Mercurial > repos > bgruening > rxdock_rbdock
changeset 2:6fe6b0e10ed6 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/rxdock commit 4a2d8ff54cacd0a755154760729058ab3cf28ee1"
| author | bgruening |
|---|---|
| date | Wed, 03 Jun 2020 12:56:21 -0400 |
| parents | 07309bad01df |
| children | b34d068c2782 |
| files | rbdock.py rbdock.xml rxdock_macros.xml |
| diffstat | 3 files changed, 22 insertions(+), 35 deletions(-) [+] |
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--- a/rbdock.py Sat Apr 25 08:58:20 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,28 +0,0 @@ -import subprocess -import argparse - -def main(): - parser = argparse.ArgumentParser(description='Simple wrapper for rbdock') - parser.add_argument('-n', '--num', type=int, help='Number of docking poses to generate') - parser.add_argument('-s', '--seed', type=int, help='Random seed') - args = parser.parse_args() - - cmd = ['rbdock', '-i', 'ligands.sdf', '-r', 'receptor.prm', '-p', 'dock.prm', '-n', str(args.num), '-o', 'rdock_output'] - if args.seed != None: - cmd += ['-s', str(args.seed)] - - ps = subprocess.Popen(cmd, stdout=subprocess.PIPE) - - error_counter = 0 - for stdout_line in iter(ps.stdout.readline, ''): - if 'RBT_DOCKING_ERROR' in str(stdout_line): - error_counter += 1 - if error_counter == 10: - print(ps.stdout) - exit(23) - if ps.poll() != None: - print(ps.stdout) - exit(int(ps.poll())) - -if __name__ == "__main__": - main()
--- a/rbdock.xml Sat Apr 25 08:58:20 2020 -0400 +++ b/rbdock.xml Wed Jun 03 12:56:21 2020 -0400 @@ -1,4 +1,4 @@ -<tool id="rxdock_rbdock" name="rxDock docking" version="0.1.4" profile="19.01"> +<tool id="rxdock_rbdock" name="rxDock docking" version="0.1.5" profile="19.01"> <description>- perform protein-ligand docking with rxDock</description> <macros> <import>rxdock_macros.xml</import> @@ -22,8 +22,11 @@ ln -s '$ligands' ligands.sdf && #end if -python '$__tool_directory__/rbdock.py' +rbdock -i ligands.sdf + -r receptor.prm + -p dock.prm -n '$num' + -o rdock_output #if $seed: -s '$seed' #end if @@ -98,7 +101,7 @@ </outputs> <tests> <!-- broken ligand test --> - <test expect_failure="true" expect_exit_code="23"> + <test> <param name="receptor" value="receptor.mol2"/> <param name="ligands" value="broken_ligand.sdf"/> <param name="active_site" value="receptor.as"/> @@ -110,6 +113,13 @@ <param name="top" value="1"/> </conditional> <param name="name" value="false"/> + <output name="output"> + <assert_contents> + <has_text text="Rbt.Current_Directory"/> + <has_n_lines n="181"/> + <has_text_matching expression="^([^\$]+?\$\$\$\$){1}?$"/> + </assert_contents> + </output> </test> <test> <param name="receptor" value="receptor.mol2"/> @@ -126,7 +136,8 @@ <output name="output"> <assert_contents> <has_text text="Rbt.Current_Directory"/> - <has_n_lines n="355"/> + <has_n_lines n="352"/> + <has_text_matching expression="^([^\$]+?\$\$\$\$){2}?$"/> </assert_contents> </output> </test> @@ -145,7 +156,8 @@ <output name="output"> <assert_contents> <has_text text="Rbt.Current_Directory"/> - <has_n_lines n="355"/> + <has_n_lines n="352"/> + <has_text_matching expression="^([^\$]+?\$\$\$\$){2}?$"/> </assert_contents> </output> </test> @@ -164,7 +176,8 @@ <output name="output"> <assert_contents> <has_text text="Rbt.Current_Directory"/> - <has_n_lines n="1059"/> + <has_n_lines n="1056"/> + <has_text_matching expression="^([^\$]+?\$\$\$\$){6}?$"/> </assert_contents> </output> </test> @@ -185,6 +198,7 @@ <assert_contents> <has_text text="Rbt.Current_Directory"/> <has_n_lines n="355"/> + <has_text_matching expression="^([^\$]+?\$\$\$\$){2}?$"/> </assert_contents> </output> </test> @@ -207,6 +221,7 @@ <assert_contents> <has_text text="Rbt.Current_Directory"/> <has_n_lines n="355"/> + <has_text_matching expression="^([^\$]+?\$\$\$\$){2}?$"/> </assert_contents> </output> </test>
--- a/rxdock_macros.xml Sat Apr 25 08:58:20 2020 -0400 +++ b/rxdock_macros.xml Wed Jun 03 12:56:21 2020 -0400 @@ -6,7 +6,7 @@ </xml> <xml name="requirements"> <requirements> - <requirement type="package" version="2013.1.0_b93747f3">rxdock</requirement> + <requirement type="package" version="2013.1.1_148c5bd1">rxdock</requirement> </requirements> </xml> </macros>