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1 <tool id="CONVERTER_cml_to_smiles" name="CML to SMILES" version="1.0.0">
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2 <description></description>
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3 <parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="10000" shared_inputs="" merge_outputs="output"></parallelism>
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4 <requirements>
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5 <requirement type="package" version="2.3.2">openbabel</requirement>
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6 </requirements>
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7 <command >
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8 obabel -icml "${input}"
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9 #if $can:
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10 -ocan
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11 #else:
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12 -osmi
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13 #end if
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14 -O "${output}" -e
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15 $remove_h
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16 #if $iso_chi or $can or $exp_h:
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17 -x$iso_chi$exp_h$can
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18 #end if
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19 #if $dative_bonds:
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20 -b
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21 #end if
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22 #if int($ph) >= 0:
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23 -p $ph
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24 #end if
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25
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26 2>&1
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27 </command>
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28 <inputs>
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29 <param name="input" type="data" format="cml" label="Molecules in CML-format"/>
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30 <param name="iso_chi" type="boolean" label="Do not include isotopic or chiral markings (-xi)" truevalue="i" falsevalue="" checked="false" />
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31 <param name="can" type="boolean" label="Output in canonical form (-xc)" truevalue="c" falsevalue="" checked="false" />
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32 <param name="exp_h" type="boolean" label="Output explicit hydrogens as such (-xh)" truevalue="h" falsevalue="" checked="false" />
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33 <param name="remove_h" type="boolean" label="Delete hydrogen atoms (-d)" truevalue="-d" falsevalue="" />
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34 <param name="ph" size="3" type="float" value="-1" label="Add hydrogens appropriate for pH (-p)" help="-1 means deactivated"/>
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35 <param name="dative_bonds" type="boolean" label="Convert dative bonds (e.g. [N+]([O-])=O to N(=O)=O) (-b)" truevalue="-b" falsevalue="" />
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36 </inputs>
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37 <outputs>
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38 <data name="output" format="smi"/>
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39 </outputs>
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40 <help>
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41 </help>
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42 </tool>
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