Mercurial > repos > iuc > pcdl_get_unit_dict

annotate pcdl_get_unit_dict.xml @ 0:24993ec6d174 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
author iuc
date Mon, 04 Aug 2025 18:57:08 +0000
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24993ec6d174 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl/ commit 7c74921b41bd7ab639e5a3f8b54e407f79ed8f16
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1 <tool id="pcdl_get_unit_dict" name="pcdl_get_unit_dict" version="3.0.1+galaxy0" profile="21.05">
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2 <macros>
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3 <import>pcdl_macros.xml</import>
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4 </macros>
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5 <requirements>
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6 <expand macro="requirement"/>
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7 </requirements>
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8 <command><![CDATA[
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9 #import re
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10 mkdir output_pc &&
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11 #for $file in $path:
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12 #set $filename = re.sub('[^\w\-\.\s]', '_', str($file.element_identifier))
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13 ln -s '$file' output_pc/$filename &&
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14 #end for
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15
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16 pcdl_get_unit_dict 'output_pc'
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17 --microenv $microenv
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18 --settingxml 'none'
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19 --verbose $verbose
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20 ]]></command>
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21 <inputs>
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22 <section name="essential" title="essential:" expanded="true">
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23 <expand macro="path"/>
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24 </section>
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25 <section name="advanced" title="advanced:" expanded="false">
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26 <expand macro="microenv"/>
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27 <expand macro="verbose"/>
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28 </section>
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29 </inputs>
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30 <outputs>
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31 <collection name="timeseries_unit" type="list">
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32 <discover_datasets pattern="(?P&lt;designation&gt;timeseries_unit)\.csv" format="csv" directory="output_pc" visible="false"/>
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33 </collection>
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34 </outputs>
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35 <tests>
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36 <test expect_num_outputs="1">
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37 <section name="essential">
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38 <param name="path">
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39 <expand macro="output"/>
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40 </param>
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41 </section>
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42 <section name="advanced">
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43 <param name="verbose" value="true"/>
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44 </section>
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45 <output_collection name="timeseries_unit" count="1">
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46 <element name="timeseries_unit">
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47 <assert_contents>
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48 <has_text text="attribute,unit"/>
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49 </assert_contents>
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50 </element>
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51 </output_collection>
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52 </test>
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53 </tests>
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54 <help><![CDATA[
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55 Function returns a csv that lists all tracked variables from metadata, cell, and microenvironment and maps them to their unit.
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56
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57 Homepage: https://github.com/elmbeech/physicelldataloader
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58 ]]></help>
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59 <citations>
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60 <expand macro="citation"/>
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61 </citations>
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62 </tool>