Mercurial > repos > ufz > lm_get_projects

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planemo upload for repository https://github.com/jw44lavo/galaxy-tools/blob/bgo/tools/lambdaminer/ commit 3f45cd07445498cefa73931cadf3d1115245ca1e
author ufz
date Mon, 17 Mar 2025 20:34:56 +0000
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a8eee1c3b6d7 planemo upload for repository https://github.com/jw44lavo/galaxy-tools/blob/bgo/tools/lambdaminer/ commit 3f45cd07445498cefa73931cadf3d1115245ca1e
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1 <tool id="lm_get_projects" name="Get LMDB Projects" version="0.1.0+galaxy0" profile="21.05">
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2 <requirements>
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3 <requirement type="package" version="2.2.2">pandas</requirement>
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4 <requirement type="package" version="2.9.9">psycopg2</requirement>
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5 <requirement type="package" version="2.0.37">sqlalchemy</requirement>
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6 </requirements>
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7 <command detect_errors="exit_code"><![CDATA[
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8 #if $test != ""
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9 export LAMBDAMINER_CREDENTIALS="$__tool_directory__/test-data/$test";
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10 #end if
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11 python '$__tool_directory__/get_projects.py'
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12 --login-name '$__user_name__'
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13 --output-file '$projects'
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14 ]]></command>
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15 <inputs>
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16 <param name="test" type="hidden"/>
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17 </inputs>
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18 <outputs>
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19 <data name="projects" format="csv"/>
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20 </outputs>
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21 <tests>
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22 <test>
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23 <param name="test" value="test_credentials.json"/>
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24 <output name="projects" value="test_projects.csv" compare="contains"/>
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25 </test>
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26 <test expect_failure="true">
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27 <param name="test" value="test_credentials_false.json"/>
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28 </test>
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29 <test expect_failure="true">
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30 <param name="test" value="test_credentials_nonexistent.json"/>
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31 </test>
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32 </tests>
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33 <help><![CDATA[
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34 **What it does**
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35
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36 This tool queries the Lambda-Miner database for the users projects.
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37
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38 **Input**
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39
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40 There is no input necessary from the user. The tool connects to the Lambda-Miner database and uses the users login name to query it.
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41
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42 **Output**
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43
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44 CSV file containing the projects (id, name, sample count) corresponding to the user.]]>
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45 </help>
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46 <citations>
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47 <citation type="doi">10.5194/egusphere-egu24-15782</citation>
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48 </citations>
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49 </tool>