Mercurial > repos > bgruening > ctb_im_constrained_conf_gen

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit d1d0ec4ebc97b2274b18a0aab99f41addd5357ae"
author bgruening
date Mon, 27 Jul 2020 11:36:47 -0400
parents 9c5121dd2fd4
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9c5121dd2fd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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1 <tool id="ctb_im_constrained_conf_gen" name="Constrained conformer generation" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
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2 <description>with RDKit</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <token name="@GALAXY_VERSION@">0</token>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code"><![CDATA[
9c5121dd2fd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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9 ln -s $refmol ./refmol.sdf &&
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10 python -m pipelines.rdkit.constrained_conf_gen
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11 -i '$infile'
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12 -if sdf
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13 -r './refmol.sdf'
9c5121dd2fd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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14 #if $core_smi
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15 -c '$core_smi'
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16 #end if
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17 -n $number
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18 --refmolidx $refmolidx
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19 --meta
9c5121dd2fd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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20 -o outp
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21 -of sdf &>> $logfile &&
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22 cat outp_metrics.txt &>> $logfile &&
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23 gzip -dc outp.sdf.gz &>> outp.sdf || :
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24 ]]></command>
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25 <inputs>
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26 <param name="infile" type="data" format="sdf" label="Input file" help="Input file in SDF format"/>
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27 <param name="refmol" type="data" format="sdf" label="SDF reference file" help="ABCD"/>
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28 <param name="refmolidx" type="integer" value="1" label="Reference molecule index" help="Index of the reference molecule index in the file, if not the first"/>
9c5121dd2fd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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29 <param name="number" type="integer" value="10" label="Number of conformers" help="Number of conformers to generate, if None then input structures are assumed to already be 3D')"/>
9c5121dd2fd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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30 <param name="core_smi" type="text" value="" label="Core substructure" help="If not specified - guessed using MCS"/>
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31 </inputs>
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32
9c5121dd2fd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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33 <expand macro="outputs" />
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9c5121dd2fd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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35 <tests>
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36 <test>
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37 <param name="infile" value="XChemReactionMaker1.sdf" ftype="sdf"/>
9c5121dd2fd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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38 <param name="refmol" value="ref_mol.sdf" ftype="sdf"/>
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39 <param name="number" value="2" />
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40 <output name="outfile" ftype="sdf" file="constrained_conf_gen_output1.sdf"/>
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41 </test>
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42 </tests>
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43 <help><![CDATA[
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44
9c5121dd2fd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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45 .. class:: infomark
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9c5121dd2fd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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47 **What this tool does**
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9c5121dd2fd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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49 This tool generates constrained conformers for a set of input molecules, using the chemistry toolkit RDKit.
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9c5121dd2fd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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51 -----
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9c5121dd2fd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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53 .. class:: infomark
9c5121dd2fd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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54
9c5121dd2fd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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55 **Input**
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9c5121dd2fd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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57 | - Molecules in `SDF format`_
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58 | - Reference molecule in SDF format.
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59
9c5121dd2fd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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60 .. _SDF format: http://en.wikipedia.org/wiki/Chemical_table_file
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63 -----
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64
9c5121dd2fd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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65 .. class:: infomark
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9c5121dd2fd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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67 **Output**
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9c5121dd2fd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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69 SD-file containing generated conformers.
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70
9c5121dd2fd4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
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71 ]]></help>
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72 <expand macro="citations" />
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73 </tool>