Mercurial > repos > iuc > beacon2_csv2xlsx

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
author iuc
date Sun, 01 Oct 2023 16:29:22 +0000
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4509627e6ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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1 <tool id="beacon2_csv2xlsx" name="Beacon2 CSV2XLSX" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
4509627e6ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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2 <description>v2 CSV Models to XLSX</description>
4509627e6ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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3 <macros>
4509627e6ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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4 <import>macros.xml</import>
4509627e6ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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5 </macros>
4509627e6ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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6 <expand macro="xrefs"/>
4509627e6ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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7 <expand macro="requirements"/>
4509627e6ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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8 <expand macro="creators"/>
4509627e6ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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9 <command detect_errors="exit_code"><![CDATA[
4509627e6ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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10 #import re
4509627e6ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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11 #set $names = []
4509627e6ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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12 #set $x=1
4509627e6ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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13 #for $x, $csv in enumerate($csvs):
4509627e6ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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14 #set $name_base = re.sub('[^\w\-_\.]', '_', $csv.element_identifier)
4509627e6ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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15 #set $name = $name_base
4509627e6ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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16 #silent $names.append( $name )
4509627e6ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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17 ln -s '$csv' ${name} &&
4509627e6ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
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18 #end for
4509627e6ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
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19 csv2xlsx
4509627e6ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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20 #for $name in $names:
4509627e6ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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21 ${name}
4509627e6ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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22 #end for
4509627e6ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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23 -o Beacon-v2-Models_template.xlsx
4509627e6ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
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24 ]]></command>
4509627e6ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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25 <inputs>
4509627e6ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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26 <param name="csvs" type="data" multiple="true" format="csv" label="CSV files" help="" />
4509627e6ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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27 </inputs>
4509627e6ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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28 <outputs>
4509627e6ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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29 <data name="Beacon_v2_Models_template" format="xlsx" label="${tool.name} on ${on_string}: Beacon-v2-Models_template file" from_work_dir="Beacon-v2-Models_template.xlsx" />
4509627e6ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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30 </outputs>
4509627e6ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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31 <tests>
4509627e6ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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32 <test expect_num_outputs="1">
4509627e6ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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33 <param name="csvs" ftype="csv" value="analyses.csv,genomicVariations.csv,runs.csv,datasets.csv,biosamples.csv,individuals.csv,cohorts.csv" />
4509627e6ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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34 <output name="Beacon_v2_Models_template" file="Beacon-v2-Models_template.xlsx" compare="sim_size">
4509627e6ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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35 <assert_contents><has_size value="12000" delta="1000" /></assert_contents>
4509627e6ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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36 </output>
4509627e6ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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37 </test>
4509627e6ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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38 </tests>
4509627e6ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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39 <help><![CDATA[
4509627e6ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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40 The Tool converts the data from multiple CSV files to the hierarchical structure of the Beacon v2 Models and creates an Excel file with seven entities.
4509627e6ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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41 The Models entities are (analyses, biosamples, cohorts, datasets, genomicVariations, individuals and runs). The Excel consisting of all Models properties ‘flattened-out’
4509627e6ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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42 The Excel file is separated into seven sheets (one per entry type). The user is responsible for filling out the Excel according to the entities and terms they want to share.
4509627e6ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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43 Once the sheets are filled out, the Beacon v2 Reference Implementation comes with a utility that validates the Excel file against the Models JSON Schemas, and, if successful, it creates a set of JSON text
4509627e6ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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44 files (JSON arrays) as an output that will be later loaded into the database.
4509627e6ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
iuc
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45 ]]></help>
4509627e6ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
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46 <expand macro="citations" />
4509627e6ee1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2 commit dcaf8046840f163143075b276dd75909d344ec3a
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47 </tool>