Mercurial > repos > bgruening > mordred
annotate mordred_descriptors.xml @ 2:d074b0c2b54f draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 7efc367809c29ff5939ea971bd00c69b7f9f5903"
author | bgruening |
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date | Wed, 06 Nov 2019 13:59:30 -0500 |
parents | ea68b86303e2 |
children | cc0f89287ecf |
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d074b0c2b54f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 7efc367809c29ff5939ea971bd00c69b7f9f5903"
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1 <tool id="ctb_mordred_descriptors" name="Calculate molecular descriptors" version="1.2.0"> |
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ea68b86303e2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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2 <description>with Mordred</description> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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3 <requirements> |
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d074b0c2b54f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 7efc367809c29ff5939ea971bd00c69b7f9f5903"
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4 <requirement type="package" version="1.2.0">mordred</requirement> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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5 </requirements> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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6 <command detect_errors="exit_code"><![CDATA[ |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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7 python '$__tool_directory__/mordred_descriptors.py' |
ea68b86303e2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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8 -i '${input}' |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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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}' |
ea68b86303e2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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11 $header |
ea68b86303e2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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12 $use_3d |
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d074b0c2b54f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 7efc367809c29ff5939ea971bd00c69b7f9f5903"
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13 $smi_col |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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14 ]]></command> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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15 <inputs> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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16 <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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17 help="SDF, SMILES or InChi format"/> |
ea68b86303e2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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18 <param name='header' type='boolean' truevalue='--header' falsevalue='' |
ea68b86303e2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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19 label='Include a header line' help='Include names of the descriptors as the first line in the output file'/> |
ea68b86303e2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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20 <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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21 label='Calculate 3D descriptors' help='Include 3D as well as 2D descriptors - only valid if an SD-file is selected'/> |
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d074b0c2b54f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 7efc367809c29ff5939ea971bd00c69b7f9f5903"
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22 <param name='smi_col' type='boolean' truevalue='--smiles' falsevalue='' |
d074b0c2b54f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 7efc367809c29ff5939ea971bd00c69b7f9f5903"
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23 label='Add column with SMILES' help='Add a column to the output file containing SMILES of all compounds'/> |
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ea68b86303e2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
bgruening
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24 </inputs> |
ea68b86303e2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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25 <outputs> |
ea68b86303e2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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26 <data name="output" format="tabular" /> |
ea68b86303e2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
bgruening
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27 </outputs> |
ea68b86303e2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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28 <tests> |
ea68b86303e2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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29 <test> |
ea68b86303e2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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30 <param name="input" ftype='sdf' value="10mol.sdf" /> |
ea68b86303e2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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31 <param name="header" value="True" /> |
ea68b86303e2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
bgruening
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32 <param name="use_3d" value="True" /> |
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d074b0c2b54f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 7efc367809c29ff5939ea971bd00c69b7f9f5903"
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33 <param name="smi_col" value="False" /> |
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ea68b86303e2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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34 <output name="output" ftype='tabular' file="10sdf.tab" /> |
ea68b86303e2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
bgruening
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35 </test> |
ea68b86303e2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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36 <test> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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37 <param name="input" ftype='smi' value="8mol.smi" /> |
ea68b86303e2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
bgruening
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38 <param name="header" value="True" /> |
ea68b86303e2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
bgruening
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39 <param name="use_3d" value="False" /> |
2
d074b0c2b54f
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 7efc367809c29ff5939ea971bd00c69b7f9f5903"
bgruening
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40 <param name="smi_col" value="True" /> |
0
ea68b86303e2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
bgruening
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41 <output name="output" ftype='tabular' file="8smi.tab" /> |
ea68b86303e2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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42 </test> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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43 </tests> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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44 |
ea68b86303e2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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45 <help><![CDATA[ |
ea68b86303e2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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46 Calculates up to 1825 molecular descriptors using the Mordred package. A list of all |
ea68b86303e2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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47 descriptors is located here_. |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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48 |
ea68b86303e2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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49 .. _here: https://github.com/simonbray/mordred-descriptors |
ea68b86303e2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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50 |
ea68b86303e2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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51 .. class:: infomark |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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52 |
ea68b86303e2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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53 **Input** |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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54 |
ea68b86303e2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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55 A file containing multiples chemical structures, either in SMILES, InChi or SDF format. |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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56 |
ea68b86303e2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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57 ----- |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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58 |
ea68b86303e2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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59 .. class:: infomark |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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60 |
ea68b86303e2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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61 **Output** |
ea68b86303e2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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62 |
ea68b86303e2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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63 A tabular file, in which each column represents a molecular descriptor (1613 in total, |
ea68b86303e2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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64 or 1825 if 3D descriptors are included). Each row describes a single molecule. Empty |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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65 cells indicate that a descriptor could not be calculated for that molecule. Rows which |
ea68b86303e2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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66 are entirely empty most likely indicate a wrongly encoded molecule. |
ea68b86303e2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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67 |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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68 ]]></help> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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69 <citations> |
ea68b86303e2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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70 <citation type="doi">10.1186/s13321-018-0258-y</citation> |
ea68b86303e2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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71 </citations> |
ea68b86303e2
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 4ce352d9c9f3f1808e2ab6c019c534fd3e805959
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72 </tool> |