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comparison confab.xml @ 4:4c4e812a67a2 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
author bgruening
date Sat, 20 May 2017 08:31:56 -0400
parents 039ef13e3676
children 119b462f0f69
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3:039ef13e3676 4:4c4e812a67a2
1 <tool id="ctb_confab" name="Conformer calculation" version="0.1"> 1 <tool id="ctb_confab" name="Conformer calculation" version="0.4">
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="2.4.1">openbabel</requirement>
6 </requirements> 6 </requirements>
7 <command> 7 <command detect_errors="aggressive">
8 <![CDATA[ 8 <![CDATA[
9 confab 9
10 obabel
11 '${infile}'
12 -O '${outfile}'
10 -i ${infile.ext} 13 -i ${infile.ext}
11 -o sdf 14 -o sdf
12 -r $RMSD 15 --confab
13 -e $energy 16 --rcutoff $RMSD
14 -c $conformers 17 --ecutoff $energy
18 --conf $conformers
15 $first_conformer 19 $first_conformer
16 $infile 20
17 $outfile 2>&1
18 ]]> 21 ]]>
19 </command> 22 </command>
20 <inputs> 23 <inputs>
21 <param name="infile" type="data" format="sdf,mol2" label="Input molecule with 3D coordinates" help="Dataset missing? See TIP below"/> 24 <param name="infile" type="data" format="sdf,mol2" label="Input molecule with 3D coordinates" help="Dataset missing? See TIP below"/>
22 <param name='RMSD' type='float' value='0.5' label='RMSD cutoff (in Angstrom)' /> 25 <param name='RMSD' type='float' value='0.5' label='RMSD cutoff (in Angstrom)' />
23 <param name='energy' type='float' value='50.0' label='Energy cutoff (in kcal/mol)' /> 26 <param name='energy' type='float' value='50.0' label='Energy cutoff (in kcal/mol)' />
24 <param name='conformers' type='integer' value='100' label='Max number of conformers to test' /> 27 <param name='conformers' type='integer' value='100' label='Max number of conformers to test' />
25 <param name='first_conformer' type='boolean' truevalue='-a' falsevalue='' label='Include the input conformation as the first conformer' /> 28 <param name='first_conformer' type='boolean' truevalue='--original' falsevalue=''
29 label='Include the input conformation as the first conformer' />
26 </inputs> 30 </inputs>
27 <outputs> 31 <outputs>
28 <data format="sdf" name="outfile" label="${tool.name} on ${on_string}"/> 32 <data format="sdf" name="outfile" label="${tool.name} on ${on_string}"/>
29 </outputs> 33 </outputs>
30 <tests> 34 <tests>
31 <test> 35 <test>
32 <param name="infile" value='CID_3033.sdf' ftype='sdf' /> 36 <param name="infile" value='CID_3033.sdf' ftype='sdf' />
33 <param name='RMSD' value='0.5' /> 37 <param name='RMSD' value='0.5' />
34 <param name='energy' value='50.0' /> 38 <param name='energy' value='50.0' />
35 <param name='conformers' value='100000' /> 39 <param name='conformers' value='10' />
36 <param name='first_conformer' value='-a' /> 40 <param name='first_conformer' value="True" />
37 <output name="outfile" file='confab_on_CID_3033.sdf' ftype='sdf' /> 41 <output name="outfile" file='confab_on_CID_3033.sdf' ftype='sdf' lines_diff="2"/>
38 </test> 42 </test>
39 </tests> 43 </tests>
40 <help> 44 <help>
41 <![CDATA[ 45 <![CDATA[
42 46
124 6 11 1 0 0 0 0 128 6 11 1 0 0 0 0
125 7 8 1 0 0 0 0 129 7 8 1 0 0 0 0
126 9 8 1 6 0 0 0 130 9 8 1 6 0 0 0
127 10 9 1 1 0 0 0 131 10 9 1 1 0 0 0
128 132
129 -----
130
131 .. class:: infomark
132
133 **Cite**
134
135 Confab_
136
137 .. _Confab: https://code.google.com/p/confab/
138 133
139 134
140 ]]> 135 ]]>
141 </help> 136 </help>
137 <citations>
138 <citation type="doi">10.1186/1758-2946-3-33</citation>
139 <citation type="doi">10.1186/1758-2946-3-8</citation>
140 </citations>
142 </tool> 141 </tool>