Mercurial > repos > bgruening > openmg

annotate openmg.xml @ 5:56482c3e63ca draft default tip

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 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
author bgruening
date Tue, 28 Jul 2020 12:04:41 +0000
parents c63a202a1ef3
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
56482c3e63ca "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
bgruening
parents: 4
diff changeset
1 <tool id="ctb_openmg" name="Open Molecule Generator" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
56482c3e63ca "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
bgruening
parents: 4
diff changeset
2 <macros>
56482c3e63ca "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
bgruening
parents: 4
diff changeset
3 <token name="@TOOL_VERSION@">0.1</token>
56482c3e63ca "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
bgruening
parents: 4
diff changeset
4 <token name="@GALAXY_VERSION@">0</token>
56482c3e63ca "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
bgruening
parents: 4
diff changeset
5 </macros>
4
c63a202a1ef3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 3
diff changeset
6 <description>- exhaustive generation of chemical structures</description>
0
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
7 <requirements>
5
56482c3e63ca "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
bgruening
parents: 4
diff changeset
8 <requirement type="package" version="@TOOL_VERSION@">openmg</requirement>
56482c3e63ca "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit 944ea4bb8a9cd4244152a4a4fecd0485fabc2ad0"
bgruening
parents: 4
diff changeset
9 <requirement type="package" version="8.0.112">java-jdk</requirement>
0
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
10 </requirements>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
11 <command detect_errors="aggressive">
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
12 <![CDATA[
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
13 openmg
3
18ed72686994 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents: 2
diff changeset
14 -ec '$ec'
0
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
15 #if $fr:
3
18ed72686994 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents: 2
diff changeset
16 -fr '$sdf_outfile'
0
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
17 #end if
3
18ed72686994 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit a44364ca5bccd47f9f331143e1abb286096e8807
bgruening
parents: 2
diff changeset
18 -o '$outfile'
0
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
19 ]]>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
20 </command>
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 <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
23 help="e.g. C2H5NO2"/>
4
c63a202a1ef3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 3
diff changeset
24 <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
bgruening
parents: 3
diff changeset
25 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
bgruening
parents:
diff changeset
26 </inputs>
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 <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
29 <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
30 <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
31 </data>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
32 </outputs>
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 <test>
1
72ce5b3d1073 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f8057aeb453aaad6ba0da0141be68dd8510bdb3a
bgruening
parents: 0
diff changeset
35 <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
36 <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
37 </test>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
38 </tests>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
39 <help>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
40 <![CDATA[
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
41 .. class:: infomark
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 **What this tool does**
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
44
4
c63a202a1ef3 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit ed9b6859de648aa5f7cde483732f5df20aaff90e
bgruening
parents: 3
diff changeset
45 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
bgruening
parents:
diff changeset
46
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
47 ]]>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
48 </help>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
49 <citations>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
50 <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
51 </citations>
c071449f22a8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit eb14d47d839cae793e34f4d61a530b563059fd4f
bgruening
parents:
diff changeset
52 </tool>