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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [Preparation]-->
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4 <tool id="SeperateMolecules" name="SeperateMolecules" version="1.1.0">
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5 <description>Split each multi molecule entry to separate single molecule entries</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">SeperateMolecules</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="stdio"/>
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11 <expand macro="requirements"/>
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12 <command>SeperateMolecules
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13
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14 #if $param_i:
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15 -i $param_i
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16 #end if
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17 #if $param_o:
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18 -o $param_o
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19 #end if
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20 #if $param_min_atoms:
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21 -min_atoms $param_min_atoms
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22 #end if
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23 #if $param_all:
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24 -all $param_all
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25 #end if
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26 </command>
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27 <inputs>
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28 <param name="param_i" type="data" format="sdf,sd,mol2,mol" optional="False" value="<class 'CTDopts.CTDopts._Null'>" label="input file (mol mol2 sd sdf)" help="(-i) "/>
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29 <param name="param_min_atoms" type="integer" value="0" label="only keep molecules having at least a minimal number of atoms" help="(-min_atoms) "/>
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30 <param name="param_all" type="integer" min="0" max="1" optional="True" value="0" label="keep all contained molecules, but each in separated entries" help="(-all) "/>
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31 </inputs>
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32 <expand macro="advanced_options"/>
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33 <outputs>
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34 <data name="param_o" metadata_source="param_i" format="input"/>
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35 </outputs>
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36 <help>This tool splits each molecule entry contained in a structure file (mol, sdf, mol2) into possibly multiple molecule entries, so that the new entries contain only a single connected molecule. The results will always be written to a single structure file in the same format as the input format, or a sdf-file in the case of a mol input file. The tool works with the given bond information, which needs to be correct.
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37
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38 Standard behaviour: only the largest molecule from each entry is retained ('largest' according to the number of atoms).
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39
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40 Optional parameters:
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41 Retain all molecules contained in a molecule entry ('-all'). Alternatively the minimal number of atoms required for a molecule to be kept can be specified ('-min_atoms').
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42
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43 </help>
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44 </tool>
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