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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex commit d42dca433f84f2540d0901a8add71d01637f5179
author recetox
date Tue, 11 Jun 2024 09:10:34 +0000
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60db8070a5c3 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/rem_complex commit d42dca433f84f2540d0901a8add71d01637f5179
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1 <tool id="rem_complex" name="Remove coordination complexes" version="@TOOL_VERSION@+galaxy4" profile="21.09">
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2 <description>Remove molecular coordination complexes from a list of structure representations</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="creator"/>
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7 <requirements>
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8 <requirement type="package" version="1.5.3">pandas</requirement>
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9 <requirement type="package" version="3.1.1">openbabel</requirement>
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10 </requirements>
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11
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12 <command detect_errors="exit_code"><![CDATA[
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13 python $__tool_directory__/rem_complex.py
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14 -i '${input}'
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15 -iformat '${input.ext}'
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16 -o '${output}'
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17 ]]></command>
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19 <environment_variables>
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20 <environment_variable name="OPENBLAS_NUM_THREADS">4</environment_variable>
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21 </environment_variables>
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22
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23 <inputs>
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24 <param name="input" format="inchi,smi,csv,tsv" type="data" help="Accepted input formats: TSV, CSV, SMI, and InChI."/>
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25 </inputs>
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26 <outputs>
3
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27 <data name="output" format="tsv" >
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28 <change_format>
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29 <when input="input.ext" value="smi" format="smi" />
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30 <when input="input.ext" value="inchi" format="inchi" />
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31 </change_format>
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32 </data>
0
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33 </outputs>
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34 <tests>
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35 <test>
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36 <param name="input" ftype="smi" value="input.smi" />
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37 <output name="output" ftype="smi" file="sample_output.smi"/>
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38 </test>
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39 <test>
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40 <param name="input" ftype="inchi" value="input.inchi"/>
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41 <output name="output" ftype="inchi" file="sample_output.inchi"/>
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42 </test>
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43 <test>
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44 <param name="input" ftype="csv" value="input.csv"/>
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45 <output name="output" ftype="tsv" file="sample_output.tsv"/>
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46 </test>
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47 <test>
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48 <param name="input" ftype="tsv" value="input.tsv"/>
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49 <output name="output" ftype="tsv" file="sample_output.tsv"/>
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50 </test>
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51 </tests>
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52 <help>
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53 <![CDATA[
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54 @HELP@
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55 ]]>
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56 </help>
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57 <citations>
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58 <citation type="doi">https://doi.org/10.5281/zenodo.6035335</citation>
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59 </citations>
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60 </tool>