Mercurial > repos > bgruening > openmg

annotate openmg.xml @ 0:a3a3fcecae1c 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 f7082d13bcea600e5a422d85f71d8164d1b9936b
author bgruening
date Thu, 19 May 2016 05:23:27 -0400
parents
children 8d2b075966d6
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
1 <tool id="ctb_openmg" name="Open Molecule Generator" version="0.1">
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
2 <description>Exhaustive generation of chemical structures</description>
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
3 <requirements>
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
4 <requirement type="package" version="0.1">openmg</requirement>
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
5 </requirements>
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
6 <command detect_errors="aggressive">
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
7 <![CDATA[
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
8 openmg
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
9 -ec "$ec"
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
10 #if $fr:
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
11 -fr "$sdf_outfile"
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
12 #end if
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
13 -o "$outfile"
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
14 ]]>
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
15 </command>
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
16 <inputs>
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
17 <param argument="-ec" type="text" label="Elemental composition of the molecules to be generated"
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
18 help="e.g. C2H5NO2"/>
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
19 <param name='fr' type='boolean' truevalue='-fr' falsevalue='' label='Output SD-file containing prescribed one or multiple substructures'
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
20 help="In the case of multiple substructures, they have to be non-overlapping" />
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
21 </inputs>
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
22 <outputs>
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
23 <data format="sdf" name="outfile" />
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
24 <data format="sdf" name="sdf_outfile">
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
25 <filter>fr is True</filter>
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
26 </data>
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
27 </outputs>
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
28 <tests>
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
29 <test>
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
30 <param name="ec" value="C6H6"/>
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
31 <output name="outfile" file="openmg_results.sdf" lines_diff="440"/>
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
32 </test>
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
33 </tests>
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
34 <help>
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
35 <![CDATA[
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
36 .. class:: infomark
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
37
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
38 **What this tool does**
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
39
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
40 Open Molecule Generator - an exhaustive generation of chemical structures
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
41
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
42
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
43 ]]>
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
44 </help>
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
45 <citations>
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
46 <citation type="doi">10.1186/1758-2946-4-21</citation>
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
47 </citations>
a3a3fcecae1c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openmg commit f7082d13bcea600e5a422d85f71d8164d1b9936b
bgruening
parents:
diff changeset
48 </tool>