| Next changeset 1:8d2b075966d6 (2017-05-20) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b |
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added:
openmg.xml test-data/openmg_results.sdf |
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| diff -r 000000000000 -r a3a3fcecae1c openmg.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/openmg.xml Thu May 19 05:23:27 2016 -0400 |
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| @@ -0,0 +1,48 @@ +<tool id="ctb_openmg" name="Open Molecule Generator" version="0.1"> + <description>Exhaustive generation of chemical structures</description> + <requirements> + <requirement type="package" version="0.1">openmg</requirement> + </requirements> + <command detect_errors="aggressive"> +<![CDATA[ + openmg + -ec "$ec" + #if $fr: + -fr "$sdf_outfile" + #end if + -o "$outfile" +]]> + </command> + <inputs> + <param argument="-ec" type="text" label="Elemental composition of the molecules to be generated" + help="e.g. C2H5NO2"/> + <param name='fr' type='boolean' truevalue='-fr' falsevalue='' label='Output SD-file containing prescribed one or multiple substructures' + help="In the case of multiple substructures, they have to be non-overlapping" /> + </inputs> + <outputs> + <data format="sdf" name="outfile" /> + <data format="sdf" name="sdf_outfile"> + <filter>fr is True</filter> + </data> + </outputs> + <tests> + <test> + <param name="ec" value="C6H6"/> + <output name="outfile" file="openmg_results.sdf" lines_diff="440"/> + </test> + </tests> + <help> +<![CDATA[ +.. class:: infomark + +**What this tool does** + +Open Molecule Generator - an exhaustive generation of chemical structures + + +]]> + </help> + <citations> + <citation type="doi">10.1186/1758-2946-4-21</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r a3a3fcecae1c test-data/openmg_results.sdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/openmg_results.sdf Thu May 19 05:23:27 2016 -0400 |
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| b'@@ -0,0 +1,5407 @@\n+\n+ CDK 0519161042\n+\n+ 6 7 0 0 0 0 0 0 0 0999 V2000\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 2 1 0 0 0 0 \n+ 1 6 1 0 0 0 0 \n+ 2 3 1 0 0 0 0 \n+ 2 5 1 0 0 0 0 \n+ 3 4 2 0 0 0 0 \n+ 4 6 1 0 0 0 0 \n+ 5 6 2 0 0 0 0 \n+M END\n+> <Id>\n+1\n+\n+> <can_string>\n+010001001010000200000001000002000000\n+\n+$$$$\n+\n+ CDK 0519161042\n+\n+ 6 7 0 0 0 0 0 0 0 0999 V2000\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 3 1 0 0 0 0 \n+ 1 4 1 0 0 0 0 \n+ 2 3 1 0 0 0 0 \n+ 2 4 1 0 0 0 0 \n+ 3 6 1 0 0 0 0 \n+ 4 5 1 0 0 0 0 \n+ 5 6 3 0 0 0 0 \n+M END\n+> <Id>\n+2\n+\n+> <can_string>\n+001100001100000001000010000003000000\n+\n+$$$$\n+\n+ CDK 0519161042\n+\n+ 6 8 0 0 0 0 0 0 0 0999 V2000\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 4 1 0 0 0 0 \n+ 1 6 1 0 0 0 0 \n+ 2 4 1 0 0 0 0 \n+ 2 6 1 0 0 0 0 \n+ 3 5 2 0 0 0 0 \n+ 3 6 1 0 0 0 0 \n+ 4 5 1 0 0 0 0 \n+ 5 6 1 0 0 0 0 \n+M END\n+> <Id>\n+3\n+\n+> <can_string>\n+000101000101000021000010000001000000\n+\n+$$$$\n+\n+ CDK 0519161042\n+\n+ 6 7 0 0 0 0 0 0 0 0999 V2000\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 4 1 0 0 0 0 \n+ 1 5 1 0 0 0 0 \n+ 2 4 1 0 0 0 0 \n+ 2 5 1 0 0 0 0 \n+ 3 4 1 0 0 0 0 \n+ 3 6 2 0 0 0 0 \n+ 5 6 2 0 0 0 0 \n+M END\n+> <Id>\n+4\n+\n+> <can_string>\n+000110000110000102000000000002000000\n+\n+$$$$\n+\n+ CDK 0519161042\n+\n+ 6 8 0 0 0 0 0 0 0 0999 V2000\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 5 1 0 0 0 0 \n+ 1 6 1 0 0 0 0 \n+ 2 5 1 0 0 0 0 \n+ 2 6 1 0 0 0 0 \n+ 3 4 2 0 0 0 0 \n+ 3 6 1 0 0 0 0 \n+ 4 5 1 0 0 0 0 \n+ 5 6 1 0 0 0 0 \n+M END\n+> <Id>\n+5\n+\n+> <can_string>\n+000011000011000201000010000001000000\n+\n+$$$$\n+\n+ CDK 0519161042\n+\n+ 6 8 0 0 0 0 0 0 0 0999 V2000\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ '..b'0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 4 1 0 0 0 0 \n+ 2 3 1 0 0 0 0 \n+ 2 6 1 0 0 0 0 \n+ 3 6 2 0 0 0 0 \n+ 4 5 3 0 0 0 0 \n+ 5 6 1 0 0 0 0 \n+M END\n+> <Id>\n+212\n+\n+> <can_string>\n+000100001001000002000030000001000000\n+\n+$$$$\n+\n+ CDK 0519161042\n+\n+ 6 7 0 0 0 0 0 0 0 0999 V2000\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 3 1 0 0 0 0 \n+ 2 4 1 0 0 0 0 \n+ 2 5 1 0 0 0 0 \n+ 3 6 2 0 0 0 0 \n+ 4 5 2 0 0 0 0 \n+ 4 6 1 0 0 0 0 \n+ 5 6 1 0 0 0 0 \n+M END\n+> <Id>\n+213\n+\n+> <can_string>\n+001000000110000002000021000001000000\n+\n+$$$$\n+\n+ CDK 0519161042\n+\n+ 6 7 0 0 0 0 0 0 0 0999 V2000\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 6 1 0 0 0 0 \n+ 2 4 1 0 0 0 0 \n+ 2 5 1 0 0 0 0 \n+ 3 5 1 0 0 0 0 \n+ 3 6 2 0 0 0 0 \n+ 4 5 2 0 0 0 0 \n+ 4 6 1 0 0 0 0 \n+M END\n+> <Id>\n+214\n+\n+> <can_string>\n+000001000110000012000021000000000000\n+\n+$$$$\n+\n+ CDK 0519161042\n+\n+ 6 7 0 0 0 0 0 0 0 0999 V2000\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 5 1 0 0 0 0 \n+ 2 3 1 0 0 0 0 \n+ 2 6 2 0 0 0 0 \n+ 3 5 1 0 0 0 0 \n+ 3 6 1 0 0 0 0 \n+ 4 5 2 0 0 0 0 \n+ 4 6 1 0 0 0 0 \n+M END\n+> <Id>\n+215\n+\n+> <can_string>\n+000010001002000011000021000000000000\n+\n+$$$$\n+\n+ CDK 0519161042\n+\n+ 6 6 0 0 0 0 0 0 0 0999 V2000\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 4 1 0 0 0 0 \n+ 2 4 2 0 0 0 0 \n+ 3 5 1 0 0 0 0 \n+ 3 6 2 0 0 0 0 \n+ 4 5 1 0 0 0 0 \n+ 5 6 2 0 0 0 0 \n+M END\n+> <Id>\n+216\n+\n+> <can_string>\n+000100000200000012000010000002000000\n+\n+$$$$\n+\n+ CDK 0519161042\n+\n+ 6 6 0 0 0 0 0 0 0 0999 V2000\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n+ 1 4 1 0 0 0 0 \n+ 2 4 2 0 0 0 0 \n+ 3 4 1 0 0 0 0 \n+ 3 5 1 0 0 0 0 \n+ 3 6 1 0 0 0 0 \n+ 5 6 3 0 0 0 0 \n+M END\n+> <Id>\n+217\n+\n+> <can_string>\n+000100000200000111000000000003000000\n+\n+$$$$\n' |