Mercurial > repos > bgruening > ctb_im_standardize

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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 15:27:03 +0000
parents 7bf099fb2027
children
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7bf099fb2027 "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_standardize" name="Standardize SD-files" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
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2 <description>using 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[
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9 standardize
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10 -i '$infile'
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11 -if sdf
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12 $fragment_opts
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13 $neutralize
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14 --meta
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15 -o outp &>> $logfile &&
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16 cat outp_metrics.txt &>> $logfile &&
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17 gzip -d outp.sdf.gz
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18 ]]></command>
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19 <inputs>
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20 <param name="infile" type="data" format="sdf" label="Input file" help="Input file in SDF format"/>
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21 <param name="fragment_opts" type="select" label="Fragment" help="The approach for choosing the largest fragment; alternatively the whole molecule is used.">
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22 <option value="" selected="true">Use whole molecule</option>
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23 <option value="--fragment-method hac">Biggest by heavy atom count</option>
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24 <option value="--fragment-method mw">Biggest by molecular weight</option>
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25 </param>
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26 <param name="neutralize" type="boolean" label="Neutralize" truevalue="--neutralize" falsevalue="" help="Remove any charge from the molecule"/>
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27 </inputs>
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28
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29 <expand macro="outputs" />
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30
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31 <tests>
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32 <test>
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33 <param name="infile" value="Kinase_inhibs.sdf" ftype="sdf"/>
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34 <param name="fragment_opts" value="--fragment-method hac"/>
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35 <output name="outfile" ftype='sdf' file="standardize_output1.sdf"/>
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36 </test>
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37 <test>
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38 <param name="infile" value="Kinase_inhibs.sdf" ftype="sdf"/>
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39 <param name="fragment_opts" value="--fragment-method mw"/>
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40 <param name="neutralize" value="true"/>
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41 <output name="outfile" ftype='sdf' file="standardize_output2.sdf"/>
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42 </test>
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43 </tests>
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44 <help><![CDATA[
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45
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46 .. class:: infomark
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47
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48 **What this tool does**
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49
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50 Standardizes an SD-file using RDKit.
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51
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52 .. class:: infomark
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53
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54 **Input**
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55
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56 | - Input file in `SDF Format`_
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57
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58 .. _SDF Format: http://en.wikipedia.org/wiki/Chemical_table_file
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59 .. _SMILES: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
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60
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61 -----
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62
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63 .. class:: infomark
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64
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65 **Output**
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66
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67 SD-file of standardized compounds.
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68
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69 ]]></help>
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70 <expand macro="citations" />
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71 </tool>