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comparison confab.xml @ 1:731ad135ddb4 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty
author bgruening
date Sun, 01 Nov 2015 10:28:54 -0500
parents 4a73b5059c22
children
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0:4a73b5059c22 1:731ad135ddb4
2 <description>for molecules (confab)</description> 2 <description>for molecules (confab)</description>
3 <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="100" shared_inputs="" merge_outputs="outfile"></parallelism> 3 <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="100" shared_inputs="" merge_outputs="outfile"></parallelism>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="1.0.1">confab</requirement> 5 <requirement type="package" version="1.0.1">confab</requirement>
6 </requirements> 6 </requirements>
7 <command> confab 7 <command>
8 <![CDATA[
9 confab
8 -i ${infile.ext} 10 -i ${infile.ext}
9 -o sdf 11 -o sdf
10 -r $RMSD 12 -r $RMSD
11 -e $energy 13 -e $energy
12 -c $conformers 14 -c $conformers
13 $first_conformer 15 $first_conformer
14 $infile 16 $infile
15 $outfile 2>&#38;1 17 $outfile 2>&1
18 ]]>
16 </command> 19 </command>
17 <inputs> 20 <inputs>
18 <param name="infile" type="data" format="sdf,mol2" label="Input molecule with 3D coordinates" help="Dataset missing? See TIP below"/> 21 <param name="infile" type="data" format="sdf,mol2" label="Input molecule with 3D coordinates" help="Dataset missing? See TIP below"/>
19 <param name='RMSD' type='float' value='0.5' label='RMSD cutoff (in Angstrom)' /> 22 <param name='RMSD' type='float' value='0.5' label='RMSD cutoff (in Angstrom)' />
20 <param name='energy' type='float' value='50.0' label='Energy cutoff (in kcal/mol)' /> 23 <param name='energy' type='float' value='50.0' label='Energy cutoff (in kcal/mol)' />
30 <param name='RMSD' value='0.5' /> 33 <param name='RMSD' value='0.5' />
31 <param name='energy' value='50.0' /> 34 <param name='energy' value='50.0' />
32 <param name='conformers' value='100000' /> 35 <param name='conformers' value='100000' />
33 <param name='first_conformer' value='-a' /> 36 <param name='first_conformer' value='-a' />
34 <output name="outfile" file='confab_on_CID_3033.sdf' ftype='sdf' /> 37 <output name="outfile" file='confab_on_CID_3033.sdf' ftype='sdf' />
35 </test> 38 </test>
36 </tests> 39 </tests>
37 <help> 40 <help>
41 <![CDATA[
38 42
39 .. class:: infomark 43 .. class:: infomark
40 44
41 **What this tool does** 45 **What this tool does**
42 46
49 .. class:: infomark 53 .. class:: infomark
50 54
51 **Input** 55 **Input**
52 56
53 * Example:: 57 * Example::
54 58
55 21.2060 9.9350 63.0810 C 0 0 0 0 0 0 0 0 0 0 0 0 59 21.2060 9.9350 63.0810 C 0 0 0 0 0 0 0 0 0 0 0 0
56 21.2410 9.4460 64.5510 C 0 0 0 0 0 0 0 0 0 0 0 0 60 21.2410 9.4460 64.5510 C 0 0 0 0 0 0 0 0 0 0 0 0
57 22.0000 8.1250 64.6300 C 0 0 0 0 0 0 0 0 0 0 0 0 61 22.0000 8.1250 64.6300 C 0 0 0 0 0 0 0 0 0 0 0 0
58 21.7010 7.3010 65.5120 O 0 0 0 0 0 0 0 0 0 0 0 0 62 21.7010 7.3010 65.5120 O 0 0 0 0 0 0 0 0 0 0 0 0
59 23.1180 7.8720 63.7340 C 0 0 0 0 0 0 0 0 0 0 0 0 63 23.1180 7.8720 63.7340 C 0 0 0 0 0 0 0 0 0 0 0 0
131 Confab_ 135 Confab_
132 136
133 .. _Confab: https://code.google.com/p/confab/ 137 .. _Confab: https://code.google.com/p/confab/
134 138
135 139
136 </help> 140 ]]>
137 141 </help>
138 </tool> 142 </tool>