Mercurial > repos > ximgchess > chap_test_20230411

annotate saxswaxs/reduce.xml @ 63:be4a6ceb0a3d draft

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planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit e280dd942513f966a9a61a3af68ee7972fb8992f-dirty
author ximgchess
date Thu, 13 Apr 2023 12:44:13 +0000
parents a560d5143348
children 17b9b4ec475b
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47d2a1f087d1 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit fe909397cd829fe9a784a810d0264ab1751ae090-dirty
ximgchess
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1 <tool id="CHAP_saxswaxs_reduce" name="SAXSWAXS Reduce Map" version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
47d2a1f087d1 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit fe909397cd829fe9a784a810d0264ab1751ae090-dirty
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2 <requirements>
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kls286
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3 <requirement type="package" version="0.0.5">chessanalysispipeline</requirement>
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4 <requirement type="package" version="2.28.1">requests</requirement>
47d2a1f087d1 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit fe909397cd829fe9a784a810d0264ab1751ae090-dirty
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5 <requirement type="package" version="2023.3.0">pyfai</requirement>
47d2a1f087d1 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit fe909397cd829fe9a784a810d0264ab1751ae090-dirty
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6 <requirement type="package" version="1.10.7">pydantic</requirement>
47d2a1f087d1 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit fe909397cd829fe9a784a810d0264ab1751ae090-dirty
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7 </requirements>
47d2a1f087d1 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit fe909397cd829fe9a784a810d0264ab1751ae090-dirty
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8 <command detect_errors="exit_code"><![CDATA[
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9 pip --exists-action i install certif-pyspec==1.5.3 &&
47d2a1f087d1 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit fe909397cd829fe9a784a810d0264ab1751ae090-dirty
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10 cp '$mapconfig' map.yaml &&
47d2a1f087d1 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit fe909397cd829fe9a784a810d0264ab1751ae090-dirty
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11 cp '$integrationconfig' integration.yaml &&
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be4a6ceb0a3d planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit e280dd942513f966a9a61a3af68ee7972fb8992f-dirty
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12 sed 's/GITLABTOKEN/$token/' '$__tool_directory__/pipeline.yaml' > pipeline.yaml &&
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13 CHAP --config pipeline.yaml
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14 ]]></command>
47d2a1f087d1 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit fe909397cd829fe9a784a810d0264ab1751ae090-dirty
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15 <inputs>
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16 <param type="text" name="token" />
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17 <param type="data" name="mapconfig" format="yaml" />
47d2a1f087d1 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit fe909397cd829fe9a784a810d0264ab1751ae090-dirty
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18 <param type="data" name="integrationconfig" format="yaml" />
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19 </inputs>
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20 <outputs>
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21 <data name="specdata" label="Map of SPEC data" format="nex" from_work_dir="map_specdata.nxs"/>
47d2a1f087d1 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit fe909397cd829fe9a784a810d0264ab1751ae090-dirty
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22 <data name="reduceddata" label="Map of reduced data" format="nex" from_work_dir="map_reduceddata.nxs"/>
47d2a1f087d1 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit fe909397cd829fe9a784a810d0264ab1751ae090-dirty
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23 </outputs>
47d2a1f087d1 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit fe909397cd829fe9a784a810d0264ab1751ae090-dirty
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24 <tests>
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25 <test>
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26 <param name="mapconfig" value="map.yaml"/>
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27 <param name="integrationconfig" value="integration.yaml"/>
47d2a1f087d1 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit fe909397cd829fe9a784a810d0264ab1751ae090-dirty
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28 <output name="specdata" value="map_specdata.nxs"/>
47d2a1f087d1 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit fe909397cd829fe9a784a810d0264ab1751ae090-dirty
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29 <output name="reduceddata" value="map_reduceddata.nxs"/>
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30 </test>
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31 </tests>
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32 <help><![CDATA[
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33 usage: PROG [-h] [--config CONFIG] [--verbose]
47d2a1f087d1 planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit fe909397cd829fe9a784a810d0264ab1751ae090-dirty
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35 options:
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36 -h, --help show this help message and exit
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37 --config CONFIG Input configuration file
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38 --verbose verbose output
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39
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40 ]]></help>
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41 <citations>
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42 <citation type="bibtex">
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43 @misc{githubChessAnalysisPipeline,
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44 author = {LastTODO, FirstTODO},
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45 year = {TODO},
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46 title = {CHAPSAXSWAXSdemo},
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47 publisher = {GitHub},
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48 journal = {GitHub repository},
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49 url = {https://github.com/CHESSComputing/ChessAnalysisPipeline},
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50 }</citation>
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51 </citations>
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52 </tool>