# HG changeset patch # User mvdbeek # Date 1468064469 14400 # Node ID 8571d1c719eee3b78ec03c32c75ff15204f37a9c # Parent ed7cf3f35799e2448976aa8e056fe2cdf0b1b9de planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ccb01d548a42beeacc01313218bff8c563da6fa9 diff -r ed7cf3f35799 -r 8571d1c719ee scriptrunner.xml --- a/scriptrunner.xml Sat Jul 09 07:12:40 2016 -0400 +++ b/scriptrunner.xml Sat Jul 09 07:41:09 2016 -0400 @@ -1,5 +1,5 @@ - - Makes scripts into tools using Docker + + Runs scripts using docker macros.xml @@ -46,13 +46,8 @@ - - - - - - @@ -120,6 +115,18 @@ make_HTML == "yes" + + + + + + + + + + + + diff -r ed7cf3f35799 -r 8571d1c719ee test-data/tf2_test.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tf2_test.html Sat Jul 09 07:41:09 2016 -0400 @@ -0,0 +1,25 @@ + + + + + + + + +
+ +
Galaxy Tool "script" run at 09/07/2016 11:37:54

+
script log output
+script_error.log is empty
+
Other log output
+/tmp/tmpG7m9zp/job_working_directory/000/1/dataset_2_files/script_runner.log is empty
+
All output files available for downloading
+ +
+ + + + +
Output File Name (click to view)Size
script.python0 B
script_error.log0 B
script_runner.log100 B

+
+ diff -r ed7cf3f35799 -r 8571d1c719ee test-data/tf2_test_in.xls --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tf2_test_in.xls Sat Jul 09 07:41:09 2016 -0400 @@ -0,0 +1,3 @@ +col1 col2 col3 +r11 r12 r13 +r21 r22 r23 diff -r ed7cf3f35799 -r 8571d1c719ee test-data/tf2_test_out.xls diff -r ed7cf3f35799 -r 8571d1c719ee test-data/tf2_test_runme.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tf2_test_runme.py Sat Jul 09 07:41:09 2016 -0400 @@ -0,0 +1,25 @@ +# bog standard argparse for 3 possible comma separated lists +# followed by some silly reverse each row code provided as an example +# you're supposed to replace it with your great code.. +import argparse +import copy + +argp = argparse.ArgumentParser() +argp.add_argument('--INNAMES', default=None) +argp.add_argument('--INPATHS', default=None) +argp.add_argument('--OUTPATH', default=None) +argp.add_argument('--additional_parameters', default=[], action="append") +argp.add_argument('otherargs', nargs=argparse.REMAINDER) +args = argp.parse_args() +fout = open(args.OUTPATH, 'w') +sins = open(args.INPATHS.split(',')[0]).readlines() +for i, sin in enumerate(sins): + row = sin.strip().split('\t') + rrow = copy.copy(row) + lrow = len(row) + if (lrow > 1): + for j in range(lrow): + rrow[j] = row[lrow - j - 1] + fout.write('\t'.join(rrow)) + fout.write('\n') +fout.close()