Mercurial > repos > bgruening > ctb_im_rxn_maker
diff rxn_maker.xml @ 0:e3c4312457b6 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/im-pipelines commit 598dd288a384481b7602a0f6322c5081dc8da5d9"
| author | bgruening |
|---|---|
| date | Tue, 21 Jul 2020 05:23:11 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rxn_maker.xml Tue Jul 21 05:23:11 2020 -0400 @@ -0,0 +1,96 @@ +<tool id="ctb_im_rxn_maker" name="Reaction maker" 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_maker + -i '$infile' + -if sdf + $multi + -r '$reagent_opts' + -rl '$reagent_file' + -rlf sdf + --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, in a Galaxy collection"/> + <param name="reagent_opts" type="select" label="Reagent options" help="Name of reaction to be run"> + <option value="Amides" selected="true">Amides</option> + <option value="SNAr">Nucleophilic aromatic substitution (SNAr mechanism)</option> + <option value="Urea">Urea</option> + <option value="Suzuki_Coupling">Suzuki coupling</option> + <option value="Sulfonamide">Sulfonamide</option> + <option value="Reductive_Amination">Reductive amination</option> + <option value="N-Alkylation">N-alkylation</option> + <option value="Ether_Coupling">Ether coupling</option> + <option value="Ester_Coupling">Ester coupling</option> + <option value="Benzimidazole">Benzimidazole</option> + <option value="Triazole">Triazole</option> + <option value="Benzoxazole">Benzoxazole</option> + <option value="Sarah_Cu">Sarah Cu</option> + <option value="Sarah_Quat_Am">Sarah Quat Am</option> + </param> + <param name="reagent_file" type="data" format="sdf" label="Reagent file" help="File in SDF format containing reagents for a 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="sulfonyl_chloride.sdf" ftype="sdf"/> + <param name="reagent_file" value="sdf-aliphatic-primary-amines-175.sdf" ftype="sdf"/> + <param name="reagent_opts" value="Sulfonamide" /> + <output name="logfile"> + <assert_contents> + <has_text text="Created 1707 molecules from a total of 1 input molecules"/> + </assert_contents> + </output> + <output name="outfile" ftype='sdf' file="rxn_maker_output1.sdf"/> + </test> + </tests> + <help><![CDATA[ +.. class:: infomark + +**What this tool does** + +Provides the output of reactions between input molecules and a list of reagents (both in SDF format). + +.. class:: infomark + +**Input** + +| - Input file in `SDF Format`_ +| - Reagent file in `SDF Format`_ + +In addition, a list of reaction types needs to be specified. + +.. _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 with reaction products. + + ]]></help> + <expand macro="citations" /> +</tool> \ No newline at end of file