Mercurial > repos > bgruening > confab
changeset 26:b0a28a5fd431 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/confab commit 01da22e4184a5a6f6a3dd4631a7b9c31d1b6d502
| author | bgruening |
|---|---|
| date | Sat, 20 May 2017 08:31:30 -0400 |
| parents | 9d019ccaa0e3 |
| children | 7198475e0755 |
| files | confab.xml test-data/confab_on_CID_3033.sdf tool_dependencies.xml |
| diffstat | 3 files changed, 8 insertions(+), 38 deletions(-) [+] |
line wrap: on
line diff
--- a/confab.xml Tue May 31 11:44:52 2016 -0400 +++ b/confab.xml Sat May 20 08:31:30 2017 -0400 @@ -1,15 +1,15 @@ -<tool id="ctb_confab" name="Conformer calculation" version="0.3"> +<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--> <requirements> - <requirement type="package" version="2.3.90dev7d621d9">openbabel</requirement> + <requirement type="package" version="2.4.1">openbabel</requirement> </requirements> <command detect_errors="aggressive"> <![CDATA[ obabel - "${infile}" - -O "${outfile}" + '${infile}' + -O '${outfile}' -i ${infile.ext} -o sdf --confab @@ -36,9 +36,9 @@ <param name="infile" value='CID_3033.sdf' ftype='sdf' /> <param name='RMSD' value='0.5' /> <param name='energy' value='50.0' /> - <param name='conformers' value='100000' /> + <param name='conformers' value='10' /> <param name='first_conformer' value="True" /> - <output name="outfile" file='confab_on_CID_3033.sdf' ftype='sdf' lines_diff="4"/> + <output name="outfile" file='confab_on_CID_3033.sdf' ftype='sdf' lines_diff="2"/> </test> </tests> <help>
--- a/test-data/confab_on_CID_3033.sdf Tue May 31 11:44:52 2016 -0400 +++ b/test-data/confab_on_CID_3033.sdf Sat May 20 08:31:30 2017 -0400 @@ -1,5 +1,5 @@ -214.7 - OpenBabel06291213403D +3033 + OpenBabel05191717063D 30 31 0 0 0 0 0 0 0 0999 V2000 1.9541 1.1500 -2.5078 Cl 0 0 0 0 0 0 0 0 0 0 0 0
--- a/tool_dependencies.xml Tue May 31 11:44:52 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,30 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="eigen2" version="2.0.17"> - <repository changeset_revision="53adc55e10f2" name="package_eigen_2_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> - <package name="confab" version="1.0.1"> - <install version="1.0"> - <actions> - <action type="download_by_url">https://github.com/bgruening/confab/archive/1.0.1.tar.gz</action> - - <!-- populate the environment variables from the dependend repos --> - <action type="set_environment_for_install"> - <repository changeset_revision="53adc55e10f2" name="package_eigen_2_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"> - <package name="eigen2" version="2.0.17" /> - </repository> - </action> - - <action type="shell_command">cmake . -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR -DEIGEN2_INCLUDE_DIR=$EIGEN2_SOURCE_PATH</action> - <action type="shell_command">make</action> - <action type="shell_command">make install</action> - <action type="set_environment"> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> - <environment_variable action="set_to" name="BABEL_DATADIR">$INSTALL_DIR/share/openbabel</environment_variable> - <environment_variable action="set_to" name="BABEL_LIBDIR">$INSTALL_DIR/lib/openbabel/2.2.99</environment_variable> - </action> - </actions> - </install> - <readme>Compiling Confab requires g++, CMake 2.4+. Optional but required for a few features is libxml2 and zlib.</readme> - </package> -</tool_dependency>