Mercurial > repos > iuc > ampvis2_setmetadata

annotate setmetadata.xml @ 0:e4e8e349c2c0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
author iuc
date Fri, 16 Aug 2024 08:55:07 +0000
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0
e4e8e349c2c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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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 '$rscript'
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9 ]]></command>
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10 <configfiles>
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11 <configfile name="rscript"><![CDATA[
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12 library(lubridate, quietly = TRUE)
e4e8e349c2c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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13 data <- readRDS("$data")
e4e8e349c2c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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14 #for col in $numbers
e4e8e349c2c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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15 data\$metadata\$$col <- as.numeric(data\$metadata\$$col)
e4e8e349c2c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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16 #end for
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17 #for col in $integers
e4e8e349c2c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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18 data\$metadata\$$col <- as.integer(data\$metadata\$$col)
e4e8e349c2c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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19 #end for
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20 #for col in $dates
e4e8e349c2c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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21 data\$metadata\$$col <- as_date(data\$metadata\$$col)
e4e8e349c2c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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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>
e4e8e349c2c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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27 <inputs>
e4e8e349c2c0 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" metadata_optional="false"/>
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29 <expand macro="metadata_select" an="name" argument="character" multiple="true" label="Character metadata variables"/>
e4e8e349c2c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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30 <expand macro="metadata_select" an="name" argument="numbers" multiple="true" label="Numerical metadata variables">
e4e8e349c2c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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31 <token name="options">
e4e8e349c2c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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32 <filter type="param_value" column="0" ref="character" keep="false"/>
e4e8e349c2c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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33 </token>
e4e8e349c2c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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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)">
e4e8e349c2c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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36 <token name="options">
e4e8e349c2c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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37 <filter type="param_value" column="0" ref="character" keep="false"/>
e4e8e349c2c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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38 <filter type="param_value" column="0" ref="numbers" keep="false"/>
e4e8e349c2c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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39 </token>
e4e8e349c2c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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40 </expand>
e4e8e349c2c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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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"/>
e4e8e349c2c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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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 </token>
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47 </expand>
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48 </inputs>
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49 <outputs>
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50 <data name="ampvis" format="ampvis2"/>
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51 <data name="metadata_list_out" format="tabular" label="${tool.name} on ${on_string}: metadata list"/>
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52 </outputs>
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53 <tests>
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54 <!-- -->
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55 <test expect_num_outputs="2">
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56 <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/>
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57 <param name="metadata_list" value="AalborgWWTPs-metadata.list"/>
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58 <param name="numbers" value="Year"/>
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59 <param name="dates" value="Date"/>
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60 <output name="ampvis" ftype="ampvis2">
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61 <assert_contents>
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62 <has_size value="11966" delta="1000"/>
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63 </assert_contents>
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64 </output>
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65 </test>
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66 </tests>
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67 <help><![CDATA[
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68 What it does
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69 ============
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70
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71 Allows to manually set the data types of metadata. `ampvis2: load` tries to
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72 detect the metadata data types automatically. If this is not as desired
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73 the data types can be set manually with this tool.
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74
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75 Input
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76 =====
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77
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78 @HELP_RDS_INPUT@
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79
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80 @HELP_METADATA_LIST_INPUT@
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81
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82 Output
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83 ======
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84
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85 **RDS**
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86
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87 The main output of the tool is an RDS data set that contains the R representation of
e4e8e349c2c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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88 the ampvis2 object containing the same data as the input, but with data types changes
e4e8e349c2c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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89 as chosen in the input form.
e4e8e349c2c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
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90
e4e8e349c2c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
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91 **Metadata list file**
e4e8e349c2c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
parents:
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92
e4e8e349c2c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
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93 Updated metadata (only column 4 should change and reflect the desired datatype changes).
e4e8e349c2c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
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94 ]]></help>
e4e8e349c2c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
iuc
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95 <expand macro="citations"/>
e4e8e349c2c0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 9ed0c3078be166bd22136771f517ae91a5198ecf
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96 </tool>