Mercurial > repos > bgruening > mordred

annotate mordred_descriptors.xml @ 1:e2f40a02f31a draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 7c47e7409a8cb19e20b4424329f5d0d9470f3b00
author bgruening
date Tue, 04 Jun 2019 10:29:10 -0400
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ea68b86303e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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1 <tool id="ctb_mordred_descriptors" name="Calculate molecular descriptors" version="0.1.0">
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2 <description>with Mordred</description>
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3 <requirements>
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4 <requirement type="package" version="1.1.2">mordred</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 python '$__tool_directory__/mordred_descriptors.py'
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8 -i '${input}'
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9 --iformat '${input.ext}'
ea68b86303e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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10 -o '${output}'
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11 $header
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12 $use_3d
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13 ]]></command>
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14 <inputs>
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15 <param name="input" format="smi,sdf,inchi" type="data" label="Molecule data"
ea68b86303e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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16 help="SDF, SMILES or InChi format"/>
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17 <param name='header' type='boolean' truevalue='--header' falsevalue=''
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18 label='Include a header line' help='Include names of the descriptors as the first line in the output file'/>
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19 <param name='use_3d' type='boolean' truevalue='--3d' falsevalue=''
ea68b86303e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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20 label='Calculate 3D descriptors' help='Include 3D as well as 2D descriptors - only valid if an SD-file is selected'/>
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21 </inputs>
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22 <outputs>
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23 <data name="output" format="tabular" />
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24 </outputs>
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25 <tests>
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26 <test>
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27 <param name="input" ftype='sdf' value="10mol.sdf" />
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28 <param name="header" value="True" />
ea68b86303e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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29 <param name="use_3d" value="True" />
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30 <output name="output" ftype='tabular' file="10sdf.tab" />
ea68b86303e2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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31 </test>
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32 <test>
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33 <param name="input" ftype='smi' value="8mol.smi" />
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34 <param name="header" value="True" />
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35 <param name="use_3d" value="False" />
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36 <output name="output" ftype='tabular' file="8smi.tab" />
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37 </test>
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38 </tests>
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39
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40 <help><![CDATA[
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41 Calculates up to 1825 molecular descriptors using the Mordred package. A list of all
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42 descriptors is located here_.
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43
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44 .. _here: https://github.com/simonbray/mordred-descriptors
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45
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46 .. class:: infomark
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47
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48 **Input**
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49
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50 A file containing multiples chemical structures, either in SMILES, InChi or SDF format.
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51
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52 -----
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53
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54 .. class:: infomark
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55
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56 **Output**
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57
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58 A tabular file, in which each column represents a molecular descriptor (1613 in total,
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59 or 1825 if 3D descriptors are included). Each row describes a single molecule. Empty
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60 cells indicate that a descriptor could not be calculated for that molecule. Rows which
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61 are entirely empty most likely indicate a wrongly encoded molecule.
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62
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63 ]]></help>
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64 <citations>
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65 <citation type="doi">10.1186/s13321-018-0258-y</citation>
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66 </citations>
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67 </tool>