Mercurial > repos > bgruening > openmg

annotate openmg.xml @ 2:a65ba7f4f8ea draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit ddd2c03ed7b04798f6aad6edb067e35515ef03f1
author bgruening
date Thu, 19 May 2016 05:27:26 -0400
parents 72ce5b3d1073
children 18ed72686994
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
1 <tool id="ctb_openmg" name="Open Molecule Generator" version="0.1">
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
2 <description>Exhaustive generation of chemical structures</description>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
3 <requirements>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
4 <requirement type="package" version="0.1">openmg</requirement>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
5 </requirements>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
6 <command detect_errors="aggressive">
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
7 <![CDATA[
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
8 openmg
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
9 -ec "$ec"
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
10 #if $fr:
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
11 -fr "$sdf_outfile"
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
12 #end if
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
13 -o "$outfile"
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
14 ]]>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
15 </command>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
16 <inputs>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
17 <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
bgruening
parents:
diff changeset
18 help="e.g. C2H5NO2"/>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
19 <param name='fr' type='boolean' truevalue='-fr' falsevalue='' label='Output SD-file containing prescribed one or multiple substructures'
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
20 help="In the case of multiple substructures, they have to be non-overlapping" />
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
21 </inputs>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
22 <outputs>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
23 <data format="sdf" name="outfile" />
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
24 <data format="sdf" name="sdf_outfile">
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
25 <filter>fr is True</filter>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
26 </data>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
27 </outputs>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
28 <tests>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
29 <test>
1
72ce5b3d1073 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f8057aeb453aaad6ba0da0141be68dd8510bdb3a
bgruening
parents: 0
diff changeset
30 <param name="ec" value="C6H6"/>
2
a65ba7f4f8ea planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit ddd2c03ed7b04798f6aad6edb067e35515ef03f1
bgruening
parents: 1
diff changeset
31 <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
bgruening
parents:
diff changeset
32 </test>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
33 </tests>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
34 <help>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
35 <![CDATA[
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
36 .. class:: infomark
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
37
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
38 **What this tool does**
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
39
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
40 Open Molecule Generator - an exhaustive generation of chemical structures
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
41
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
42
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
43 ]]>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
44 </help>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
45 <citations>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
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
bgruening
parents:
diff changeset
47 </citations>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
48 </tool>