Mercurial > repos > bgruening > ctb_im_constrained_conf_gen
diff constrained_conf_gen.xml @ 0:9c5121dd2fd4 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
author | bgruening |
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date | Tue, 21 Jul 2020 05:25:31 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/constrained_conf_gen.xml Tue Jul 21 05:25:31 2020 -0400 @@ -0,0 +1,73 @@ +<tool id="ctb_im_constrained_conf_gen" name="Constrained conformer generation" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> + <description>with RDKit</description> + <macros> + <import>macros.xml</import> + <token name="@GALAXY_VERSION@">0</token> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + ln -s $refmol ./refmol.sdf && + python -m pipelines.rdkit.constrained_conf_gen + -i '$infile' + -if sdf + -r './refmol.sdf' + #if $core_smi + -c '$core_smi' + #end if + -n $number + --refmolidx $refmolidx + --meta + -o outp + -of sdf &>> $logfile && + cat outp_metrics.txt &>> $logfile && + gzip -dc outp.sdf.gz &>> outp.sdf || : + ]]></command> + <inputs> + <param name="infile" type="data" format="sdf" label="Input file" help="Input file in SDF format"/> + <param name="refmol" type="data" format="sdf" label="SDF reference file" help="ABCD"/> + <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"/> + <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')"/> + <param name="core_smi" type="text" value="" label="Core substructure" help="If not specified - guessed using MCS"/> + </inputs> + + <expand macro="outputs" /> + + <tests> + <test> + <param name="infile" value="XChemReactionMaker1.sdf" ftype="sdf"/> + <param name="refmol" value="ref_mol.sdf" ftype="sdf"/> + <param name="number" value="2" /> + <output name="outfile" ftype="sdf" file="constrained_conf_gen_output1.sdf"/> + </test> + </tests> + <help><![CDATA[ + +.. class:: infomark + +**What this tool does** + +This tool generates constrained conformers for a set of input molecules, using the chemistry toolkit RDKit. + +----- + +.. class:: infomark + +**Input** + +| - Molecules in `SDF format`_ +| - Reference molecule in SDF format. + +.. _SDF format: http://en.wikipedia.org/wiki/Chemical_table_file + + +----- + +.. class:: infomark + + **Output** + +SD-file containing generated conformers. + + ]]></help> + <expand macro="citations" /> +</tool>