Mercurial > repos > iuc > ampvis2_setmetadata

annotate setmetadata.xml @ 2:20a46ce12854 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 09b56ef3e09ad6c5923c88616fea5cbd77d87616
author iuc
date Mon, 18 Dec 2023 09:45:59 +0000
parents 7499e3a586c0
children 0d18b4bb08cb
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1 <tool id="ampvis2_setmetadata" name="ampvis2 set metadata" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
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2 <description>types</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 '$rscript'
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9 ]]></command>
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10 <configfiles>
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11 <configfile name="rscript"><![CDATA[
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12 library(lubridate, quietly = TRUE)
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13 data <- readRDS("$data")
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14 #for col in $numbers
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15 data\$metadata\$$col <- as.numeric(data\$metadata\$$col)
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16 #end for
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17 #for col in $integers
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18 data\$metadata\$$col <- as.integer(data\$metadata\$$col)
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19 #end for
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20 #for col in $dates
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21 data\$metadata\$$col <- as_datetime(data\$metadata\$$col)
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22 #end for
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23 saveRDS(data, "$ampvis")
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24 @SAVE_METADATA_LIST@
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25 ]]></configfile>
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26 </configfiles>
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27 <inputs>
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28 <expand macro="rds_metadata_input_macro" metadata_optional="false"/>
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29 <expand macro="metadata_select" an="name" argument="character" multiple="true" label="Character metadata variables"/>
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30 <expand macro="metadata_select" an="name" argument="numbers" multiple="true" label="Numerical metadata variables">
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31 <token name="options">
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32 <filter type="param_value" column="0" ref="character" keep="false"/>
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33 </token>
0
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34 </expand>
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35 <expand macro="metadata_select" an="name" argument="integers" multiple="true" label="Discrete numerical metadata variables (integers)">
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36 <token name="options">
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37 <filter type="param_value" column="0" ref="character" keep="false"/>
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38 <filter type="param_value" column="0" ref="numbers" keep="false"/>
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39 </token>
0
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40 </expand>
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41 <expand macro="metadata_select" an="name" argument="dates" multiple="true" label="Date metadata variables">
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42 <token name="options">
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43 <filter type="param_value" column="0" ref="character" keep="false"/>
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44 <filter type="param_value" column="0" ref="numbers" keep="false"/>
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45 <filter type="param_value" column="0" ref="integers" keep="false"/>
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46
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47 </token>
0
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48 </expand>
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49 </inputs>
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50 <outputs>
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51 <data name="ampvis" format="ampvis2"/>
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52 <data name="metadata_list_out" format="tabular" label="${tool.name} on ${on_string}: metadata list"/>
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53 </outputs>
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54 <tests>
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55 <!-- -->
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56 <test expect_num_outputs="2">
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57 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
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58 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
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59 <param name="numbers" value="Year"/>
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60 <param name="dates" value="Date"/>
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61 <output name="ampvis" ftype="ampvis2">
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62 <assert_contents>
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63 <has_size value="11966" delta="1000"/>
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64 </assert_contents>
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65 </output>
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66 </test>
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67 </tests>
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68 <help><![CDATA[
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69 What it does
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70 ============
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71
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72 Allows to manually set the data types of metadata. `ampvis2: load` tries to
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73 detect the metadata data types automatically. If this is not as desired
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74 the data types can be set manually with this tool.
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75
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76 Input
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77 =====
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78
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79 @HELP_RDS_INPUT@
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80
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81 @HELP_METADATA_LIST_INPUT@
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82
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83 Output
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84 ======
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85
7499e3a586c0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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86 **RDS**
7499e3a586c0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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87
7499e3a586c0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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88 The main output of the tool is an RDS data set that contains the R representation of
7499e3a586c0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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89 the ampvis2 object containing the same data as the input, but with data types changes
7499e3a586c0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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90 as chosen in the input form.
7499e3a586c0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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91
7499e3a586c0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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92 **Metadata list file**
7499e3a586c0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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93
7499e3a586c0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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94 Updated metadata (only column 4 should change and reflect the desired datatype changes).
7499e3a586c0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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95 ]]></help>
7499e3a586c0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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96 <expand macro="citations"/>
7499e3a586c0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
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97 </tool>