Mercurial > repos > bgruening > confab
diff confab.xml @ 4:4c4e812a67a2 draft
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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--- a/confab.xml Sun Nov 01 10:34:34 2015 -0500 +++ b/confab.xml Sat May 20 08:31:56 2017 -0400 @@ -1,20 +1,23 @@ -<tool id="ctb_confab" name="Conformer calculation" version="0.1"> +<tool id="ctb_confab" name="Conformer calculation" version="0.4"> <description>for molecules (confab)</description> - <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="100" shared_inputs="" merge_outputs="outfile"></parallelism> + <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="100" shared_inputs="" merge_outputs="outfile"></parallelism--> <requirements> - <requirement type="package" version="1.0.1">confab</requirement> + <requirement type="package" version="2.4.1">openbabel</requirement> </requirements> - <command> + <command detect_errors="aggressive"> <![CDATA[ - confab + + obabel + '${infile}' + -O '${outfile}' -i ${infile.ext} -o sdf - -r $RMSD - -e $energy - -c $conformers + --confab + --rcutoff $RMSD + --ecutoff $energy + --conf $conformers $first_conformer - $infile - $outfile 2>&1 + ]]> </command> <inputs> @@ -22,7 +25,8 @@ <param name='RMSD' type='float' value='0.5' label='RMSD cutoff (in Angstrom)' /> <param name='energy' type='float' value='50.0' label='Energy cutoff (in kcal/mol)' /> <param name='conformers' type='integer' value='100' label='Max number of conformers to test' /> - <param name='first_conformer' type='boolean' truevalue='-a' falsevalue='' label='Include the input conformation as the first conformer' /> + <param name='first_conformer' type='boolean' truevalue='--original' falsevalue='' + label='Include the input conformation as the first conformer' /> </inputs> <outputs> <data format="sdf" name="outfile" label="${tool.name} on ${on_string}"/> @@ -32,9 +36,9 @@ <param name="infile" value='CID_3033.sdf' ftype='sdf' /> <param name='RMSD' value='0.5' /> <param name='energy' value='50.0' /> - <param name='conformers' value='100000' /> - <param name='first_conformer' value='-a' /> - <output name="outfile" file='confab_on_CID_3033.sdf' ftype='sdf' /> + <param name='conformers' value='10' /> + <param name='first_conformer' value="True" /> + <output name="outfile" file='confab_on_CID_3033.sdf' ftype='sdf' lines_diff="2"/> </test> </tests> <help> @@ -126,17 +130,12 @@ 9 8 1 6 0 0 0 10 9 1 1 0 0 0 ------ - -.. class:: infomark - -**Cite** - -Confab_ - -.. _Confab: https://code.google.com/p/confab/ ]]> </help> + <citations> + <citation type="doi">10.1186/1758-2946-3-33</citation> + <citation type="doi">10.1186/1758-2946-3-8</citation> + </citations> </tool>