Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species".
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219
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220 Generally avoid special characters and spaces in row- and column names.
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221
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222 The OTU table can also contain the taxonomic information in additional columns:
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223 Kingdom, Phylum, Class, Order, Family, Genus.
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224
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225 Check `here <https://biom-format.org/>`_ for information on the BIOM formats.
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226
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227 **The metadata**
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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228
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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229 contains additional information about the samples, for example where each sample
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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230 was taken, date, pH, treatment etc, which is used to compare and group the
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231 samples during analysis. The amount of information in the metadata is unlimited,
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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232 it can contain any number of columns (variables), however there are a few
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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233 requirements:
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234
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235 - The sample IDs must be in the first column and the column must be named
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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236 ``SampleID``. These sample IDs must match exactly to those in the OTU-table. Any
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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237 unmatched samples between the otutable and metadata will be removed with a
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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238 warning.
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239 - Generally avoid special characters and spaces in row- and column names.
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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240
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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241 By default the data types of metadata columns are guessed with
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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242 ``readr::type_convert``. The guessed column types can be seen in the last (4th)
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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243 column of the ``metadata list`` output and also stdout of the tool. Guessing of
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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244 data types can be disabled using the parameter ``Guess metadata column types``.
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245 If disabled matadata from separate tabular input is treated as character data,
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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246 and if loaded from biom files that data is used as is. Metadata types can be set
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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247 manually using the tool ``ampvis2: set metadata``
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248
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249 Dates should be given in the format ``YYYY-MM-DD`` (Y: year, M: month, D: day).
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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250
474bbc45ddd9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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251 In addition to the RDS data set a metadata (resp. taxonomy) list data set is returned
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252 if metadata (resp. taxonomic information) is given to this tool. It contains
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iuc
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253 restructured metadata (taxonomic information) that is used in downstream ampvis2
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254 Galaxy tools in order to select metadata / metadata values (resp. taxonomic levels).
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255
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256 **Taxonomy**
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257
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258 is a tabular data set with 7 columns and one row per ASV/OTU:
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259
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260 - the 1st column is identical to the 1st column of the OTU table parameter
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261 - the remaining columns contain data for Kingdom, Phylum, Class, Order, Family, Genus
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262
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263 Note that the taxonomic information can also be embedded in the OTU table.
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264
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265 **Tree**
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266
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267 a tree with branch lengths in Newick format.
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268
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269 This is needed / usefull only if the data is used as input of: ``ampvis2:
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270 ordination plot`` for ordination methods NNDS / MMDS with (un)weighted UniFrac
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271 distances. Note that the loaded tree is also filtered by the ``ampvis2: subset
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272 ...`` tools.
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273
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274 **Fasta**
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275
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276 a fasta file containing the sequences of the OTUs. Note that this information is
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277 only used in ``ampvis2: export fasta``. If the OTU table is modified by
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278 ``ampvis2: mergereplicates`` or the ``ampvis2: subset ...`` tools this might be
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279 useful to obtain a filtered list of sequences.
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280
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281
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282 Output
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283 ======
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284
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285 **RDS**
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286
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287 The main output of the tool is an RDS data set that contains the R representation of
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288 the ampvis2 object containing the provided data (OTU table, metadata, taxonomy,
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289 phylogenetic tree, and fasta).
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290
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291 **List files**
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292
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293 Summarize the metadata and taxonomy information:
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294
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295 - the taxonomy list file lists all taxa in a 1 column tabular data set
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296 - the metadata list file lists the Metadata variables (column 1), and the corresponding
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297 available metadata values (column 2), if the variable is the SampleID (column 3), and
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298 the data type of the corresponding metadata variable (column 4)
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299
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300 These files are auxilliary files that are needed in downstream ``ampvis2`` Galaxy tools
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301 to allow selecting metadata and taxonomy. They are not passed to the underlying R functions.
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302
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303 Note that, if the no taxonomy (or metadata) is given then the underlying ``ampvis2`` R
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304 function adds dummy taxonomy (resp. metadata). In this case the output of the list datasets
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305 can be disabled with the ``Output list data sets`` parameter.
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306 ]]></help>
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307 <expand macro="citations"/>
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308 </tool>