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comparison mordred_descriptors.xml @ 2:d074b0c2b54f draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/mordred commit 7efc367809c29ff5939ea971bd00c69b7f9f5903"
author bgruening
date Wed, 06 Nov 2019 13:59:30 -0500
parents ea68b86303e2
children cc0f89287ecf
comparison
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1:e2f40a02f31a 2:d074b0c2b54f
1 <tool id="ctb_mordred_descriptors" name="Calculate molecular descriptors" version="0.1.0"> 1 <tool id="ctb_mordred_descriptors" name="Calculate molecular descriptors" version="1.2.0">
2 <description>with Mordred</description> 2 <description>with Mordred</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.1.2">mordred</requirement> 4 <requirement type="package" version="1.2.0">mordred</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
7 python '$__tool_directory__/mordred_descriptors.py' 7 python '$__tool_directory__/mordred_descriptors.py'
8 -i '${input}' 8 -i '${input}'
9 --iformat '${input.ext}' 9 --iformat '${input.ext}'
10 -o '${output}' 10 -o '${output}'
11 $header 11 $header
12 $use_3d 12 $use_3d
13 $smi_col
13 ]]></command> 14 ]]></command>
14 <inputs> 15 <inputs>
15 <param name="input" format="smi,sdf,inchi" type="data" label="Molecule data" 16 <param name="input" format="smi,sdf,inchi" type="data" label="Molecule data"
16 help="SDF, SMILES or InChi format"/> 17 help="SDF, SMILES or InChi format"/>
17 <param name='header' type='boolean' truevalue='--header' falsevalue='' 18 <param name='header' type='boolean' truevalue='--header' falsevalue=''
18 label='Include a header line' help='Include names of the descriptors as the first line in the output file'/> 19 label='Include a header line' help='Include names of the descriptors as the first line in the output file'/>
19 <param name='use_3d' type='boolean' truevalue='--3d' falsevalue='' 20 <param name='use_3d' type='boolean' truevalue='--3d' falsevalue=''
20 label='Calculate 3D descriptors' help='Include 3D as well as 2D descriptors - only valid if an SD-file is selected'/> 21 label='Calculate 3D descriptors' help='Include 3D as well as 2D descriptors - only valid if an SD-file is selected'/>
22 <param name='smi_col' type='boolean' truevalue='--smiles' falsevalue=''
23 label='Add column with SMILES' help='Add a column to the output file containing SMILES of all compounds'/>
21 </inputs> 24 </inputs>
22 <outputs> 25 <outputs>
23 <data name="output" format="tabular" /> 26 <data name="output" format="tabular" />
24 </outputs> 27 </outputs>
25 <tests> 28 <tests>
26 <test> 29 <test>
27 <param name="input" ftype='sdf' value="10mol.sdf" /> 30 <param name="input" ftype='sdf' value="10mol.sdf" />
28 <param name="header" value="True" /> 31 <param name="header" value="True" />
29 <param name="use_3d" value="True" /> 32 <param name="use_3d" value="True" />
33 <param name="smi_col" value="False" />
30 <output name="output" ftype='tabular' file="10sdf.tab" /> 34 <output name="output" ftype='tabular' file="10sdf.tab" />
31 </test> 35 </test>
32 <test> 36 <test>
33 <param name="input" ftype='smi' value="8mol.smi" /> 37 <param name="input" ftype='smi' value="8mol.smi" />
34 <param name="header" value="True" /> 38 <param name="header" value="True" />
35 <param name="use_3d" value="False" /> 39 <param name="use_3d" value="False" />
40 <param name="smi_col" value="True" />
36 <output name="output" ftype='tabular' file="8smi.tab" /> 41 <output name="output" ftype='tabular' file="8smi.tab" />
37 </test> 42 </test>
38 </tests> 43 </tests>
39 44
40 <help><![CDATA[ 45 <help><![CDATA[