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annotate openmg.xml @ 4:c63a202a1ef3 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit ed9b6859de648aa5f7cde483732f5df20aaff90e
author bgruening
date Tue, 07 May 2019 13:27:40 -0400
parents 18ed72686994
children 56482c3e63ca
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c63a202a1ef3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
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1 <tool id="ctb_openmg" name="Open Molecule Generator" version="0.2">
c63a202a1ef3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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2 <description>- exhaustive generation of chemical structures</description>
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c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
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3 <requirements>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
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4 <requirement type="package" version="0.1">openmg</requirement>
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c63a202a1ef3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
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5 <requirement type="package">java-jdk</requirement>
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c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
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6 </requirements>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
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7 <command detect_errors="aggressive">
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
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8 <![CDATA[
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
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9 openmg
3
18ed72686994 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit a44364ca5bccd47f9f331143e1abb286096e8807
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10 -ec '$ec'
0
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
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11 #if $fr:
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18ed72686994 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit a44364ca5bccd47f9f331143e1abb286096e8807
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12 -fr '$sdf_outfile'
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c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
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13 #end if
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18ed72686994 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit a44364ca5bccd47f9f331143e1abb286096e8807
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14 -o '$outfile'
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c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
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15 ]]>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
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16 </command>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
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17 <inputs>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
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18 <param argument="-ec" type="text" label="Elemental composition of the molecules to be generated"
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
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19 help="e.g. C2H5NO2"/>
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c63a202a1ef3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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20 <param name='fr' type='boolean' truevalue='-fr' falsevalue='' label='Output SD-file containing prescribed (single or multiple) substructure(s)'
c63a202a1ef3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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21 help="In the case of multiple substructures, they must be non-overlapping" />
0
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
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22 </inputs>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
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23 <outputs>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
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24 <data format="sdf" name="outfile" />
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
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25 <data format="sdf" name="sdf_outfile">
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
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26 <filter>fr is True</filter>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
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27 </data>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
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28 </outputs>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
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29 <tests>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
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30 <test>
1
72ce5b3d1073 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f8057aeb453aaad6ba0da0141be68dd8510bdb3a
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31 <param name="ec" value="C6H6"/>
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a65ba7f4f8ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit ddd2c03ed7b04798f6aad6edb067e35515ef03f1
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32 <output name="outfile" file="openmg_results.sdf" lines_diff="440"/>
0
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
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33 </test>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
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34 </tests>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
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35 <help>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
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36 <![CDATA[
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
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37 .. class:: infomark
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
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38
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
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39 **What this tool does**
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
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40
4
c63a202a1ef3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit ed9b6859de648aa5f7cde483732f5df20aaff90e
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41 Takes an molecular formula (such as C6H6, C2H5NO2) and returns all possible structures with this elemental composition.
0
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
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42
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
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43 ]]>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
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44 </help>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
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45 <citations>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
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46 <citation type="doi">10.1186/1758-2946-4-21</citation>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
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47 </citations>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
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48 </tool>