| Previous changeset 20:df8c4f142ae3 (2013-07-23) Next changeset 22:70b28a917515 (2015-11-01) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit a44c0a13283e873a740eabcad04f021208290dfe-dirty |
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modified:
confab.xml repository_dependencies.xml tool_dependencies.xml |
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added:
confab.tar.bz2 |
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| diff -r df8c4f142ae3 -r ff23947232d0 confab.tar.bz2 |
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| Binary file confab.tar.bz2 has changed |
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| diff -r df8c4f142ae3 -r ff23947232d0 confab.xml --- a/confab.xml Tue Jul 23 14:53:58 2013 +0200 +++ b/confab.xml Sun Nov 01 10:29:42 2015 -0500 |
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| @@ -4,15 +4,18 @@ <requirements> <requirement type="package" version="1.0.1">confab</requirement> </requirements> - <command> confab + <command> +<![CDATA[ + confab -i ${infile.ext} -o sdf - -r $RMSD - -e $energy - -c $conformers - $first_conformer + -r $RMSD + -e $energy + -c $conformers + $first_conformer $infile - $outfile 2>&1 + $outfile 2>&1 +]]> </command> <inputs> <param name="infile" type="data" format="sdf,mol2" label="Input molecule with 3D coordinates" help="Dataset missing? See TIP below"/> @@ -32,9 +35,10 @@ <param name='conformers' value='100000' /> <param name='first_conformer' value='-a' /> <output name="outfile" file='confab_on_CID_3033.sdf' ftype='sdf' /> - </test> + </test> </tests> <help> +<![CDATA[ .. class:: infomark @@ -51,7 +55,7 @@ **Input** * Example:: - + 21.2060 9.9350 63.0810 C 0 0 0 0 0 0 0 0 0 0 0 0 21.2410 9.4460 64.5510 C 0 0 0 0 0 0 0 0 0 0 0 0 22.0000 8.1250 64.6300 C 0 0 0 0 0 0 0 0 0 0 0 0 @@ -133,6 +137,6 @@ .. _Confab: https://code.google.com/p/confab/ - </help> - +]]> + </help> </tool> |
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| diff -r df8c4f142ae3 -r ff23947232d0 repository_dependencies.xml --- a/repository_dependencies.xml Tue Jul 23 14:53:58 2013 +0200 +++ b/repository_dependencies.xml Sun Nov 01 10:29:42 2015 -0500 |
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| @@ -1,4 +1,4 @@ -<?xml version='1.0' encoding='utf-8'?> +<?xml version="1.0"?> <repositories description="This requires the Molecule datatype definitions (e.g. SMILES, InChI, SD-format)."> - <repository changeset_revision="18ff2d6e1dca" name="molecule_datatypes" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> -</repositories> \ No newline at end of file + <repository changeset_revision="8714f927a6ee" name="molecule_datatypes" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> +</repositories> |
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| diff -r df8c4f142ae3 -r ff23947232d0 tool_dependencies.xml --- a/tool_dependencies.xml Tue Jul 23 14:53:58 2013 +0200 +++ b/tool_dependencies.xml Sun Nov 01 10:29:42 2015 -0500 |
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| @@ -1,16 +1,16 @@ -<?xml version='1.0' encoding='utf-8'?> +<?xml version="1.0"?> <tool_dependency> <package name="eigen2" version="2.0.17"> - <repository changeset_revision="7293f118efef" name="package_eigen_2_0" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" /> + <repository changeset_revision="08253ca817b7" name="package_eigen_2_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="confab" version="1.0.1"> <install version="1.0"> <actions> - <action type="download_by_url">http://confab.googlecode.com/files/Confab-1.0.1.tar.gz</action> + <action type="download_by_url">https://github.com/bgruening/confab/archive/1.0.1.tar.gz</action> <!-- populate the environment variables from the dependend repos --> <action type="set_environment_for_install"> - <repository changeset_revision="7293f118efef" name="package_eigen_2_0" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu/"> + <repository changeset_revision="08253ca817b7" name="package_eigen_2_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> <package name="eigen2" version="2.0.17" /> </repository> </action> @@ -27,4 +27,4 @@ </install> <readme>Compiling Confab requires g++, CMake 2.4+. Optional but required for a few features is libxml2 and zlib.</readme> </package> -</tool_dependency> \ No newline at end of file +</tool_dependency> |