Mercurial > repos > bgruening > ctb_im_o3dalign
diff o3dalign.xml @ 0:b760f006cb6b 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 05:24:46 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/o3dalign.xml Tue Jul 21 05:24:46 2020 -0400 @@ -0,0 +1,103 @@ +<tool id="ctb_im_o3dalign" name="Open 3D Align" 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 $molquery ./molquery.sdf && + o3dAlign + ./molquery.sdf ##positional arg + -i '$infile' + -if sdf + --qmolidx '$qmolidx' + $crippen + -n '$number' + -t '$threshold' + -a '$attempts' + -r '$rmsd' + -e '$emin' + --meta + -of sdf + -o outp &>> $logfile && + cat outp_metrics.txt &>> $logfile && + gzip -d outp.sdf.gz + ]]></command> + <inputs> + <param name="infile" type="data" format="sdf" label="Input file" help="Input file in SDF format"/> + <param name="molquery" type="data" format="sdf,mol" label="Mol query file" help="Mol file to align against"/> + <param name="qmolidx" type="integer" value="1" label="Query molecule index" help="Query molecule index in SD-file if not the first"/> + <param name="threshold" type="float" min="0" value="1" label="Threshold" help="Score cutoff relative to alignment of query to itself"/> + <param name="number" type="integer" value="0" label="Number of conformers" help="Number of conformers to generate, if 0 then input structures are assumed to already be)"/> + <param name="rmsd" type="float" min="0" value="1.0" label="RMSD Threshold" help="Prune RMSD threshold for excluding conformers"/> + <param name="attempts" type="integer" min="0" value="0" label="Number of attempts" help="If confomers fall below the RMSD threshold, number of attempts at regeneration before giving up."/> + <param name="emin" type="integer" value="0" label="Energy minimisation iterations" help="Number of EM iterations using the MMFF force field. Default is 0 (i.e. no EM)."/> + <param name="crippen" type="boolean" label="Crippen" truevalue="--crippen" falsevalue="" help="Use Crippen (logP) contributions"/> + </inputs> + + <expand macro="outputs" /> + + <tests> + <test> + <param name="infile" value="Kinase_inhibs.sdf" ftype="sdf"/> + <param name="molquery" value="pyrimethamine.mol" ftype="mol"/> + <param name="threshold" value="30" /> + <param name="number" value="2" /> + <output name="outfile"> + <assert_contents> + <has_text text="Fc1ccc(Sc2ccc3c(c4c(Cl)cccc4Cl)c(=O)ncn3n2)c(F)c1"/> + </assert_contents> + </output> + <output name="logfile"> + <assert_contents> + <has_text text="Perfect score: 0.0 134.34 CCc1nc(N)nc(N)c1-c1ccc(Cl)cc1 17"/> + </assert_contents> + </output> + </test> + <test> + <param name="infile" value="Kinase_inhibs.sdf" ftype="sdf"/> + <param name="molquery" value="pyrimethamine.mol" ftype="mol"/> + <param name="threshold" value="30" /> + <param name="number" value="2" /> + <param name="crippen" value="--crippen" /> + <output name="outfile"> + <assert_contents> + <has_text text="Fc1ccc(Sc2ccc3c(c4c(Cl)cccc4Cl)c(=O)ncn3n2)c(F)c1"/> + </assert_contents> + </output> + <output name="logfile"> + <assert_contents> + <has_text text="Perfect score: 0.0 114.13359999999997 CCc1nc(N)nc(N)c1-c1ccc(Cl)cc1 17"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + +.. class:: infomark + +**What this tool does** + +Aligns molecules using RDKit's Open 3D Align. + +.. class:: infomark + +**Input** + +| - Input file in `SDF Format`_ + +.. _SDF Format: http://en.wikipedia.org/wiki/Chemical_table_file +.. _SMILES: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification + +----- + +.. class:: infomark + + **Output** + +SD-file of aligned compounds. + +]]></help> + <expand macro="citations" /> +</tool> \ No newline at end of file