Mercurial > repos > bgruening > ctb_im_rxn_smarts_filter
view rxn_smarts_filter.xml @ 1:d219d934cf1c draft default tip
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit d1d0ec4ebc97b2274b18a0aab99f41addd5357ae"
author | bgruening |
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date | Mon, 27 Jul 2020 11:38:00 -0400 |
parents | ce27129127e0 |
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<tool id="ctb_im_rxn_smarts_filter" name="Reaction SMARTS filter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> <description>using RDKit</description> <macros> <import>macros.xml</import> <token name="@GALAXY_VERSION@">0</token> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ rxn_smarts_filter -i '$infile' -if sdf $multi --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="multi" type="boolean" label="Multi mode" truevalue="--multi" falsevalue="" help="Output one file for each reaction"/> </inputs> <outputs> <data name="outfile" format="sdf" label="SDF output for ${tool.name}" from_work_dir="outp.sdf"/> <data name="logfile" format="txt" label="Logfile for ${tool.name}"/> <collection name="output_list" type="list"> <filter>multi</filter> <discover_datasets pattern="(?P<designation>.+)\.sdf$" ext="sdf" /> </collection> </outputs> <tests> <test> <param name="infile" value="Kinase_inhibs.sdf" ftype="sdf"/> <param name="multi" value="" /> <output name="outfile" ftype="sdf"> <assert_contents> <has_line line=" -5.0090 3.0685 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0"/> <has_line line="OB(O)c1nc(N2CCOCC2)c2oc3ncccc3c2n1"/> <has_line line="CO[C@@H]1[C@H](NC(=O)c2ccccc2)C[C@H]2O[C@]1(C)n1c3ccccc3c3c4c(c5c6ccccc6n2c5c31)C(=O)NC4"/> <has_text_matching expression="^([^\$]+?\$\$\$\$){36}?$"/> </assert_contents> </output> <output name="logfile"> <assert_contents> <has_text text="Matched 36 molecules from a total of 36"/> </assert_contents> </output> </test> <test> <param name="infile" value="Kinase_inhibs.sdf" ftype="sdf"/> <param name="multi" value="--multi" /> <output name="outfile" ftype="sdf"> <assert_contents> <has_line line=" -5.0090 3.0685 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0"/> <has_line line="OB(O)c1nc(N2CCOCC2)c2oc3ncccc3c2n1"/> <has_line line="CO[C@@H]1[C@H](NC(=O)c2ccccc2)C[C@H]2O[C@]1(C)n1c3ccccc3c3c4c(c5c6ccccc6n2c5c31)C(=O)NC4"/> <has_text_matching expression="^([^\$]+?\$\$\$\$){36}?$"/> </assert_contents> </output> <output name="logfile"> <assert_contents> <has_text text="Matched 36 molecules from a total of 36"/> </assert_contents> </output> <output_collection name="output_list" type="list"> <element name="Sonogashira" ftype="sdf" > <assert_contents> <has_text text="COCCOc1cc2ncnc(Nc3cccc(C#C)c3)c2cc1OCCOC"/> <has_text_matching expression="^([^\$]+?\$\$\$\$){1}?$"/> </assert_contents> </element> </output_collection> </test> </tests> <help><![CDATA[ ABCCDEFGHIJKLMNOPQRSTUVWXYZ ]]></help> <expand macro="citations" /> </tool>