Mercurial > repos > bgruening > sdf_to_tab

annotate sdf_to_tab.xml @ 3:71bc02c59d3a 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/rdkit commit a03b1b7b283901a1510562f1e6eba41f70afaac4"
author bgruening
date Mon, 23 Mar 2020 15:57:35 -0400
parents 40ff81f67f5e
children 55553120df69
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
71bc02c59d3a "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit a03b1b7b283901a1510562f1e6eba41f70afaac4"
bgruening
parents: 2
diff changeset
1 <tool id="sdf_to_tab" name="Extract values from an SD-file" version="@VERSION@.2">
0
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
2 <macros>
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
3 <token name="@VERSION@">2019.03.1</token>
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
4 </macros>
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
5 <description>into a tabular file using RDKit</description>
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
6 <requirements>
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
7 <requirement type="package" version="@VERSION@">rdkit</requirement>
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
8 </requirements>
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
9 <command detect_errors="exit_code">
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
10 <![CDATA[
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
11 python '$__tool_directory__/sdf_to_tab.py'
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
12 -i '${infile}'
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
13 -o '${outfile}'
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
14 -p '$props'
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
15 $header
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
16 $smiles
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
17 $name
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
18 ]]>
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
19 </command>
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
20 <inputs>
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
21 <param name="infile" format="sdf" type="data" label="Input SD-file"/>
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
22 <param name="header" type="boolean" label="Include the property name as header"
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
23 truevalue="--header" falsevalue="" checked="false" />
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
24 <param name="smiles" type="boolean" label="Include SMILES as column in output"
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
25 truevalue="--smiles" falsevalue="" checked="false" />
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
26 <param name="name" type="boolean" label="Include molecule name as column in output"
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
27 truevalue="--name" falsevalue="" checked="false" />
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
28 <param name="props" type="text" optional="true" label="Properties to extract from the SD-file" help="Separated with a comma, e.g. RMSD_UB,RMSD_LB,SCORE. To extract values for all properties in the file, leave the field blank."/>
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
29 </inputs>
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
30 <outputs>
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
31 <data format="tabular" name="outfile" />
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
32 </outputs>
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
33 <tests>
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
34 <test>
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
35 <param name="infile" ftype='sdf' value="CID_3037.sdf" />
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
36 <param name="header" value="True" />
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
37 <param name="props" value="" />
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
38 <param name="name" value="True" />
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
39 <output name="outfile" ftype='tabular' file="CID_3037.tab" />
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
40
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
41 </test>
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
42 <test>
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
43 <param name="infile" ftype='sdf' value="ligand.sdf" />
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
44 <param name="header" value="True" />
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
45 <param name="props" value="RMSD_UB,RMSD_LB,SCORE" />
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
46 <param name="smiles" value="True" />
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
47 <output name="outfile" ftype='tabular' file="ligand.tab" />
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
48 </test>
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
49 </tests>
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
50 <help>
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
51 <![CDATA[
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
52
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
53 .. class:: infomark
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
54
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
55 **What this tool does**
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
56
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
57 Structure-data (SD-) files may contain values for various properties saved under each of the records. These are indicated using angled brackets, as in the following extract::
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
58
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
59 > <TORSDO>
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
60 F 3
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
61
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
62 > <SCORE>
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
63 -4.9
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
64
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
65 > <RMSD_LB>
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
66 0.000
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
67
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
68 > <RMSD_UB>
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
69 0.000
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
70
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
71 This tool extracts properties for all molecules saved within an input SD-file, using RDKit, and saves them to tabular format.
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
72
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
73
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
74 -----
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
75
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
76 .. class:: infomark
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
77
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
78 **Input**
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
79
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
80 An SD-file. The properties to be extracted can also be specified, separated with a comma; for example, SCORE,RMSD_LB,RMSD_UB.
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
81
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
82 If the field is left blank, all properties found in the SD-file will be saved, excluding properties with values that contain newline or tab characters, which would disrupt the tabular format.
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
83
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
84 -----
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
85
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
86 .. class:: infomark
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
87
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
88 **Output**
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
89
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
90 Tabular file, where each property is shown in a separate column, with compounds found in the SD-file listed in each row::
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
91
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
92 Name RMSD_LB RMSD_UB SCORE
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
93 pose1 0.0 0.0 -4.9
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
94 pose2 0.118 2.246 -4.9
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
95 pose3 2.96 5.795 -4.9
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
96 pose4 2.958 5.379 -4.8
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
97 pose5 2.763 5.379 -4.5
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
98 pose6 3.106 4.85 -4.4
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
99 pose7 2.847 5.816 -4.4
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
100 pose8 3.964 5.892 -4.3
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
101 pose9 3.971 6.363 -4.3
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
102
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
103 ]]>
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
104 </help>
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
105 <citations>
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
106 <citation type="bibtex">
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
107 @article{rdkit,
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
108 author = {Greg Landrum and others},
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
109 title = {RDKit: Open-source cheminformatics},
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
110 url ={http://www.rdkit.org}
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
111 }</citation>
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
112 </citations>
06828e0cc8a7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rdkit commit 714e984db6ba1198cacf4dcf325320a5889fa02c"
bgruening
parents:
diff changeset
113 </tool>